From 2aae4689f351ebf2be008f62bb9e389d7010aaee Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Sun, 15 May 2022 21:37:12 +0200 Subject: [PATCH 01/60] switch to lineup 4.6.0 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index c2f3c64..c22f762 100644 --- a/package.json +++ b/package.json @@ -69,7 +69,7 @@ "d3-selection": "^3.0.0", "d3-transition": "^3.0.1", "jquery": "^3.5.0", - "lineupjs": "next", + "lineupjs": "~4.6.0", "lodash.merge": "^4.x", "lodash.pick": "^4.4.0", "loglevel": "^1.6.4", From 5fe296fccebce9440d2c30f406a24dad14453ffe Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Mon, 23 May 2022 11:33:48 +0200 Subject: [PATCH 02/60] also copy templates folder --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index c22f762..fcf0ab1 100644 --- a/package.json +++ b/package.json @@ -23,7 +23,7 @@ "clean": "rimraf build dist lib", "compile:watch": "tsc -w", "compile": "tsc", - "copy-assets": "if [ -d src/assets ]; then cp -rv src/assets/. dist/assets/; fi && if [ -d src/template ]; then shx --verbose cp -R src/template/. dist/template/; fi", + "copy-assets": "if [ -d src/assets ]; then cp -rv src/assets/. dist/assets/; fi && if [ -d src/template ]; then shx --verbose cp -R src/template/. dist/template/; fi && if [ -d src/templates ]; then shx --verbose cp -R src/templates/. dist/templates/; fi", "copy-styles": "if [ -d src/scss ]; then shx --verbose cp -R src/scss/. dist/scss/; fi", "copy": "npm run copy-assets && npm run copy-styles", "delete-dependencies": "rimraf node_modules", From 6f33257cc3d079c3f748686dc65151fe57f1ce85 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Mon, 23 May 2022 11:33:58 +0200 Subject: [PATCH 03/60] add 2nd compare tasks --- dist/Taskview/tasks/Compadre.d.ts | 20 ++++ dist/Taskview/tasks/Compadre.js | 123 +++++++++++++++++++++++ dist/Taskview/tasks/Compadre.js.map | 1 + dist/Taskview/tasks/TaskList.js | 4 +- dist/Taskview/tasks/TaskList.js.map | 2 +- dist/templates/SearchColumn.html | 6 ++ src/Taskview/tasks/Compadre.ts | 146 ++++++++++++++++++++++++++++ src/Taskview/tasks/TaskList.ts | 4 +- src/templates/SearchColumn.html | 6 ++ 9 files changed, 309 insertions(+), 3 deletions(-) create mode 100644 dist/Taskview/tasks/Compadre.d.ts create mode 100644 dist/Taskview/tasks/Compadre.js create mode 100644 dist/Taskview/tasks/Compadre.js.map create mode 100644 src/Taskview/tasks/Compadre.ts diff --git a/dist/Taskview/tasks/Compadre.d.ts b/dist/Taskview/tasks/Compadre.d.ts new file mode 100644 index 0000000..4c95b44 --- /dev/null +++ b/dist/Taskview/tasks/Compadre.d.ts @@ -0,0 +1,20 @@ +import { Cohort } from '../../Cohort'; +import { ICohort } from '../../CohortInterfaces'; +import { IAttribute } from '../../data/Attribute'; +import { ATask } from './ATask'; +export declare class Compadre extends ATask { + label: string; + id: string; + hasOutput: boolean; + private eventID; + private _entityName; + private ids; + supports(attributes: IAttribute[], cohorts: ICohort[]): boolean; + showSearchBar(): boolean; + show(columnHeader: HTMLDivElement, container: HTMLDivElement, attributes: IAttribute[], cohorts: ICohort[]): Promise; + appendTable(): void; + sendData(ids: any): Promise; + visualize(response: any): void; + getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; + postData(url?: string, data?: {}): Promise; +} diff --git a/dist/Taskview/tasks/Compadre.js b/dist/Taskview/tasks/Compadre.js new file mode 100644 index 0000000..563eb80 --- /dev/null +++ b/dist/Taskview/tasks/Compadre.js @@ -0,0 +1,123 @@ +import * as aq from 'arquero'; +import { getCohortLabel } from '../../Cohort'; +import { ServerColumnAttribute } from '../../data/Attribute'; +import { getAnimatedLoadingText } from '../../util'; +import { DATA_LABEL } from '../visualizations'; +import { ATask } from './ATask'; +export class Compadre extends ATask { + constructor() { + super(...arguments); + this.label = `Compare ++`; + this.id = `compadre`; + this.hasOutput = false; + this.eventID = 0; + this._entityName = null; + } + supports(attributes, cohorts) { + return cohorts.length >= 2; + } + showSearchBar() { + return false; + } + async show(columnHeader, container, attributes, cohorts) { + super.show(columnHeader, container, attributes, cohorts); + const eventId = ++this.eventID; // get new eventID, we will compare it with the field again to see if it is still up to date + if (cohorts.length >= 2) { + this.$container = this.body + .append('div') + .classed('compadre-container', true) + .node(); + this.$container.insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); + const attrCohort = cohorts[0]; + attributes = [ + new ServerColumnAttribute(attrCohort.idColumn.column, attrCohort.view, attrCohort.database, attrCohort.idColumn), + ]; + this.ids = await this.getData(attributes, cohorts); + if (eventId !== this.eventID) { + return; + } + this.appendTable(); + } + } + appendTable() { + this.$container.innerHTML = ` +
+

Differences in:

+ + + + + + Mutated State + + + Mutation Type + +

+ +
+
+ `; + this.$container.querySelector('button').addEventListener('click', () => { + this.$container + .querySelector('.output') + .insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); + this.sendData(this.ids); + }); + } + async sendData(ids) { + const response = await this.postData('http://localhost:8444/cmp_meta/', { + exclude: ['tissuename', 'tdpid'], + ids, + }); + console.log('Request complete! response:', JSON.stringify(response)); + this.visualize(response); + } + visualize(response) { + this.$container.querySelector('.output').innerHTML = + 'Response is here ' + JSON.stringify(response); + } + async getData(attributes, cohorts) { + const dataPromises = cohorts + .map((cht, chtIndex) => { + const promise = new Promise(async (resolve, reject) => { + const chtDataPromises = attributes.map((attr) => attr.getData(cht.dbId)); + try { + const chtData = await Promise.all(chtDataPromises); // array with one entry per attribute, which contains an array with one value for every item in the cohort + let joinedData = aq.from(chtData[0]); + for (let i = 1; i < chtData.length; i++) { + joinedData = joinedData.join_full(aq.from(chtData[i])); + } + const labelTable = aq.table({ [DATA_LABEL]: [getCohortLabel(cht)] }); + joinedData = joinedData.join_left(labelTable, (data, label) => true); + resolve(joinedData.objects()); + } + catch (e) { + reject(e); + } + }); + return promise; + }); + const data = await Promise.all(dataPromises); + return data; + } + // Example POST method implementation: + async postData(url = '', data = {}) { + // Default options are marked with * + const response = await fetch(url, { + method: 'POST', + mode: 'cors', + cache: 'no-cache', + credentials: 'same-origin', + headers: { + 'Content-Type': 'application/json' + // 'Content-Type': 'application/x-www-form-urlencoded', + }, + redirect: 'follow', + referrerPolicy: 'no-referrer', + body: JSON.stringify(data) // body data type must match "Content-Type" header + }); + return response.json(); // parses JSON response into native JavaScript objects + } +} +//# sourceMappingURL=Compadre.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Compadre.js.map b/dist/Taskview/tasks/Compadre.js.map new file mode 100644 index 0000000..c4b90e1 --- /dev/null +++ b/dist/Taskview/tasks/Compadre.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/TaskList.js b/dist/Taskview/tasks/TaskList.js index 7d78748..be634a1 100644 --- a/dist/Taskview/tasks/TaskList.js +++ b/dist/Taskview/tasks/TaskList.js @@ -2,10 +2,12 @@ import { Compare } from './Compare'; import { Details } from './Details'; import { Filter } from './Filter'; import { Prevalence } from './Prevalence'; +import { Compadre } from './Compadre'; export const TASKLIST = [ new Filter(), new Details(), new Prevalence(), - new Compare() + new Compare(), + new Compadre() ]; // Add new tasks to this array //# sourceMappingURL=TaskList.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/TaskList.js.map b/dist/Taskview/tasks/TaskList.js.map index 9234c81..e463ddc 100644 --- a/dist/Taskview/tasks/TaskList.js.map +++ b/dist/Taskview/tasks/TaskList.js.map @@ -1 +1 @@ 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a/dist/templates/SearchColumn.html b/dist/templates/SearchColumn.html index f2d57bd..a36d333 100644 --- a/dist/templates/SearchColumn.html +++ b/dist/templates/SearchColumn.html @@ -60,6 +60,12 @@
Compare
+
+
+ +
+
Compare ++
+
+ +
+ + + +
+ +
+ + `; + this.$container.querySelector('button#meta').addEventListener('click', () => { + this.$container.querySelector('.output').innerHTML = ''; + this.$container.querySelector('.output') + .insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); + this.sendData(`cmp_meta`, this.ids); + }); + this.$container.querySelector('button#stop').addEventListener('click', () => { var _a; return (_a = this.reader) === null || _a === void 0 ? void 0 : _a.cancel(); }); + } + async sendData(endpoint, ids) { + const response = await this.postData(`http://localhost:8444/${endpoint}/`, { + exclude: ['tissuename', 'tdpid'], + ids, + }); + this.visualize(response); + } + async visualize(response) { + this.reader = response.body.getReader(); + const decoder = new TextDecoder('utf-8'); + let first = true; + while (true) { + const { value, done } = await this.reader.read(); //variable names are important for destructuring + if (done) { + break; + } // if done, value is undefined + console.log(value); + if (first) { + this.$container.querySelector('.output').innerHTML = ''; + first = false; + } + this.$container.querySelector('.output').insertAdjacentHTML('beforeend', `

Response is here ${JSON.stringify(decoder.decode(value))}

`); + } + } + async getData(attributes, cohorts) { + const dataPromises = cohorts + .map((cht, chtIndex) => { + const promise = new Promise(async (resolve, reject) => { + const chtDataPromises = attributes.map((attr) => attr.getData(cht.dbId)); + try { + const chtData = await Promise.all(chtDataPromises); // array with one entry per attribute, which contains an array with one value for every item in the cohort + let joinedData = aq.from(chtData[0]); + for (let i = 1; i < chtData.length; i++) { + joinedData = joinedData.join_full(aq.from(chtData[i])); + } + const labelTable = aq.table({ [DATA_LABEL]: [getCohortLabel(cht)] }); + joinedData = joinedData.join_left(labelTable, (data, label) => true); + resolve(joinedData.objects()); + } + catch (e) { + reject(e); + } + }); + return promise; + }); + const data = await Promise.all(dataPromises); + return data; + } + // Example POST method implementation: + async postData(url = '', data = {}) { + // Default options are marked with * + const response = await fetch(url, { + method: 'POST', + mode: 'cors', + cache: 'no-cache', + credentials: 'same-origin', + headers: { + 'Content-Type': 'application/json' + // 'Content-Type': 'application/x-www-form-urlencoded', + }, + redirect: 'follow', + referrerPolicy: 'no-referrer', + body: JSON.stringify(data) // body data type must match "Content-Type" header + }); + return response; + } +} +//# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map new file mode 100644 index 0000000..d5406f7 --- /dev/null +++ b/dist/Taskview/tasks/Characterize.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Compadre.d.ts b/dist/Taskview/tasks/Compadre.d.ts index 4c95b44..76987d9 100644 --- a/dist/Taskview/tasks/Compadre.d.ts +++ b/dist/Taskview/tasks/Compadre.d.ts @@ -2,7 +2,7 @@ import { Cohort } from '../../Cohort'; import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; -export declare class Compadre extends ATask { +export declare class Characterize extends ATask { label: string; id: string; hasOutput: boolean; diff --git a/dist/Taskview/tasks/Compadre.js b/dist/Taskview/tasks/Compadre.js index 563eb80..c83c510 100644 --- a/dist/Taskview/tasks/Compadre.js +++ b/dist/Taskview/tasks/Compadre.js @@ -4,11 +4,11 @@ import { ServerColumnAttribute } from '../../data/Attribute'; import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; -export class Compadre extends ATask { +export class Characterize extends ATask { constructor() { super(...arguments); - this.label = `Compare ++`; - this.id = `compadre`; + this.label = `Characterize`; + this.id = `characterize`; this.hasOutput = false; this.eventID = 0; this._entityName = null; @@ -25,7 +25,7 @@ export class Compadre extends ATask { if (cohorts.length >= 2) { this.$container = this.body .append('div') - .classed('compadre-container', true) + .classed('characterize-container', true) .node(); this.$container.insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); const attrCohort = cohorts[0]; @@ -53,17 +53,31 @@ export class Compadre extends ATask { Mutation Type -

+

+ +

`; - this.$container.querySelector('button').addEventListener('click', () => { + this.$container.querySelector('button#meta').addEventListener('click', () => { this.$container .querySelector('.output') .insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); this.sendData(this.ids); }); + this.$container.querySelector('button#stream').addEventListener('click', async () => { + const response = await fetch('http://localhost:8444/'); + const body = response.body; + const reader = body.getReader(); + const decoder = new TextDecoder('utf-8'); + while (true) { + const { value, done } = await reader.read(); //variable names are important for destructuring + console.log(decoder.decode(value)); + if (done) + break; // if done, value is undefined + } + }); } async sendData(ids) { const response = await this.postData('http://localhost:8444/cmp_meta/', { diff --git a/dist/Taskview/tasks/Compadre.js.map b/dist/Taskview/tasks/Compadre.js.map index c4b90e1..61a83b1 100644 --- 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\ No newline at end of file diff --git a/dist/Taskview/tasks/TaskList.js b/dist/Taskview/tasks/TaskList.js index be634a1..0ae2447 100644 --- a/dist/Taskview/tasks/TaskList.js +++ b/dist/Taskview/tasks/TaskList.js @@ -2,12 +2,12 @@ import { Compare } from './Compare'; import { Details } from './Details'; import { Filter } from './Filter'; import { Prevalence } from './Prevalence'; -import { Compadre } from './Compadre'; +import { Characterize } from './Characterize'; export const TASKLIST = [ new Filter(), new Details(), new Prevalence(), new Compare(), - new Compadre() + new Characterize() ]; // Add new tasks to this array //# sourceMappingURL=TaskList.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/TaskList.js.map b/dist/Taskview/tasks/TaskList.js.map index e463ddc..830ed84 100644 --- a/dist/Taskview/tasks/TaskList.js.map +++ b/dist/Taskview/tasks/TaskList.js.map @@ -1 +1 @@ -{"version":3,"file":"TaskList.js","sourceRoot":"","sources":["../../../src/Taskview/tasks/TaskList.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,OAAO,EAAC,MAAM,WAAW,CAAC;AAClC,OAAO,EAAC,OAAO,EAAC,MAAM,WAAW,CAAC;AAClC,OAAO,EAAC,MAAM,EAAC,MAAM,UAAU,CAAC;AAChC,OAAO,EAAC,UAAU,EAAC,MAAM,cAAc,CAAC;AACxC,OAAO,EAAC,QAAQ,EAAC,MAAM,YAAY,CAAC;AAEpC,MAAM,CAAC,MAAM,QAAQ,GAAiB;IACpC,IAAI,MAAM,EAAE;IACZ,IAAI,OAAO,EAAE;IACb,IAAI,UAAU,EAAE;IAChB,IAAI,OAAO,EAAE;IACb,IAAI,QAAQ,EAAE;CACf,CAAC,CAAC,8BAA8B"} \ No newline at end of file +{"version":3,"file":"TaskList.js","sourceRoot":"","sources":["../../../src/Taskview/tasks/TaskList.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,OAAO,EAAC,MAAM,WAAW,CAAC;AAClC,OAAO,EAAC,OAAO,EAAC,MAAM,WAAW,CAAC;AAClC,OAAO,EAAC,MAAM,EAAC,MAAM,UAAU,CAAC;AAChC,OAAO,EAAC,UAAU,EAAC,MAAM,cAAc,CAAC;AACxC,OAAO,EAAC,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE5C,MAAM,CAAC,MAAM,QAAQ,GAAiB;IACpC,IAAI,MAAM,EAAE;IACZ,IAAI,OAAO,EAAE;IACb,IAAI,UAAU,EAAE;IAChB,IAAI,OAAO,EAAE;IACb,IAAI,YAAY,EAAE;CACnB,CAAC,CAAC,8BAA8B"} \ No newline at end of file diff --git a/dist/templates/SearchColumn.html b/dist/templates/SearchColumn.html index a36d333..c48059b 100644 --- a/dist/templates/SearchColumn.html +++ b/dist/templates/SearchColumn.html @@ -60,18 +60,12 @@
Compare
-
+
- -
-
Compare ++
-
- +
diff --git a/package.json b/package.json index 35d5086..3cf0075 100644 --- a/package.json +++ b/package.json @@ -75,6 +75,7 @@ "lodash.merge": "^4.x", "lodash.pick": "^4.4.0", "loglevel": "^1.6.4", + "ndjson": "^2.0.0", "react": "^16.13.0", "react-dom": "^16.13.0", "react-router-dom": "^5.2.0", diff --git a/src/Taskview/tasks/Compadre.ts b/src/Taskview/tasks/Characterize.ts similarity index 63% rename from src/Taskview/tasks/Compadre.ts rename to src/Taskview/tasks/Characterize.ts index 15c9627..fa81c18 100644 --- a/src/Taskview/tasks/Compadre.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,21 +1,21 @@ import * as aq from 'arquero'; -import {table} from 'console'; -import { Cohort, getCohortLabel } from '../../Cohort'; -import { ICohort } from '../../CohortInterfaces'; -import { IAttribute, ServerColumnAttribute } from '../../data/Attribute'; -import { getCohortData } from '../../rest'; -import { CohortColorSchema, getAnimatedLoadingText } from '../../util'; -import { getIdTypeFromCohort } from '../../utilIdTypes'; -import { DATA_LABEL } from '../visualizations'; -import { ATask } from './ATask'; - -export class Compadre extends ATask { - public label = `Compare ++`; - public id = `compadre`; +import {Cohort, getCohortLabel} from '../../Cohort'; +import {ICohort} from '../../CohortInterfaces'; +import {IAttribute, ServerColumnAttribute} from '../../data/Attribute'; +import {getCohortData} from '../../rest'; +import {CohortColorSchema, getAnimatedLoadingText} from '../../util'; +import {getIdTypeFromCohort} from '../../utilIdTypes'; +import {DATA_LABEL} from '../visualizations'; +import {ATask} from './ATask'; + +export class Characterize extends ATask { + public label = `Characterize`; + public id = `characterize`; public hasOutput = false; private eventID = 0; private _entityName: string = null; private ids: any[]; + private reader: ReadableStreamDefaultReader; supports(attributes: IAttribute[], cohorts: ICohort[]) { return cohorts.length >= 2; @@ -37,8 +37,9 @@ export class Compadre extends ATask { if (cohorts.length >= 2) { this.$container = this.body .append('div') - .classed('compadre-container', true) + .classed('characterize-container', true) .node(); + this.$container.insertAdjacentElement( 'beforeend', getAnimatedLoadingText('data') @@ -61,8 +62,9 @@ export class Compadre extends ATask { appendTable() { this.$container.innerHTML = `
-

Differences in:

+

Find Differences in:

+ -

+
+ + + +
`; - this.$container.querySelector('button').addEventListener('click', () => { - this.$container - .querySelector('.output') + this.$container.querySelector('button#meta').addEventListener('click', () => { + this.$container.querySelector('.output').innerHTML = ''; + this.$container.querySelector('.output') .insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); - this.sendData(this.ids); + this.sendData(`cmp_meta`, this.ids); }); + + this.$container.querySelector('button#stop').addEventListener('click', () => this.reader?.cancel()); } - async sendData(ids) { + async sendData(endpoint, ids) { const response = await this.postData( - 'http://localhost:8444/cmp_meta/', { + `http://localhost:8444/${endpoint}/`, { exclude: ['tissuename', 'tdpid'], ids, }); - console.log('Request complete! response:', JSON.stringify(response)); this.visualize(response); } - visualize(response) { - this.$container.querySelector('.output').innerHTML = - 'Response is here ' + JSON.stringify(response); + async visualize(response) { + this.reader = response.body.getReader(); + const decoder = new TextDecoder('utf-8'); + let first = true; + while (true) { + const { value, done } = await this.reader.read(); //variable names are important for destructuring + if (done) { break; } // if done, value is undefined + console.log(value); + if (first) { + this.$container.querySelector('.output').innerHTML = ''; + first = false; + } + this.$container.querySelector('.output').insertAdjacentHTML( + 'beforeend', + `

Response is here ${JSON.stringify(decoder.decode(value))}

` + ); + } } async getData(attributes: IAttribute[], cohorts: Cohort[]) { @@ -139,8 +161,8 @@ export class Compadre extends ATask { }, redirect: 'follow', // manual, *follow, error referrerPolicy: 'no-referrer', // no-referrer, *no-referrer-when-downgrade, origin, origin-when-cross-origin, same-origin, strict-origin, strict-origin-when-cross-origin, unsafe-url - body: JSON.stringify(data) // body data type must match "Content-Type" header + body: JSON.stringify(data) // body data type must match "Content-Type" header }); - return response.json(); // parses JSON response into native JavaScript objects + return response; } } diff --git a/src/Taskview/tasks/TaskList.ts b/src/Taskview/tasks/TaskList.ts index 9a0c3d2..6a403f0 100644 --- a/src/Taskview/tasks/TaskList.ts +++ b/src/Taskview/tasks/TaskList.ts @@ -3,12 +3,12 @@ import {Compare} from './Compare'; import {Details} from './Details'; import {Filter} from './Filter'; import {Prevalence} from './Prevalence'; -import {Compadre} from './Compadre'; +import {Characterize} from './Characterize'; export const TASKLIST: Array = [ new Filter(), new Details(), new Prevalence(), new Compare(), - new Compadre() + new Characterize() ]; // Add new tasks to this array diff --git a/src/templates/SearchColumn.html b/src/templates/SearchColumn.html index a36d333..c48059b 100644 --- a/src/templates/SearchColumn.html +++ b/src/templates/SearchColumn.html @@ -60,18 +60,12 @@
Compare
-
+
- -
-
Compare ++
-
- +
From cdec4f07e7ddc0fa2ec466e86d97e3020c86b07b Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 1 Jun 2022 11:50:08 +0200 Subject: [PATCH 05/60] Add Upset & Lineup --- dist/Taskview/tasks/Characterize.d.ts | 17 +- dist/Taskview/tasks/Characterize.js | 168 +++++++++++++--- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 7 + dist/scss/components/task/_filter.scss | 28 --- dist/scss/components/task/_tasks.scss | 30 +++ package.json | 1 + src/Taskview/tasks/Characterize.ts | 201 +++++++++++++++---- src/scss/components/task/_characterize.scss | 7 + src/scss/components/task/_filter.scss | 28 --- src/scss/components/task/_tasks.scss | 30 +++ 11 files changed, 397 insertions(+), 122 deletions(-) create mode 100644 dist/scss/components/task/_characterize.scss create mode 100644 src/scss/components/task/_characterize.scss diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 82215c3..3de7e78 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -1,21 +1,36 @@ +/// +import * as LineUpJS from 'lineupjs'; import { Cohort } from '../../Cohort'; import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; export declare class Characterize extends ATask { + static readonly TREES = 500; label: string; id: string; hasOutput: boolean; private eventID; - private _entityName; private ids; private reader; + progressBar: any; + lineup: LineUpJS.Taggle; + dataProv: LineUpJS.LocalDataProvider; supports(attributes: IAttribute[], cohorts: ICohort[]): boolean; showSearchBar(): boolean; show(columnHeader: HTMLDivElement, container: HTMLDivElement, attributes: IAttribute[], cohorts: ICohort[]): Promise; appendTable(): void; + appendUpset(container: HTMLDivElement): void; + getSetData(ids: any[]): { + name: string; + sets: string[]; + }[]; sendData(endpoint: any, ids: any): Promise; visualize(response: any): Promise; getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; postData(url?: string, data?: {}): Promise; + addProgressBar(): void; + setProgress(iteration: number): void; + fadeOutProgressBar(delay?: number): Promise; + createLineUp(data: any): Promise; + updateLineUp(importances: any): void; } diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index c545cb3..e2c11e8 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -1,9 +1,12 @@ import * as aq from 'arquero'; +import * as LineUpJS from 'lineupjs'; +import { extractCombinations, extractSets, generateCombinations, renderUpSet } from '@upsetjs/bundle'; import { getCohortLabel } from '../../Cohort'; import { ServerColumnAttribute } from '../../data/Attribute'; import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; +import { colors } from '../../colors'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -11,7 +14,6 @@ export class Characterize extends ATask { this.id = `characterize`; this.hasOutput = false; this.eventID = 0; - this._entityName = null; } supports(attributes, cohorts) { return cohorts.length >= 2; @@ -41,36 +43,72 @@ export class Characterize extends ATask { } appendTable() { this.$container.innerHTML = ` -
-

Find Differences in:

- - - +
-
-
-
+
+ +
`; this.$container.querySelector('button#meta').addEventListener('click', () => { - this.$container.querySelector('.output').innerHTML = ''; - this.$container.querySelector('.output') - .insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); + if (this.lineup) { + this.lineup.destroy(); + } + this.$container.querySelector('.lineup-container').innerHTML = ''; + this.addProgressBar(); this.sendData(`cmp_meta`, this.ids); }); - this.$container.querySelector('button#stop').addEventListener('click', () => { var _a; return (_a = this.reader) === null || _a === void 0 ? void 0 : _a.cancel(); }); + this.appendUpset(this.$container.querySelector('div.upset-container')); + } + appendUpset(container) { + const elems = this.getSetData(this.ids); + const { sets, combinations } = extractCombinations(elems, ({ name, sets }) => sets, { type: 'intersection' }); + const sets2 = extractSets(elems, ({ name, sets }) => sets, {}); + const combinations2 = generateCombinations(sets2, { type: 'intersection', min: 2, empty: true, max: 2 }); + let selection = null; + function onHover(set) { + selection = set; + rerender(); + } + function rerender() { + renderUpSet(container, { + sets: sets2, combinations: combinations2, + width: 800, height: 200, + // title: 'Cohort Overlap', + // description: 'Intersection of selected cohorts', + // selection, onHover, + exportButtons: false, + setLabelAlignment: 'right', + // setName: 'Size', + color: colors.barColor + }); + } + rerender(); + // remove set size barchar + container.querySelectorAll('g[data-upset="setaxis"]').forEach((d) => d.remove()); + container.querySelectorAll('text[class^="sBarTextStyle-upset"]').forEach((d) => d.remove()); + container.querySelectorAll('g[data-upset="sets"] rect[class^="fillPrimary-upset"]').forEach((d) => d.remove()); + // remove clipping of cohort labels + container.querySelectorAll('text[class^="setTextStyle-upset"]').forEach((d) => d.removeAttribute('clip-path')); + } + getSetData(ids) { + const setMap = new Map(); + const idList = ids.flat(); + idList.forEach((d) => { + if (!setMap.has(d.tissuename)) { + setMap.set(d.tissuename, [d.Cohort]); + } + else { + setMap.get(d.tissuename).push(d.Cohort); + } + }); + const setArr = Array + .from(setMap) + .map(([key, value]) => ({ name: key, sets: value })); + return setArr; } async sendData(endpoint, ids) { const response = await this.postData(`http://localhost:8444/${endpoint}/`, { @@ -86,14 +124,23 @@ export class Characterize extends ATask { while (true) { const { value, done } = await this.reader.read(); //variable names are important for destructuring if (done) { + console.log('done'); break; } // if done, value is undefined - console.log(value); - if (first) { - this.$container.querySelector('.output').innerHTML = ''; - first = false; + const response = decoder.decode(value); + console.log('response', response); + try { + const responseData = JSON.parse(response); + if (first) { + await this.createLineUp(responseData.importances); // await so its ready for the next response + first = false; + } + this.setProgress(responseData.trees); + this.updateLineUp(responseData.importances); + } + catch (e) { + console.error('could not read JSON data', e); } - this.$container.querySelector('.output').insertAdjacentHTML('beforeend', `

Response is here ${JSON.stringify(decoder.decode(value))}

`); } } async getData(attributes, cohorts) { @@ -134,9 +181,74 @@ export class Characterize extends ATask { }, redirect: 'follow', referrerPolicy: 'no-referrer', - body: JSON.stringify(data) // body data type must match "Content-Type" header + body: JSON.stringify(data), // body data type must match "Content-Type" header + //TODO abortController }); return response; } + addProgressBar() { + const wrapper = this.$container.querySelector('.progress-wrapper'); + wrapper.innerHTML = ''; + wrapper.insertAdjacentHTML('beforeend', ` +
+ +
+
+
+ 0/${Characterize.TREES} +
+
+ `); + this.progressBar = wrapper.querySelector('.progress .progress-bar'); + wrapper + .querySelector(('a.run')) + .addEventListener('click', () => { + var _a; + (_a = this.reader) === null || _a === void 0 ? void 0 : _a.cancel(); + wrapper.querySelector('.progress-ctrl').remove(); + this.progressBar.textContent = 'Stopped'; + this.fadeOutProgressBar(); + }); + } + setProgress(iteration) { + this.progressBar.textContent = `${iteration}/${Characterize.TREES}`; + this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; + if (iteration === Characterize.TREES) { + this.progressBar.textContent = 'Done'; + this.fadeOutProgressBar(); + } + } + async fadeOutProgressBar(delay = 2500) { + return setTimeout(() => { + const wrapper = this.$container.querySelector('.progress-wrapper'); + wrapper.innerHTML = ''; + }, delay); + } + async createLineUp(data) { + const builder = LineUpJS.builder(data); + this.lineup = builder + .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) + .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) + .column(LineUpJS.buildNumberColumn('importance').label('Importance').width(150)) + .deriveColors() + .ranking(LineUpJS.buildRanking() + .supportTypes() + .allColumns() + .sortBy('Importance', 'desc') + .groupBy('Attribute') + .groupSortBy('Importance', 'desc')) + .buildTaggle(this.$container.querySelector('.lineup-container')); + this.dataProv = this.lineup.data; + const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + children[children.length - 1].setFilter({ + filterMissing: true, + min: 0.001, + max: Infinity + }); + } + updateLineUp(importances) { + this.dataProv.setData(importances); + } } +Characterize.TREES = 500; //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss new file mode 100644 index 0000000..599e1ca --- /dev/null +++ b/dist/scss/components/task/_characterize.scss @@ -0,0 +1,7 @@ +.characterize-container { + height: 100%; + display: grid; + grid-template-columns: 1fr; + grid-template-rows: auto auto 1fr; + row-gap: 1em; +} diff --git a/dist/scss/components/task/_filter.scss b/dist/scss/components/task/_filter.scss index 6458351..4d43fa8 100644 --- a/dist/scss/components/task/_filter.scss +++ b/dist/scss/components/task/_filter.scss @@ -118,34 +118,6 @@ width: auto; //needed to adjust to css grid 🤷‍♀️ } } - - .progress-wrapper { - display: flex; - - .progress-ctrl { - width: 2em; // constant width - display: flex; // move button to bottom - align-items: flex-end; - - .run { - color: $color-text; - &:hover { - color: $color-hover; - } - } - } - - .progress { - flex-grow: 1; // variable width - flex-shrink: 1; - margin-bottom: unset; - - .progress-bar { - min-width: 3em; - background-color: $color-bar; - } - } - } } button img { diff --git a/dist/scss/components/task/_tasks.scss b/dist/scss/components/task/_tasks.scss index 025d06d..ddb0a99 100644 --- a/dist/scss/components/task/_tasks.scss +++ b/dist/scss/components/task/_tasks.scss @@ -32,6 +32,36 @@ @import "./details"; @import "./prevalence"; @import "./compare"; + @import "./characterize"; + + + .progress-wrapper { + display: flex; + + .progress-ctrl { + width: 2em; // constant width + display: flex; // move button to bottom + align-items: flex-end; + + .run { + color: $color-text; + &:hover { + color: $color-hover; + } + } + } + + .progress { + flex-grow: 1; // variable width + flex-shrink: 1; + margin-bottom: unset; + + .progress-bar { + min-width: 3em; + background-color: $color-bar; + } + } + } } } diff --git a/package.json b/package.json index 3cf0075..a67df59 100644 --- a/package.json +++ b/package.json @@ -62,6 +62,7 @@ }, "dependencies": { "@keckelt/tsne": "^1.0.0", + "@upsetjs/bundle" : "^1.0.0", "arquero": "^4.8.0", "canvas-confetti": "^1.4.0", "clone": "^2.1.2", diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index fa81c18..eca2e4c 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,21 +1,27 @@ + import * as aq from 'arquero'; +import * as LineUpJS from 'lineupjs'; +import {extractCombinations, extractSets, generateCombinations, isGenerateSetCombinationOptions, renderUpSet} from '@upsetjs/bundle'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; import {IAttribute, ServerColumnAttribute} from '../../data/Attribute'; -import {getCohortData} from '../../rest'; -import {CohortColorSchema, getAnimatedLoadingText} from '../../util'; -import {getIdTypeFromCohort} from '../../utilIdTypes'; +import {getAnimatedLoadingText} from '../../util'; import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; +import {colors} from '../../colors'; export class Characterize extends ATask { + static readonly TREES = 500; + public label = `Characterize`; public id = `characterize`; public hasOutput = false; private eventID = 0; - private _entityName: string = null; private ids: any[]; private reader: ReadableStreamDefaultReader; + progressBar: any; + lineup: LineUpJS.Taggle; + dataProv: LineUpJS.LocalDataProvider; supports(attributes: IAttribute[], cohorts: ICohort[]) { return cohorts.length >= 2; @@ -61,38 +67,81 @@ export class Characterize extends ATask { appendTable() { this.$container.innerHTML = ` -
-

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+
+ +
`; this.$container.querySelector('button#meta').addEventListener('click', () => { - this.$container.querySelector('.output').innerHTML = ''; - this.$container.querySelector('.output') - .insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); + if (this.lineup) { + this.lineup.destroy(); + } + this.$container.querySelector('.lineup-container').innerHTML = ''; + this.addProgressBar(); this.sendData(`cmp_meta`, this.ids); }); - this.$container.querySelector('button#stop').addEventListener('click', () => this.reader?.cancel()); + this.appendUpset(this.$container.querySelector('div.upset-container')); + } + + + appendUpset(container: HTMLDivElement) { + const elems = this.getSetData(this.ids); + const {sets, combinations} = extractCombinations(elems, ({name, sets}) => sets, {type: 'intersection'}); + const sets2 = extractSets(elems, ({name, sets}) => sets, {}); + const combinations2 = generateCombinations(sets2, {type: 'intersection', min: 2, empty: true, max: 2}); + + let selection = null; + + function onHover(set) { + selection = set; + rerender(); + } + + function rerender() { + renderUpSet(container, { + sets: sets2, combinations: combinations2, + width: 800, height: 200, + // title: 'Cohort Overlap', + // description: 'Intersection of selected cohorts', + // selection, onHover, + exportButtons: false, + setLabelAlignment: 'right', + // setName: 'Size', + color: colors.barColor + }); + } + + rerender(); + // remove set size barchar + container.querySelectorAll('g[data-upset="setaxis"]').forEach((d) => d.remove()); + container.querySelectorAll('text[class^="sBarTextStyle-upset"]').forEach((d) => d.remove()); + container.querySelectorAll('g[data-upset="sets"] rect[class^="fillPrimary-upset"]').forEach((d) => d.remove()); + // remove clipping of cohort labels + container.querySelectorAll('text[class^="setTextStyle-upset"]').forEach((d) => d.removeAttribute('clip-path')); + } + + getSetData(ids: any[]) { + const setMap = new Map(); + const idList = ids.flat(); + idList.forEach((d) => { + if (!setMap.has(d.tissuename)) { + setMap.set(d.tissuename, [d.Cohort]); + } else { + setMap.get(d.tissuename).push(d.Cohort); + } + }); + + const setArr = Array + .from(setMap) + .map(([key, value]) => ({name: key, sets: value})); + return setArr; } async sendData(endpoint, ids) { @@ -109,17 +158,24 @@ export class Characterize extends ATask { const decoder = new TextDecoder('utf-8'); let first = true; while (true) { - const { value, done } = await this.reader.read(); //variable names are important for destructuring - if (done) { break; } // if done, value is undefined - console.log(value); - if (first) { - this.$container.querySelector('.output').innerHTML = ''; - first = false; + const {value, done} = await this.reader.read(); //variable names are important for destructuring + if (done) {console.log('done'); break;} // if done, value is undefined + + const response = decoder.decode(value); + console.log('response', response); + + try { + const responseData = JSON.parse(response); + if (first) { + await this.createLineUp(responseData.importances); // await so its ready for the next response + first = false; + } + this.setProgress(responseData.trees); + this.updateLineUp(responseData.importances); + + } catch (e) { + console.error('could not read JSON data', e); } - this.$container.querySelector('.output').insertAdjacentHTML( - 'beforeend', - `

Response is here ${JSON.stringify(decoder.decode(value))}

` - ); } } @@ -161,8 +217,81 @@ export class Characterize extends ATask { }, redirect: 'follow', // manual, *follow, error referrerPolicy: 'no-referrer', // no-referrer, *no-referrer-when-downgrade, origin, origin-when-cross-origin, same-origin, strict-origin, strict-origin-when-cross-origin, unsafe-url - body: JSON.stringify(data) // body data type must match "Content-Type" header + body: JSON.stringify(data), // body data type must match "Content-Type" header + //TODO abortController }); return response; } + + addProgressBar() { + const wrapper = this.$container.querySelector('.progress-wrapper'); + wrapper.innerHTML = ''; + wrapper.insertAdjacentHTML('beforeend', ` +
+ +
+
+
+ 0/${Characterize.TREES} +
+
+ `); + this.progressBar = wrapper.querySelector('.progress .progress-bar'); + wrapper + .querySelector(('a.run')) + .addEventListener('click', () => { + this.reader?.cancel(); + wrapper.querySelector('.progress-ctrl').remove(); + this.progressBar.textContent = 'Stopped'; + this.fadeOutProgressBar(); + }); + } + + setProgress(iteration: number) { + this.progressBar.textContent = `${iteration}/${Characterize.TREES}`; + this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; + + if (iteration === Characterize.TREES) { + this.progressBar.textContent = 'Done'; + this.fadeOutProgressBar(); + } + } + + async fadeOutProgressBar(delay = 2500) { + return setTimeout(() => { + const wrapper = this.$container.querySelector('.progress-wrapper'); + wrapper.innerHTML = ''; + }, delay); + } + + + async createLineUp(data) { + const builder = LineUpJS.builder(data); + this.lineup = builder + .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) + .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) + .column(LineUpJS.buildNumberColumn('importance').label('Importance').width(150)) + .deriveColors() + .ranking(LineUpJS.buildRanking() + .supportTypes() + .allColumns() + .sortBy('Importance', 'desc') + .groupBy('Attribute') + .groupSortBy('Importance', 'desc') + ) + .buildTaggle(this.$container.querySelector('.lineup-container')); + + this.dataProv = this.lineup.data as LineUpJS.LocalDataProvider; + + const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ + filterMissing: true, + min: 0.001, + max: Infinity + }); + } + + updateLineUp(importances: any) { + this.dataProv.setData(importances); + } } diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss new file mode 100644 index 0000000..599e1ca --- /dev/null +++ b/src/scss/components/task/_characterize.scss @@ -0,0 +1,7 @@ +.characterize-container { + height: 100%; + display: grid; + grid-template-columns: 1fr; + grid-template-rows: auto auto 1fr; + row-gap: 1em; +} diff --git a/src/scss/components/task/_filter.scss b/src/scss/components/task/_filter.scss index 6458351..4d43fa8 100644 --- a/src/scss/components/task/_filter.scss +++ b/src/scss/components/task/_filter.scss @@ -118,34 +118,6 @@ width: auto; //needed to adjust to css grid 🤷‍♀️ } } - - .progress-wrapper { - display: flex; - - .progress-ctrl { - width: 2em; // constant width - display: flex; // move button to bottom - align-items: flex-end; - - .run { - color: $color-text; - &:hover { - color: $color-hover; - } - } - } - - .progress { - flex-grow: 1; // variable width - flex-shrink: 1; - margin-bottom: unset; - - .progress-bar { - min-width: 3em; - background-color: $color-bar; - } - } - } } button img { diff --git a/src/scss/components/task/_tasks.scss b/src/scss/components/task/_tasks.scss index 025d06d..ddb0a99 100644 --- a/src/scss/components/task/_tasks.scss +++ b/src/scss/components/task/_tasks.scss @@ -32,6 +32,36 @@ @import "./details"; @import "./prevalence"; @import "./compare"; + @import "./characterize"; + + + .progress-wrapper { + display: flex; + + .progress-ctrl { + width: 2em; // constant width + display: flex; // move button to bottom + align-items: flex-end; + + .run { + color: $color-text; + &:hover { + color: $color-hover; + } + } + } + + .progress { + flex-grow: 1; // variable width + flex-shrink: 1; + margin-bottom: unset; + + .progress-bar { + min-width: 3em; + background-color: $color-bar; + } + } + } } } From 999b0a90b2fe7fdd7d560df78f746321f2d71dec Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 1 Jun 2022 17:28:06 +0200 Subject: [PATCH 06/60] remove grouping by attribute --- dist/Taskview/tasks/Characterize.js | 2 +- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index e2c11e8..6b88da7 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -235,7 +235,7 @@ export class Characterize extends ATask { .supportTypes() .allColumns() .sortBy('Importance', 'desc') - .groupBy('Attribute') + // .groupBy('Attribute') .groupSortBy('Importance', 'desc')) .buildTaggle(this.$container.querySelector('.lineup-container')); this.dataProv = this.lineup.data; diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index d90f9ef..056ee67 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index eca2e4c..a269e28 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -276,7 +276,7 @@ export class Characterize extends ATask { .supportTypes() .allColumns() .sortBy('Importance', 'desc') - .groupBy('Attribute') + // .groupBy('Attribute') .groupSortBy('Importance', 'desc') ) .buildTaggle(this.$container.querySelector('.lineup-container')); From 0586163b706a538487c84fadcf6a7e25b58e9b0d Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 07:34:01 +0200 Subject: [PATCH 07/60] Custom Upset and defining Attributes --- dist/Taskview/tasks/Characterize.d.ts | 3 + dist/Taskview/tasks/Characterize.js | 93 +++++++++++++++-- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 39 ++++++- src/Taskview/tasks/Characterize.ts | 102 ++++++++++++++++--- src/scss/components/task/_characterize.scss | 39 ++++++- 6 files changed, 252 insertions(+), 26 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 3de7e78..722a993 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -15,10 +15,13 @@ export declare class Characterize extends ATask { progressBar: any; lineup: LineUpJS.Taggle; dataProv: LineUpJS.LocalDataProvider; + cohorts: Cohort[]; supports(attributes: IAttribute[], cohorts: ICohort[]): boolean; showSearchBar(): boolean; show(columnHeader: HTMLDivElement, container: HTMLDivElement, attributes: IAttribute[], cohorts: ICohort[]): Promise; appendTable(): void; + appendCustomUpset(container: HTMLDivElement): void; + definingAttributeTooltip(hintText: HTMLElement): void; appendUpset(container: HTMLDivElement): void; getSetData(ids: any[]): { name: string; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 6b88da7..3a1a5cc 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -1,12 +1,13 @@ +import { extractSets, generateCombinations, renderUpSet } from '@upsetjs/bundle'; import * as aq from 'arquero'; import * as LineUpJS from 'lineupjs'; -import { extractCombinations, extractSets, generateCombinations, renderUpSet } from '@upsetjs/bundle'; +import tippy from 'tippy.js'; import { getCohortLabel } from '../../Cohort'; +import { colors } from '../../colors'; import { ServerColumnAttribute } from '../../data/Attribute'; import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; -import { colors } from '../../colors'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -24,17 +25,18 @@ export class Characterize extends ATask { async show(columnHeader, container, attributes, cohorts) { super.show(columnHeader, container, attributes, cohorts); const eventId = ++this.eventID; // get new eventID, we will compare it with the field again to see if it is still up to date - if (cohorts.length >= 2) { + this.cohorts = cohorts; + if (this.cohorts.length >= 2) { this.$container = this.body .append('div') .classed('characterize-container', true) .node(); this.$container.insertAdjacentElement('beforeend', getAnimatedLoadingText('data')); - const attrCohort = cohorts[0]; + const attrCohort = (this.cohorts[0]); attributes = [ new ServerColumnAttribute(attrCohort.idColumn.column, attrCohort.view, attrCohort.database, attrCohort.idColumn), ]; - this.ids = await this.getData(attributes, cohorts); + this.ids = await this.getData(attributes, this.cohorts); if (eventId !== this.eventID) { return; } @@ -43,10 +45,12 @@ export class Characterize extends ATask { } appendTable() { this.$container.innerHTML = ` -
+
+

Cohort Differences

+ Exclude the cohorts' defining attributes
@@ -61,13 +65,80 @@ export class Characterize extends ATask { this.addProgressBar(); this.sendData(`cmp_meta`, this.ids); }); - this.appendUpset(this.$container.querySelector('div.upset-container')); + this.definingAttributeTooltip(this.$container.querySelector('.hint')); + this.appendCustomUpset(this.$container.querySelector('div.custom-upset-container')); + } + appendCustomUpset(container) { + container.insertAdjacentHTML('beforeend', ` +

Overlap between Cohorts

+ `); //in line to display "no overlap" note on the same line + let localChtCopy = this.cohorts.slice(); + const aqData = this.ids.flat(); + const idsAndTheirCohorts = aq.from(aqData) + .groupby('tissuename') + .pivot('Cohort', 'Cohort'); + const intersections = new Map(); + let maxIntersection = 0; + while (localChtCopy.length > 1) { + const drawCht = localChtCopy.shift(); + for (const remainingCht of localChtCopy) { + // To use copied code replace "data" with your own variable + const { count } = idsAndTheirCohorts + .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) + .count() // still a aq table + .object(); + intersections.set(`${drawCht.id}-${remainingCht.id}`, count); + if (count > maxIntersection) { + maxIntersection = count; + } + } + } + if (maxIntersection === 0) { // still zero --> no intersection + container.insertAdjacentHTML('beforeend', ` + Cohorts do not overlap. + `); + } + else { + localChtCopy = this.cohorts.slice(); + while (localChtCopy.length > 1) { + const drawCht = localChtCopy.shift(); + for (const remainingCht of localChtCopy) { + const count = intersections.get(`${drawCht.id}-${remainingCht.id}`); + if (count > 0) { + container.insertAdjacentHTML('beforeend', ` +
+
+
+
+
+
 ${count}
+
+
+ `); + } + } + } + } + } + definingAttributeTooltip(hintText) { + let attributes = []; + for (const cht of this.cohorts) { + const bloodline = cht.getBloodline(); + // get all tasks from the bloodline + // fist task is the one before the cohort + let tasks = bloodline.filter((elem) => elem.elemType === 'task').map((elem) => elem.obj); + // reverse order of tasks -> now the first element is the first task after root cohort + tasks = tasks.reverse(); + tasks.forEach((task) => attributes.push(...task.attributes.map((attr) => attr.label))); + } + attributes = Array.from(new Set(attributes)); // remove duplicates + const attributeList = attributes.reduce((text, attr) => text + `
  • ${attr}
    • `, '
      ') + '
    '; + tippy(hintText, { content: attributeList }); } appendUpset(container) { const elems = this.getSetData(this.ids); - const { sets, combinations } = extractCombinations(elems, ({ name, sets }) => sets, { type: 'intersection' }); - const sets2 = extractSets(elems, ({ name, sets }) => sets, {}); - const combinations2 = generateCombinations(sets2, { type: 'intersection', min: 2, empty: true, max: 2 }); + const sets = extractSets(elems, ({ name, sets }) => sets, {}); + const combinations = generateCombinations(sets, { type: 'intersection', min: 2, empty: true, max: 2 }); let selection = null; function onHover(set) { selection = set; @@ -75,7 +146,7 @@ export class Characterize extends ATask { } function rerender() { renderUpSet(container, { - sets: sets2, combinations: combinations2, + sets, combinations, width: 800, height: 200, // title: 'Cohort Overlap', // description: 'Intersection of selected cohorts', diff --git a/dist/Taskview/tasks/Characterize.js.map 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 599e1ca..b63d633 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -1,7 +1,44 @@ .characterize-container { + $border-radius: 0.2em; + height: 100%; display: grid; grid-template-columns: 1fr; grid-template-rows: auto auto 1fr; row-gap: 1em; -} + +.cht-icon { + width: 1.5em; + height: 1em; + border-radius: $border-radius; + opacity: 0.8; + display: inline-block; + &:nth-child(2) { + transform: translate(-0.75em, 0.25em); + } + } + + .cht-intersect { + display: inline-flex; + width: 40%; //don't want thae bars to be too long + height: 1em; + align-items: center; + border-left: 2px solid $color-bar; + } + + .cht-intersect-bar { + background: $color-bar; + height: 60%; + border-top-right-radius: $border-radius; + border-bottom-right-radius: $border-radius; + } + + .cht-intersect-label { + display: inline-block; + white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container + } + + h1 { + font-size: 1.1em; + } +} \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index a269e28..6d1c0ae 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,14 +1,15 @@ - +import {extractSets, generateCombinations, renderUpSet} from '@upsetjs/bundle'; import * as aq from 'arquero'; import * as LineUpJS from 'lineupjs'; -import {extractCombinations, extractSets, generateCombinations, isGenerateSetCombinationOptions, renderUpSet} from '@upsetjs/bundle'; +import tippy from 'tippy.js'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; +import {colors} from '../../colors'; import {IAttribute, ServerColumnAttribute} from '../../data/Attribute'; +import {Task} from '../../Tasks'; import {getAnimatedLoadingText} from '../../util'; import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; -import {colors} from '../../colors'; export class Characterize extends ATask { static readonly TREES = 500; @@ -22,6 +23,7 @@ export class Characterize extends ATask { progressBar: any; lineup: LineUpJS.Taggle; dataProv: LineUpJS.LocalDataProvider; + cohorts: Cohort[]; supports(attributes: IAttribute[], cohorts: ICohort[]) { return cohorts.length >= 2; @@ -40,7 +42,9 @@ export class Characterize extends ATask { super.show(columnHeader, container, attributes, cohorts); const eventId = ++this.eventID; // get new eventID, we will compare it with the field again to see if it is still up to date - if (cohorts.length >= 2) { + this.cohorts = cohorts as Cohort[]; + + if (this.cohorts.length >= 2) { this.$container = this.body .append('div') .classed('characterize-container', true) @@ -51,11 +55,11 @@ export class Characterize extends ATask { getAnimatedLoadingText('data') ); - const attrCohort = (cohorts[0] as Cohort); + const attrCohort = (this.cohorts[0]); attributes = [ new ServerColumnAttribute(attrCohort.idColumn.column, attrCohort.view, attrCohort.database, attrCohort.idColumn), ]; - this.ids = await this.getData(attributes, cohorts as Cohort[]); + this.ids = await this.getData(attributes, this.cohorts); if (eventId !== this.eventID) { return; @@ -67,10 +71,12 @@ export class Characterize extends ATask { appendTable() { this.$container.innerHTML = ` -
    +
    +

    Cohort Differences

    + Exclude the cohorts' defining attributes
    @@ -87,15 +93,87 @@ export class Characterize extends ATask { this.sendData(`cmp_meta`, this.ids); }); - this.appendUpset(this.$container.querySelector('div.upset-container')); + this.definingAttributeTooltip(this.$container.querySelector('.hint')); + this.appendCustomUpset(this.$container.querySelector('div.custom-upset-container')); + } + appendCustomUpset(container: HTMLDivElement) { + container.insertAdjacentHTML('beforeend', ` +

    Overlap between Cohorts

    + `); //in line to display "no overlap" note on the same line + let localChtCopy = this.cohorts.slice(); + + const aqData = this.ids.flat(); + const idsAndTheirCohorts = aq.from(aqData) + .groupby('tissuename') + .pivot('Cohort', 'Cohort'); + const intersections = new Map(); + let maxIntersection = 0; + + while (localChtCopy.length > 1) { + const drawCht = localChtCopy.shift(); + for (const remainingCht of localChtCopy) { + // To use copied code replace "data" with your own variable + const {count} = idsAndTheirCohorts + .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) + .count() // still a aq table + .object() as {count: number}; + intersections.set(`${drawCht.id}-${remainingCht.id}`, count); + if (count > maxIntersection) { + maxIntersection = count; + } + } + } + + if (maxIntersection === 0) { // still zero --> no intersection + container.insertAdjacentHTML('beforeend', ` + Cohorts do not overlap. + `); + } else { + localChtCopy = this.cohorts.slice(); + while (localChtCopy.length > 1) { + const drawCht = localChtCopy.shift(); + for (const remainingCht of localChtCopy) { + const count = intersections.get(`${drawCht.id}-${remainingCht.id}`); + if (count > 0) { + container.insertAdjacentHTML('beforeend', ` +
    +
    +
    +
    +
    +
     ${count}
    +
    +
    + `); + } + } + } + } + + } + + definingAttributeTooltip(hintText: HTMLElement) { + let attributes = []; + for (const cht of this.cohorts) { + const bloodline = cht.getBloodline(); + // get all tasks from the bloodline + // fist task is the one before the cohort + let tasks = bloodline.filter((elem) => elem.elemType === 'task').map((elem) => elem.obj) as Task[]; + // reverse order of tasks -> now the first element is the first task after root cohort + tasks = tasks.reverse(); + + tasks.forEach((task) => attributes.push(...task.attributes.map((attr) => attr.label))); + } + attributes = Array.from(new Set(attributes)); // remove duplicates + const attributeList = attributes.reduce((text, attr) => text + `
  • ${attr}
    • `, '
      ') + '
    '; + tippy(hintText, {content: attributeList}); } appendUpset(container: HTMLDivElement) { const elems = this.getSetData(this.ids); - const {sets, combinations} = extractCombinations(elems, ({name, sets}) => sets, {type: 'intersection'}); - const sets2 = extractSets(elems, ({name, sets}) => sets, {}); - const combinations2 = generateCombinations(sets2, {type: 'intersection', min: 2, empty: true, max: 2}); + const sets = extractSets(elems, ({name, sets}) => sets, {}); + const combinations = generateCombinations(sets, {type: 'intersection', min: 2, empty: true, max: 2}); let selection = null; @@ -106,7 +184,7 @@ export class Characterize extends ATask { function rerender() { renderUpSet(container, { - sets: sets2, combinations: combinations2, + sets, combinations, width: 800, height: 200, // title: 'Cohort Overlap', // description: 'Intersection of selected cohorts', diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 599e1ca..b63d633 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -1,7 +1,44 @@ .characterize-container { + $border-radius: 0.2em; + height: 100%; display: grid; grid-template-columns: 1fr; grid-template-rows: auto auto 1fr; row-gap: 1em; -} + +.cht-icon { + width: 1.5em; + height: 1em; + border-radius: $border-radius; + opacity: 0.8; + display: inline-block; + &:nth-child(2) { + transform: translate(-0.75em, 0.25em); + } + } + + .cht-intersect { + display: inline-flex; + width: 40%; //don't want thae bars to be too long + height: 1em; + align-items: center; + border-left: 2px solid $color-bar; + } + + .cht-intersect-bar { + background: $color-bar; + height: 60%; + border-top-right-radius: $border-radius; + border-bottom-right-radius: $border-radius; + } + + .cht-intersect-label { + display: inline-block; + white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container + } + + h1 { + font-size: 1.1em; + } +} \ No newline at end of file From 56357f0786750aa300c9f84a688a0a6efaaa0611 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 08:22:42 +0200 Subject: [PATCH 08/60] remove upset and refactor code --- dist/Taskview/tasks/Characterize.d.ts | 35 +-- dist/Taskview/tasks/Characterize.js | 245 +++++++--------- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 2 +- dist/scss/components/task/_tasks.scss | 1 + src/Taskview/tasks/Characterize.ts | 280 ++++++++----------- src/scss/components/task/_characterize.scss | 2 +- src/scss/components/task/_tasks.scss | 1 + 8 files changed, 242 insertions(+), 326 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 722a993..bed648f 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -1,5 +1,4 @@ /// -import * as LineUpJS from 'lineupjs'; import { Cohort } from '../../Cohort'; import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; @@ -12,28 +11,24 @@ export declare class Characterize extends ATask { private eventID; private ids; private reader; - progressBar: any; - lineup: LineUpJS.Taggle; - dataProv: LineUpJS.LocalDataProvider; - cohorts: Cohort[]; + private progressBar; + private lineup; + private dataProv; + private cohorts; + private definingAttributes; supports(attributes: IAttribute[], cohorts: ICohort[]): boolean; showSearchBar(): boolean; show(columnHeader: HTMLDivElement, container: HTMLDivElement, attributes: IAttribute[], cohorts: ICohort[]): Promise; - appendTable(): void; - appendCustomUpset(container: HTMLDivElement): void; - definingAttributeTooltip(hintText: HTMLElement): void; - appendUpset(container: HTMLDivElement): void; - getSetData(ids: any[]): { - name: string; - sets: string[]; - }[]; - sendData(endpoint: any, ids: any): Promise; - visualize(response: any): Promise; - getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; - postData(url?: string, data?: {}): Promise; - addProgressBar(): void; - setProgress(iteration: number): void; - fadeOutProgressBar(delay?: number): Promise; + private createView; + private showOverlap; + setDefiningAttributeTooltip(hintText: HTMLElement): void; + private compare; createLineUp(data: any): Promise; updateLineUp(importances: any): void; + addProgressBar(): void; + setProgress(iteration: number, done?: boolean): void; + setProgressDone(): void; + fadeOutProgressBar(delay?: number): Promise; + getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; + postData(url?: string, data?: {}): Promise; } diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 3a1a5cc..6ea79dc 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -1,9 +1,7 @@ -import { extractSets, generateCombinations, renderUpSet } from '@upsetjs/bundle'; import * as aq from 'arquero'; import * as LineUpJS from 'lineupjs'; import tippy from 'tippy.js'; import { getCohortLabel } from '../../Cohort'; -import { colors } from '../../colors'; import { ServerColumnAttribute } from '../../data/Attribute'; import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; @@ -40,10 +38,10 @@ export class Characterize extends ATask { if (eventId !== this.eventID) { return; } - this.appendTable(); + this.createView(); } } - appendTable() { + createView() { this.$container.innerHTML = `
    @@ -63,12 +61,12 @@ export class Characterize extends ATask { } this.$container.querySelector('.lineup-container').innerHTML = ''; this.addProgressBar(); - this.sendData(`cmp_meta`, this.ids); + this.compare(`cmp_meta`, this.ids); }); - this.definingAttributeTooltip(this.$container.querySelector('.hint')); - this.appendCustomUpset(this.$container.querySelector('div.custom-upset-container')); + this.showOverlap(this.$container.querySelector('div.custom-upset-container')); + this.setDefiningAttributeTooltip(this.$container.querySelector('.hint')); } - appendCustomUpset(container) { + showOverlap(container) { container.insertAdjacentHTML('beforeend', `

    Overlap between Cohorts

    `); //in line to display "no overlap" note on the same line @@ -94,9 +92,7 @@ export class Characterize extends ATask { } } if (maxIntersection === 0) { // still zero --> no intersection - container.insertAdjacentHTML('beforeend', ` - Cohorts do not overlap. - `); + container.insertAdjacentHTML('beforeend', `Cohorts do not overlap.`); } else { localChtCopy = this.cohorts.slice(); @@ -106,22 +102,22 @@ export class Characterize extends ATask { const count = intersections.get(`${drawCht.id}-${remainingCht.id}`); if (count > 0) { container.insertAdjacentHTML('beforeend', ` -
    -
    -
    -
    -
    -
     ${count}
    +
    +
    +
    +
    +
    +
     ${count}
    +
    -
    `); } } } } } - definingAttributeTooltip(hintText) { - let attributes = []; + setDefiningAttributeTooltip(hintText) { + const attributes = []; for (const cht of this.cohorts) { const bloodline = cht.getBloodline(); // get all tasks from the bloodline @@ -129,91 +125,117 @@ export class Characterize extends ATask { let tasks = bloodline.filter((elem) => elem.elemType === 'task').map((elem) => elem.obj); // reverse order of tasks -> now the first element is the first task after root cohort tasks = tasks.reverse(); - tasks.forEach((task) => attributes.push(...task.attributes.map((attr) => attr.label))); + tasks.forEach((task) => attributes.push(...task.attributes)); } - attributes = Array.from(new Set(attributes)); // remove duplicates - const attributeList = attributes.reduce((text, attr) => text + `
  • ${attr}
    • `, '
      ') + '
    '; + this.definingAttributes = attributes.filter((attr, i, arr) => arr.findIndex((attr2) => (attr2.id === attr.id)) === i // if there are multiple attributes with the same id, keep the first + ); + const attributeList = this.definingAttributes + .map((attr) => attr.label) + .reduce((text, attr) => text + `
  • ${attr}
    • `, '
      ') + '
    '; tippy(hintText, { content: attributeList }); } - appendUpset(container) { - const elems = this.getSetData(this.ids); - const sets = extractSets(elems, ({ name, sets }) => sets, {}); - const combinations = generateCombinations(sets, { type: 'intersection', min: 2, empty: true, max: 2 }); - let selection = null; - function onHover(set) { - selection = set; - rerender(); - } - function rerender() { - renderUpSet(container, { - sets, combinations, - width: 800, height: 200, - // title: 'Cohort Overlap', - // description: 'Intersection of selected cohorts', - // selection, onHover, - exportButtons: false, - setLabelAlignment: 'right', - // setName: 'Size', - color: colors.barColor - }); - } - rerender(); - // remove set size barchar - container.querySelectorAll('g[data-upset="setaxis"]').forEach((d) => d.remove()); - container.querySelectorAll('text[class^="sBarTextStyle-upset"]').forEach((d) => d.remove()); - container.querySelectorAll('g[data-upset="sets"] rect[class^="fillPrimary-upset"]').forEach((d) => d.remove()); - // remove clipping of cohort labels - container.querySelectorAll('text[class^="setTextStyle-upset"]').forEach((d) => d.removeAttribute('clip-path')); - } - getSetData(ids) { - const setMap = new Map(); - const idList = ids.flat(); - idList.forEach((d) => { - if (!setMap.has(d.tissuename)) { - setMap.set(d.tissuename, [d.Cohort]); - } - else { - setMap.get(d.tissuename).push(d.Cohort); - } - }); - const setArr = Array - .from(setMap) - .map(([key, value]) => ({ name: key, sets: value })); - return setArr; - } - async sendData(endpoint, ids) { + async compare(endpoint, ids) { const response = await this.postData(`http://localhost:8444/${endpoint}/`, { exclude: ['tissuename', 'tdpid'], ids, }); - this.visualize(response); - } - async visualize(response) { + // start to read response stream this.reader = response.body.getReader(); const decoder = new TextDecoder('utf-8'); let first = true; while (true) { const { value, done } = await this.reader.read(); //variable names are important for destructuring if (done) { - console.log('done'); - break; - } // if done, value is undefined + console.log('the reader is done'); + this.setProgressDone(); + break; // if done, value is undefined --> skip the rest + } const response = decoder.decode(value); - console.log('response', response); + // console.log('response', response); try { const responseData = JSON.parse(response); + console.log(responseData.trees); + this.setProgress(responseData.trees); if (first) { await this.createLineUp(responseData.importances); // await so its ready for the next response first = false; } - this.setProgress(responseData.trees); - this.updateLineUp(responseData.importances); + else { + this.updateLineUp(responseData.importances); + } } catch (e) { - console.error('could not read JSON data', e); + // console.error('could not read JSON data', e); } } } + async createLineUp(data) { + const builder = LineUpJS.builder(data); + this.lineup = builder + .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) + .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) + .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) + .deriveColors() + .ranking(LineUpJS.buildRanking() + .supportTypes() + .allColumns() + .sortBy('Importance', 'desc') + // .groupBy('Attribute') + .groupSortBy('Importance', 'desc')) + .buildTaggle(this.$container.querySelector('.lineup-container')); + this.dataProv = this.lineup.data; + const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + children[children.length - 1].setFilter({ + filterMissing: true, + min: 0.001, + max: Infinity + }); + } + updateLineUp(importances) { + var _a; + (_a = this.dataProv) === null || _a === void 0 ? void 0 : _a.setData(importances); + } + addProgressBar() { + const wrapper = this.$container.querySelector('.progress-wrapper'); + wrapper.innerHTML = ''; + wrapper.insertAdjacentHTML('beforeend', ` +
    + +
    +
    +
    + 0/${Characterize.TREES} +
    +
    + `); + this.progressBar = wrapper.querySelector('.progress .progress-bar'); + wrapper + .querySelector(('a.run')) + .addEventListener('click', () => { + var _a; + (_a = this.reader) === null || _a === void 0 ? void 0 : _a.cancel(); + wrapper.querySelector('.progress-ctrl').remove(); + this.progressBar.textContent = 'Stopped'; + this.fadeOutProgressBar(); + }); + } + setProgress(iteration, done = false) { + this.progressBar.textContent = `${iteration}/${Characterize.TREES}`; + this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; + if (iteration === Characterize.TREES) { + this.setProgressDone(); + } + } + setProgressDone() { + this.progressBar.textContent = 'Done'; + this.fadeOutProgressBar(); + } + async fadeOutProgressBar(delay = 2500) { + return setTimeout(() => { + const wrapper = this.$container.querySelector('.progress-wrapper'); + wrapper.innerHTML = ''; + }, delay); + } async getData(attributes, cohorts) { const dataPromises = cohorts .map((cht, chtIndex) => { @@ -257,69 +279,6 @@ export class Characterize extends ATask { }); return response; } - addProgressBar() { - const wrapper = this.$container.querySelector('.progress-wrapper'); - wrapper.innerHTML = ''; - wrapper.insertAdjacentHTML('beforeend', ` -
    - -
    -
    -
    - 0/${Characterize.TREES} -
    -
    - `); - this.progressBar = wrapper.querySelector('.progress .progress-bar'); - wrapper - .querySelector(('a.run')) - .addEventListener('click', () => { - var _a; - (_a = this.reader) === null || _a === void 0 ? void 0 : _a.cancel(); - wrapper.querySelector('.progress-ctrl').remove(); - this.progressBar.textContent = 'Stopped'; - this.fadeOutProgressBar(); - }); - } - setProgress(iteration) { - this.progressBar.textContent = `${iteration}/${Characterize.TREES}`; - this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; - if (iteration === Characterize.TREES) { - this.progressBar.textContent = 'Done'; - this.fadeOutProgressBar(); - } - } - async fadeOutProgressBar(delay = 2500) { - return setTimeout(() => { - const wrapper = this.$container.querySelector('.progress-wrapper'); - wrapper.innerHTML = ''; - }, delay); - } - async createLineUp(data) { - const builder = LineUpJS.builder(data); - this.lineup = builder - .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) - .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) - .column(LineUpJS.buildNumberColumn('importance').label('Importance').width(150)) - .deriveColors() - .ranking(LineUpJS.buildRanking() - .supportTypes() - .allColumns() - .sortBy('Importance', 'desc') - // .groupBy('Attribute') - .groupSortBy('Importance', 'desc')) - .buildTaggle(this.$container.querySelector('.lineup-container')); - this.dataProv = this.lineup.data; - const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... - children[children.length - 1].setFilter({ - filterMissing: true, - min: 0.001, - max: Infinity - }); - } - updateLineUp(importances) { - this.dataProv.setData(importances); - } } Characterize.TREES = 500; //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index b63d633..2c235e4 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto 1fr; + grid-template-rows: auto auto auto 1fr; // 1fr for lineup row-gap: 1em; .cht-icon { diff --git a/dist/scss/components/task/_tasks.scss b/dist/scss/components/task/_tasks.scss index ddb0a99..47cc435 100644 --- a/dist/scss/components/task/_tasks.scss +++ b/dist/scss/components/task/_tasks.scss @@ -37,6 +37,7 @@ .progress-wrapper { display: flex; + align-items: center; .progress-ctrl { width: 2em; // constant width diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 6d1c0ae..f0fd2a2 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,10 +1,8 @@ -import {extractSets, generateCombinations, renderUpSet} from '@upsetjs/bundle'; import * as aq from 'arquero'; import * as LineUpJS from 'lineupjs'; import tippy from 'tippy.js'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; -import {colors} from '../../colors'; import {IAttribute, ServerColumnAttribute} from '../../data/Attribute'; import {Task} from '../../Tasks'; import {getAnimatedLoadingText} from '../../util'; @@ -18,12 +16,15 @@ export class Characterize extends ATask { public id = `characterize`; public hasOutput = false; private eventID = 0; + private ids: any[]; private reader: ReadableStreamDefaultReader; - progressBar: any; - lineup: LineUpJS.Taggle; - dataProv: LineUpJS.LocalDataProvider; - cohorts: Cohort[]; + + private progressBar: any; + private lineup: LineUpJS.Taggle; + private dataProv: LineUpJS.LocalDataProvider; + private cohorts: Cohort[]; + private definingAttributes: any[]; supports(attributes: IAttribute[], cohorts: ICohort[]) { return cohorts.length >= 2; @@ -65,11 +66,11 @@ export class Characterize extends ATask { return; } - this.appendTable(); + this.createView(); } } - appendTable() { + private createView() { this.$container.innerHTML = `
    @@ -90,13 +91,14 @@ export class Characterize extends ATask { } this.$container.querySelector('.lineup-container').innerHTML = ''; this.addProgressBar(); - this.sendData(`cmp_meta`, this.ids); + this.compare(`cmp_meta`, this.ids); }); - this.definingAttributeTooltip(this.$container.querySelector('.hint')); - this.appendCustomUpset(this.$container.querySelector('div.custom-upset-container')); + this.showOverlap(this.$container.querySelector('div.custom-upset-container')); + this.setDefiningAttributeTooltip(this.$container.querySelector('.hint')); } - appendCustomUpset(container: HTMLDivElement) { + + private showOverlap(container: HTMLDivElement) { container.insertAdjacentHTML('beforeend', `

    Overlap between Cohorts

    `); //in line to display "no overlap" note on the same line @@ -125,9 +127,7 @@ export class Characterize extends ATask { } if (maxIntersection === 0) { // still zero --> no intersection - container.insertAdjacentHTML('beforeend', ` - Cohorts do not overlap. - `); + container.insertAdjacentHTML('beforeend', `Cohorts do not overlap.`); } else { localChtCopy = this.cohorts.slice(); while (localChtCopy.length > 1) { @@ -136,24 +136,23 @@ export class Characterize extends ATask { const count = intersections.get(`${drawCht.id}-${remainingCht.id}`); if (count > 0) { container.insertAdjacentHTML('beforeend', ` -
    -
    -
    -
    -
    -
     ${count}
    +
    +
    +
    +
    +
    +
     ${count}
    +
    -
    `); } } } } - } - definingAttributeTooltip(hintText: HTMLElement) { - let attributes = []; + setDefiningAttributeTooltip(hintText: HTMLElement) { + const attributes = []; for (const cht of this.cohorts) { const bloodline = cht.getBloodline(); // get all tasks from the bloodline @@ -162,143 +161,87 @@ export class Characterize extends ATask { // reverse order of tasks -> now the first element is the first task after root cohort tasks = tasks.reverse(); - tasks.forEach((task) => attributes.push(...task.attributes.map((attr) => attr.label))); - } - attributes = Array.from(new Set(attributes)); // remove duplicates - const attributeList = attributes.reduce((text, attr) => text + `
  • ${attr}
    • `, '
      ') + '
    '; - tippy(hintText, {content: attributeList}); - } - - - appendUpset(container: HTMLDivElement) { - const elems = this.getSetData(this.ids); - const sets = extractSets(elems, ({name, sets}) => sets, {}); - const combinations = generateCombinations(sets, {type: 'intersection', min: 2, empty: true, max: 2}); - - let selection = null; - - function onHover(set) { - selection = set; - rerender(); - } - - function rerender() { - renderUpSet(container, { - sets, combinations, - width: 800, height: 200, - // title: 'Cohort Overlap', - // description: 'Intersection of selected cohorts', - // selection, onHover, - exportButtons: false, - setLabelAlignment: 'right', - // setName: 'Size', - color: colors.barColor - }); + tasks.forEach( + (task) => attributes.push(...task.attributes) + ); } - rerender(); - // remove set size barchar - container.querySelectorAll('g[data-upset="setaxis"]').forEach((d) => d.remove()); - container.querySelectorAll('text[class^="sBarTextStyle-upset"]').forEach((d) => d.remove()); - container.querySelectorAll('g[data-upset="sets"] rect[class^="fillPrimary-upset"]').forEach((d) => d.remove()); - // remove clipping of cohort labels - container.querySelectorAll('text[class^="setTextStyle-upset"]').forEach((d) => d.removeAttribute('clip-path')); - } + this.definingAttributes = attributes.filter( + (attr, i, arr) => arr.findIndex((attr2) => (attr2.id === attr.id)) === i // if there are multiple attributes with the same id, keep the first + ); + const attributeList = this.definingAttributes + .map((attr) => attr.label) + .reduce((text, attr) => text + `
  • ${attr}
    • `, '
      ') + '
    '; - getSetData(ids: any[]) { - const setMap = new Map(); - const idList = ids.flat(); - idList.forEach((d) => { - if (!setMap.has(d.tissuename)) { - setMap.set(d.tissuename, [d.Cohort]); - } else { - setMap.get(d.tissuename).push(d.Cohort); - } - }); - - const setArr = Array - .from(setMap) - .map(([key, value]) => ({name: key, sets: value})); - return setArr; + tippy(hintText, {content: attributeList}); } - async sendData(endpoint, ids) { + private async compare(endpoint, ids) { const response = await this.postData( `http://localhost:8444/${endpoint}/`, { exclude: ['tissuename', 'tdpid'], ids, }); - this.visualize(response); - } - async visualize(response) { + // start to read response stream this.reader = response.body.getReader(); const decoder = new TextDecoder('utf-8'); let first = true; while (true) { const {value, done} = await this.reader.read(); //variable names are important for destructuring - if (done) {console.log('done'); break;} // if done, value is undefined + if (done) { + console.log('the reader is done'); + this.setProgressDone(); + break; // if done, value is undefined --> skip the rest + } const response = decoder.decode(value); - console.log('response', response); + // console.log('response', response); try { const responseData = JSON.parse(response); + console.log(responseData.trees); + this.setProgress(responseData.trees); if (first) { await this.createLineUp(responseData.importances); // await so its ready for the next response first = false; + } else { + this.updateLineUp(responseData.importances); } - this.setProgress(responseData.trees); - this.updateLineUp(responseData.importances); - } catch (e) { - console.error('could not read JSON data', e); + // console.error('could not read JSON data', e); } } } - async getData(attributes: IAttribute[], cohorts: Cohort[]) { - const dataPromises = cohorts - .map((cht, chtIndex) => { - const promise = new Promise(async (resolve, reject) => { - const chtDataPromises = attributes.map((attr) => attr.getData(cht.dbId)); - try { - const chtData = await Promise.all(chtDataPromises); // array with one entry per attribute, which contains an array with one value for every item in the cohort - let joinedData = aq.from(chtData[0]); - for (let i = 1; i < chtData.length; i++) { - joinedData = joinedData.join_full(aq.from(chtData[i])); - } - const labelTable = aq.table({[DATA_LABEL]: [getCohortLabel(cht)]}); - joinedData = joinedData.join_left(labelTable, (data, label) => true); - resolve(joinedData.objects()); - } catch (e) { - reject(e); - } - }); - return promise; - }); - const data = await Promise.all(dataPromises); - return data; - } + async createLineUp(data) { + const builder = LineUpJS.builder(data); + this.lineup = builder + .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) + .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) + .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) + .deriveColors() + .ranking(LineUpJS.buildRanking() + .supportTypes() + .allColumns() + .sortBy('Importance', 'desc') + // .groupBy('Attribute') + .groupSortBy('Importance', 'desc') + ) + .buildTaggle(this.$container.querySelector('.lineup-container')); - // Example POST method implementation: - async postData(url = '', data = {}) { - // Default options are marked with * - const response = await fetch(url, { - method: 'POST', // *GET, POST, PUT, DELETE, etc. - mode: 'cors', // no-cors, *cors, same-origin - cache: 'no-cache', // *default, no-cache, reload, force-cache, only-if-cached - credentials: 'same-origin', // include, *same-origin, omit - headers: { - 'Content-Type': 'application/json' - // 'Content-Type': 'application/x-www-form-urlencoded', - }, - redirect: 'follow', // manual, *follow, error - referrerPolicy: 'no-referrer', // no-referrer, *no-referrer-when-downgrade, origin, origin-when-cross-origin, same-origin, strict-origin, strict-origin-when-cross-origin, unsafe-url - body: JSON.stringify(data), // body data type must match "Content-Type" header - //TODO abortController + this.dataProv = this.lineup.data as LineUpJS.LocalDataProvider; + + const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ + filterMissing: true, + min: 0.001, + max: Infinity }); - return response; + } + + updateLineUp(importances: any) { + this.dataProv?.setData(importances); } addProgressBar() { @@ -325,16 +268,20 @@ export class Characterize extends ATask { }); } - setProgress(iteration: number) { + setProgress(iteration: number, done=false) { this.progressBar.textContent = `${iteration}/${Characterize.TREES}`; this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; if (iteration === Characterize.TREES) { - this.progressBar.textContent = 'Done'; - this.fadeOutProgressBar(); + this.setProgressDone(); } } + setProgressDone() { + this.progressBar.textContent = 'Done'; + this.fadeOutProgressBar(); + } + async fadeOutProgressBar(delay = 2500) { return setTimeout(() => { const wrapper = this.$container.querySelector('.progress-wrapper'); @@ -342,34 +289,47 @@ export class Characterize extends ATask { }, delay); } - - async createLineUp(data) { - const builder = LineUpJS.builder(data); - this.lineup = builder - .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) - .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) - .column(LineUpJS.buildNumberColumn('importance').label('Importance').width(150)) - .deriveColors() - .ranking(LineUpJS.buildRanking() - .supportTypes() - .allColumns() - .sortBy('Importance', 'desc') - // .groupBy('Attribute') - .groupSortBy('Importance', 'desc') - ) - .buildTaggle(this.$container.querySelector('.lineup-container')); - - this.dataProv = this.lineup.data as LineUpJS.LocalDataProvider; - - const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... - (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ - filterMissing: true, - min: 0.001, - max: Infinity - }); + async getData(attributes: IAttribute[], cohorts: Cohort[]) { + const dataPromises = cohorts + .map((cht, chtIndex) => { + const promise = new Promise(async (resolve, reject) => { + const chtDataPromises = attributes.map((attr) => attr.getData(cht.dbId)); + try { + const chtData = await Promise.all(chtDataPromises); // array with one entry per attribute, which contains an array with one value for every item in the cohort + let joinedData = aq.from(chtData[0]); + for (let i = 1; i < chtData.length; i++) { + joinedData = joinedData.join_full(aq.from(chtData[i])); + } + const labelTable = aq.table({[DATA_LABEL]: [getCohortLabel(cht)]}); + joinedData = joinedData.join_left(labelTable, (data, label) => true); + resolve(joinedData.objects()); + } catch (e) { + reject(e); + } + }); + return promise; + }); + const data = await Promise.all(dataPromises); + return data; } - updateLineUp(importances: any) { - this.dataProv.setData(importances); + // Example POST method implementation: + async postData(url = '', data = {}) { + // Default options are marked with * + const response = await fetch(url, { + method: 'POST', // *GET, POST, PUT, DELETE, etc. + mode: 'cors', // no-cors, *cors, same-origin + cache: 'no-cache', // *default, no-cache, reload, force-cache, only-if-cached + credentials: 'same-origin', // include, *same-origin, omit + headers: { + 'Content-Type': 'application/json' + // 'Content-Type': 'application/x-www-form-urlencoded', + }, + redirect: 'follow', // manual, *follow, error + referrerPolicy: 'no-referrer', // no-referrer, *no-referrer-when-downgrade, origin, origin-when-cross-origin, same-origin, strict-origin, strict-origin-when-cross-origin, unsafe-url + body: JSON.stringify(data), // body data type must match "Content-Type" header + //TODO abortController + }); + return response; } } diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index b63d633..2c235e4 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto 1fr; + grid-template-rows: auto auto auto 1fr; // 1fr for lineup row-gap: 1em; .cht-icon { diff --git a/src/scss/components/task/_tasks.scss b/src/scss/components/task/_tasks.scss index ddb0a99..47cc435 100644 --- a/src/scss/components/task/_tasks.scss +++ b/src/scss/components/task/_tasks.scss @@ -37,6 +37,7 @@ .progress-wrapper { display: flex; + align-items: center; .progress-ctrl { width: 2em; // constant width From b0b8ecf40e1e5a3dd09094e7a379b36d9583ce6c Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 08:37:01 +0200 Subject: [PATCH 09/60] exclude bloodline --- dist/Taskview/tasks/Characterize.js | 16 ++++++++++------ dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 19 ++++++++++++------- 3 files changed, 23 insertions(+), 14 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 6ea79dc..48fbcaf 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -61,7 +61,7 @@ export class Characterize extends ATask { } this.$container.querySelector('.lineup-container').innerHTML = ''; this.addProgressBar(); - this.compare(`cmp_meta`, this.ids); + this.compare(`cmp_meta`); }); this.showOverlap(this.$container.querySelector('div.custom-upset-container')); this.setDefiningAttributeTooltip(this.$container.querySelector('.hint')); @@ -134,10 +134,14 @@ export class Characterize extends ATask { .reduce((text, attr) => text + `
  • ${attr}
    • `, '
      ') + '
    '; tippy(hintText, { content: attributeList }); } - async compare(endpoint, ids) { + async compare(endpoint) { + const excludeChechbox = this.$container.querySelector('input#exclude-attributes'); + const excludeBloodline = excludeChechbox.checked; + const excludeAttributes = excludeBloodline ? this.definingAttributes.map((attr) => attr.id) : []; + const exclude = ['tissuename', 'tdpid', ...excludeAttributes]; const response = await this.postData(`http://localhost:8444/${endpoint}/`, { - exclude: ['tissuename', 'tdpid'], - ids, + exclude, + ids: this.ids, }); // start to read response stream this.reader = response.body.getReader(); @@ -151,7 +155,7 @@ export class Characterize extends ATask { break; // if done, value is undefined --> skip the rest } const response = decoder.decode(value); - // console.log('response', response); + console.log('response', response); try { const responseData = JSON.parse(response); console.log(responseData.trees); @@ -165,7 +169,7 @@ export class Characterize extends ATask { } } catch (e) { - // console.error('could not read JSON data', e); + console.error('could not read JSON data', e); } } } diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index e178e7e..01a1b1c 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index f0fd2a2..fbc8f3d 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -24,7 +24,7 @@ export class Characterize extends ATask { private lineup: LineUpJS.Taggle; private dataProv: LineUpJS.LocalDataProvider; private cohorts: Cohort[]; - private definingAttributes: any[]; + private definingAttributes: IAttribute[]; supports(attributes: IAttribute[], cohorts: ICohort[]) { return cohorts.length >= 2; @@ -91,7 +91,7 @@ export class Characterize extends ATask { } this.$container.querySelector('.lineup-container').innerHTML = ''; this.addProgressBar(); - this.compare(`cmp_meta`, this.ids); + this.compare(`cmp_meta`); }); this.showOverlap(this.$container.querySelector('div.custom-upset-container')); @@ -176,11 +176,16 @@ export class Characterize extends ATask { tippy(hintText, {content: attributeList}); } - private async compare(endpoint, ids) { + private async compare(endpoint) { + const excludeChechbox = this.$container.querySelector('input#exclude-attributes') as HTMLInputElement; + const excludeBloodline = excludeChechbox.checked; + const excludeAttributes = excludeBloodline ? this.definingAttributes.map((attr) => attr.id) : []; + const exclude = ['tissuename', 'tdpid', ...excludeAttributes]; + const response = await this.postData( `http://localhost:8444/${endpoint}/`, { - exclude: ['tissuename', 'tdpid'], - ids, + exclude, + ids: this.ids, }); // start to read response stream @@ -196,7 +201,7 @@ export class Characterize extends ATask { } const response = decoder.decode(value); - // console.log('response', response); + console.log('response', response); try { const responseData = JSON.parse(response); @@ -209,7 +214,7 @@ export class Characterize extends ATask { this.updateLineUp(responseData.importances); } } catch (e) { - // console.error('could not read JSON data', e); + console.error('could not read JSON data', e); } } } From 83cc6a21779a0df95610f072be38fabb8aee7e72 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 09:37:47 +0200 Subject: [PATCH 10/60] move hardcoded exlcuded attributes to backend --- dist/Taskview/tasks/Characterize.js | 3 +-- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 3 +-- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 48fbcaf..8cd314d 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -138,9 +138,8 @@ export class Characterize extends ATask { const excludeChechbox = this.$container.querySelector('input#exclude-attributes'); const excludeBloodline = excludeChechbox.checked; const excludeAttributes = excludeBloodline ? this.definingAttributes.map((attr) => attr.id) : []; - const exclude = ['tissuename', 'tdpid', ...excludeAttributes]; const response = await this.postData(`http://localhost:8444/${endpoint}/`, { - exclude, + exclude: excludeAttributes, ids: this.ids, }); // start to read response stream diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 01a1b1c..b0af289 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index fbc8f3d..4ca04ec 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -180,11 +180,10 @@ export class Characterize extends ATask { const excludeChechbox = this.$container.querySelector('input#exclude-attributes') as HTMLInputElement; const excludeBloodline = excludeChechbox.checked; const excludeAttributes = excludeBloodline ? this.definingAttributes.map((attr) => attr.id) : []; - const exclude = ['tissuename', 'tdpid', ...excludeAttributes]; const response = await this.postData( `http://localhost:8444/${endpoint}/`, { - exclude, + exclude: excludeAttributes, ids: this.ids, }); From 68b21e6e3a272b8353f49eb7377c79ce1de946a3 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 12:02:46 +0200 Subject: [PATCH 11/60] adapt for mutated data --- dist/Taskview/tasks/Characterize.js | 21 +++++++++++++++------ dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 22 +++++++++++++++------- 3 files changed, 31 insertions(+), 14 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 8cd314d..8e3a97d 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -55,14 +55,14 @@ export class Characterize extends ATask {
    `; - this.$container.querySelector('button#meta').addEventListener('click', () => { + this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { if (this.lineup) { this.lineup.destroy(); } this.$container.querySelector('.lineup-container').innerHTML = ''; this.addProgressBar(); - this.compare(`cmp_meta`); - }); + this.compare(`cmp_${btn.id}`); + })); this.showOverlap(this.$container.querySelector('div.custom-upset-container')); this.setDefiningAttributeTooltip(this.$container.querySelector('.hint')); } @@ -80,8 +80,7 @@ export class Characterize extends ATask { while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { - // To use copied code replace "data" with your own variable - const { count } = idsAndTheirCohorts + const { count } = idsAndTheirCohorts // cmp: https://observablehq.com/d/59236004518c5729 .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table .object(); @@ -137,7 +136,17 @@ export class Characterize extends ATask { async compare(endpoint) { const excludeChechbox = this.$container.querySelector('input#exclude-attributes'); const excludeBloodline = excludeChechbox.checked; - const excludeAttributes = excludeBloodline ? this.definingAttributes.map((attr) => attr.id) : []; + const excludeAttributes = !excludeBloodline ? [] : this.definingAttributes + .filter((attr) => { + if (endpoint === 'cmp_meta') { + return 'serverColumn' in attr; + } + else if (endpoint === 'cmp_mutated') { + return 'gene' in attr; + } + return true; + }) + .map((attr) => 'gene' in attr ? attr.gene : attr.id); const response = await this.postData(`http://localhost:8444/${endpoint}/`, { exclude: excludeAttributes, ids: this.ids, diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index b0af289..a81ce3e 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 4ca04ec..d3f9fa5 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -3,7 +3,7 @@ import * as LineUpJS from 'lineupjs'; import tippy from 'tippy.js'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; -import {IAttribute, ServerColumnAttribute} from '../../data/Attribute'; +import {IAttribute, ServerColumnAttribute, GeneScoreAttribute} from '../../data/Attribute'; import {Task} from '../../Tasks'; import {getAnimatedLoadingText} from '../../util'; import {DATA_LABEL} from '../visualizations'; @@ -85,14 +85,14 @@ export class Characterize extends ATask {
    `; - this.$container.querySelector('button#meta').addEventListener('click', () => { + this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { if (this.lineup) { this.lineup.destroy(); } this.$container.querySelector('.lineup-container').innerHTML = ''; this.addProgressBar(); - this.compare(`cmp_meta`); - }); + this.compare(`cmp_${btn.id}`); + })); this.showOverlap(this.$container.querySelector('div.custom-upset-container')); this.setDefiningAttributeTooltip(this.$container.querySelector('.hint')); @@ -114,8 +114,7 @@ export class Characterize extends ATask { while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { - // To use copied code replace "data" with your own variable - const {count} = idsAndTheirCohorts + const {count} = idsAndTheirCohorts // cmp: https://observablehq.com/d/59236004518c5729 .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table .object() as {count: number}; @@ -179,7 +178,16 @@ export class Characterize extends ATask { private async compare(endpoint) { const excludeChechbox = this.$container.querySelector('input#exclude-attributes') as HTMLInputElement; const excludeBloodline = excludeChechbox.checked; - const excludeAttributes = excludeBloodline ? this.definingAttributes.map((attr) => attr.id) : []; + const excludeAttributes = !excludeBloodline ? [] : this.definingAttributes + .filter((attr) => { + if (endpoint === 'cmp_meta') { + return 'serverColumn' in attr; + } else if (endpoint === 'cmp_mutated') { + return 'gene' in attr; + } + return true; + }) + .map((attr) => 'gene' in attr ? (attr as GeneScoreAttribute).gene : attr.id); const response = await this.postData( `http://localhost:8444/${endpoint}/`, { From 84f95ce3afed6708c1d80ae1b33c23f02119e05c Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 14:08:16 +0200 Subject: [PATCH 12/60] Show overlap with Jaccard Similarity --- dist/Taskview/tasks/Characterize.d.ts | 3 ++ dist/Taskview/tasks/Characterize.js | 38 +++++++++++++++++------ dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 41 ++++++++++++++++++------- 4 files changed, 62 insertions(+), 22 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index bed648f..f568719 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -5,6 +5,9 @@ import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; export declare class Characterize extends ATask { static readonly TREES = 500; + static readonly jaccardFormat: (n: number | { + valueOf(): number; + }) => string; label: string; id: string; hasOutput: boolean; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 8e3a97d..644973f 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -1,11 +1,13 @@ import * as aq from 'arquero'; import * as LineUpJS from 'lineupjs'; +import { format } from 'd3-format'; import tippy from 'tippy.js'; import { getCohortLabel } from '../../Cohort'; import { ServerColumnAttribute } from '../../data/Attribute'; import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; +import { colors } from '../../colors'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -68,7 +70,7 @@ export class Characterize extends ATask { } showOverlap(container) { container.insertAdjacentHTML('beforeend', ` -

    Overlap between Cohorts

    +

    Item Similarity of Cohorts

    `); //in line to display "no overlap" note on the same line let localChtCopy = this.cohorts.slice(); const aqData = this.ids.flat(); @@ -76,7 +78,7 @@ export class Characterize extends ATask { .groupby('tissuename') .pivot('Cohort', 'Cohort'); const intersections = new Map(); - let maxIntersection = 0; + let maxJaccard = 0; while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { @@ -84,13 +86,15 @@ export class Characterize extends ATask { .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table .object(); - intersections.set(`${drawCht.id}-${remainingCht.id}`, count); - if (count > maxIntersection) { - maxIntersection = count; + const jaccardIndex = count / aqData.length; + intersections.set(`${drawCht.id}-${remainingCht.id}`, jaccardIndex); + if (jaccardIndex > maxJaccard) { + maxJaccard = jaccardIndex; } } } - if (maxIntersection === 0) { // still zero --> no intersection + let noOverlapCounter = 0; + if (maxJaccard === 0) { // still zero --> no intersection container.insertAdjacentHTML('beforeend', `Cohorts do not overlap.`); } else { @@ -98,21 +102,34 @@ export class Characterize extends ATask { while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { - const count = intersections.get(`${drawCht.id}-${remainingCht.id}`); - if (count > 0) { + const jaccard = intersections.get(`${drawCht.id}-${remainingCht.id}`); + if (jaccard > 0) { container.insertAdjacentHTML('beforeend', `
    -
    -
     ${count}
    +
    +
     ${Characterize.jaccardFormat(jaccard)}
    `); } + else { + noOverlapCounter++; + } } } + if (noOverlapCounter > 0) { + container.insertAdjacentHTML('beforeend', ` +

    + + + ${noOverlapCounter} other cohort combinations have no overlap. + +

    + `); + } } } setDefiningAttributeTooltip(hintText) { @@ -293,4 +310,5 @@ export class Characterize extends ATask { } } Characterize.TREES = 500; +Characterize.jaccardFormat = format('.1~%'); //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index a81ce3e..4412dab 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index d3f9fa5..a2a6e23 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,5 +1,6 @@ import * as aq from 'arquero'; import * as LineUpJS from 'lineupjs'; +import {format} from 'd3-format'; import tippy from 'tippy.js'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; @@ -8,9 +9,11 @@ import {Task} from '../../Tasks'; import {getAnimatedLoadingText} from '../../util'; import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; +import {colors} from '../../colors'; export class Characterize extends ATask { static readonly TREES = 500; + static readonly jaccardFormat = format('.1~%'); public label = `Characterize`; public id = `characterize`; @@ -26,6 +29,7 @@ export class Characterize extends ATask { private cohorts: Cohort[]; private definingAttributes: IAttribute[]; + supports(attributes: IAttribute[], cohorts: ICohort[]) { return cohorts.length >= 2; } @@ -100,7 +104,7 @@ export class Characterize extends ATask { private showOverlap(container: HTMLDivElement) { container.insertAdjacentHTML('beforeend', ` -

    Overlap between Cohorts

    +

    Item Similarity of Cohorts

    `); //in line to display "no overlap" note on the same line let localChtCopy = this.cohorts.slice(); @@ -109,7 +113,7 @@ export class Characterize extends ATask { .groupby('tissuename') .pivot('Cohort', 'Cohort'); const intersections = new Map(); - let maxIntersection = 0; + let maxJaccard = 0; while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); @@ -118,35 +122,50 @@ export class Characterize extends ATask { .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table .object() as {count: number}; - intersections.set(`${drawCht.id}-${remainingCht.id}`, count); - if (count > maxIntersection) { - maxIntersection = count; + const jaccardIndex = count / aqData.length; + intersections.set(`${drawCht.id}-${remainingCht.id}`, jaccardIndex); + if (jaccardIndex > maxJaccard) { + maxJaccard = jaccardIndex; } } } - if (maxIntersection === 0) { // still zero --> no intersection + let noOverlapCounter = 0; + if (maxJaccard === 0) { // still zero --> no intersection container.insertAdjacentHTML('beforeend', `Cohorts do not overlap.`); } else { localChtCopy = this.cohorts.slice(); while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { - const count = intersections.get(`${drawCht.id}-${remainingCht.id}`); - if (count > 0) { + const jaccard = intersections.get(`${drawCht.id}-${remainingCht.id}`); + if (jaccard > 0) { container.insertAdjacentHTML('beforeend', `
    -
    -
     ${count}
    +
    +
     ${Characterize.jaccardFormat(jaccard)}
    `); + } else { + noOverlapCounter++; } } } + + if (noOverlapCounter > 0) { + container.insertAdjacentHTML('beforeend', ` +

    + + + ${noOverlapCounter} other cohort combinations have no overlap. + +

    + `); + } } } @@ -280,7 +299,7 @@ export class Characterize extends ATask { }); } - setProgress(iteration: number, done=false) { + setProgress(iteration: number, done = false) { this.progressBar.textContent = `${iteration}/${Characterize.TREES}`; this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; From ed49d3cb60c71bcc714b57102808c33e6cea5647 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 14:13:24 +0200 Subject: [PATCH 13/60] fix jaccard similarity remove duplicate tissues --- dist/Taskview/tasks/Characterize.js | 3 ++- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 8 +++++--- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 644973f..28b79de 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -77,6 +77,7 @@ export class Characterize extends ATask { const idsAndTheirCohorts = aq.from(aqData) .groupby('tissuename') .pivot('Cohort', 'Cohort'); + const uniqueIds = idsAndTheirCohorts.count().object().count; const intersections = new Map(); let maxJaccard = 0; while (localChtCopy.length > 1) { @@ -86,7 +87,7 @@ export class Characterize extends ATask { .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table .object(); - const jaccardIndex = count / aqData.length; + const jaccardIndex = count / uniqueIds; intersections.set(`${drawCht.id}-${remainingCht.id}`, jaccardIndex); if (jaccardIndex > maxJaccard) { maxJaccard = jaccardIndex; diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 4412dab..5b0d3e2 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index a2a6e23..1ed6e18 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -110,11 +110,13 @@ export class Characterize extends ATask { const aqData = this.ids.flat(); const idsAndTheirCohorts = aq.from(aqData) - .groupby('tissuename') - .pivot('Cohort', 'Cohort'); + .groupby('tissuename') + .pivot('Cohort', 'Cohort'); + const uniqueIds = (idsAndTheirCohorts.count().object() as {count: number}).count; const intersections = new Map(); let maxJaccard = 0; + while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { @@ -122,7 +124,7 @@ export class Characterize extends ATask { .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table .object() as {count: number}; - const jaccardIndex = count / aqData.length; + const jaccardIndex = count / uniqueIds; intersections.set(`${drawCht.id}-${remainingCht.id}`, jaccardIndex); if (jaccardIndex > maxJaccard) { maxJaccard = jaccardIndex; From 7f539f6b01ef069a7a1001dfc6af84a93ff9d111 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 2 Jun 2022 17:24:11 +0200 Subject: [PATCH 14/60] Shoe jaccard and exclusive share --- dist/Taskview/tasks/Characterize.js | 55 ++++++++++++----- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 37 +++++++---- src/Taskview/tasks/Characterize.ts | 65 ++++++++++++++------ src/scss/components/task/_characterize.scss | 37 +++++++---- 5 files changed, 137 insertions(+), 59 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 28b79de..759e88d 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -77,22 +77,39 @@ export class Characterize extends ATask { const idsAndTheirCohorts = aq.from(aqData) .groupby('tissuename') .pivot('Cohort', 'Cohort'); - const uniqueIds = idsAndTheirCohorts.count().object().count; const intersections = new Map(); let maxJaccard = 0; + let i = 0; while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); - for (const remainingCht of localChtCopy) { - const { count } = idsAndTheirCohorts // cmp: https://observablehq.com/d/59236004518c5729 + for (const [j, remainingCht] of localChtCopy.entries()) { + const uniqueCohortIds = idsAndTheirCohorts.filter(aq.escape((d) => d[drawCht.label] !== undefined || d[remainingCht.label] !== undefined)); + const uniqueIds = uniqueCohortIds.count().object().count; + const intersectingItems = uniqueCohortIds // cmp: https://observablehq.com/d/59236004518c5729 .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table - .object(); - const jaccardIndex = count / uniqueIds; - intersections.set(`${drawCht.id}-${remainingCht.id}`, jaccardIndex); + .object().count; + const jaccardIndex = intersectingItems / uniqueIds; + const onlyAItems = uniqueCohortIds // cmp: https://observablehq.com/d/59236004518c5729 + .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] === undefined)) + .count() // still a aq table + .object().count; + const exclusiveInA = onlyAItems / uniqueIds; + const onlyBItems = uniqueCohortIds // cmp: https://observablehq.com/d/59236004518c5729 + .filter(aq.escape((d) => d[drawCht.label] === undefined && d[remainingCht.label] !== undefined)) + .count() // still a aq table + .object().count; + const exclusiveInB = onlyBItems / uniqueIds; + intersections.set(`${drawCht.id}-${remainingCht.id}`, { + intersection: jaccardIndex, + exclusiveInA, + exclusiveInB + }); if (jaccardIndex > maxJaccard) { maxJaccard = jaccardIndex; } } + i++; } let noOverlapCounter = 0; if (maxJaccard === 0) { // still zero --> no intersection @@ -103,15 +120,25 @@ export class Characterize extends ATask { while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { - const jaccard = intersections.get(`${drawCht.id}-${remainingCht.id}`); - if (jaccard > 0) { + const { intersection, exclusiveInA, exclusiveInB } = intersections.get(`${drawCht.id}-${remainingCht.id}`); + if (intersection > 0) { container.insertAdjacentHTML('beforeend', ` -
    -
    -
    -
    -
    -
     ${Characterize.jaccardFormat(jaccard)}
    +
    +
    +
    +
    +
    +
    +
     ${Characterize.jaccardFormat(exclusiveInA)} are only in
    +
    +
    +
    +
     ${Characterize.jaccardFormat(intersection)} are in both
    +
    +
    +
    +
     ${Characterize.jaccardFormat(exclusiveInB)} are only in
    +
    `); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 5b0d3e2..6ab1451 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 2c235e4..d8bae95 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -13,29 +13,40 @@ border-radius: $border-radius; opacity: 0.8; display: inline-block; - &:nth-child(2) { + + &.up { + transform: translate(0, -0.25em); + } + + &.left.down { // transformations don't stack, so combine into one rule transform: translate(-0.75em, 0.25em); } } - .cht-intersect { + .cht-overlap { + display: inline-flex; + flex-direction: column; + width: 500px; + } + + .cht-bar { display: inline-flex; - width: 40%; //don't want thae bars to be too long + // width: 40%; //don't want thae bars to be too long height: 1em; align-items: center; border-left: 2px solid $color-bar; - } - .cht-intersect-bar { - background: $color-bar; - height: 60%; - border-top-right-radius: $border-radius; - border-bottom-right-radius: $border-radius; - } + .cht-bar-bar { + background: $color-bar; + height: 60%; + border-top-right-radius: $border-radius; + border-bottom-right-radius: $border-radius; + } - .cht-intersect-label { - display: inline-block; - white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container + .cht-bar-label { + display: inline-block; + white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container + } } h1 { diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 1ed6e18..b4e1257 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -110,26 +110,45 @@ export class Characterize extends ATask { const aqData = this.ids.flat(); const idsAndTheirCohorts = aq.from(aqData) - .groupby('tissuename') - .pivot('Cohort', 'Cohort'); - const uniqueIds = (idsAndTheirCohorts.count().object() as {count: number}).count; - const intersections = new Map(); + .groupby('tissuename') + .pivot('Cohort', 'Cohort'); + const intersections = new Map(); let maxJaccard = 0; - + let i = 0; while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); - for (const remainingCht of localChtCopy) { - const {count} = idsAndTheirCohorts // cmp: https://observablehq.com/d/59236004518c5729 + for (const [j, remainingCht] of localChtCopy.entries()) { + const uniqueCohortIds = idsAndTheirCohorts.filter(aq.escape((d) => d[drawCht.label] !== undefined || d[remainingCht.label] !== undefined)); + const uniqueIds = (uniqueCohortIds.count().object() as {count: number}).count; + const intersectingItems = (uniqueCohortIds // cmp: https://observablehq.com/d/59236004518c5729 .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] !== undefined)) .count() // still a aq table - .object() as {count: number}; - const jaccardIndex = count / uniqueIds; - intersections.set(`${drawCht.id}-${remainingCht.id}`, jaccardIndex); + .object() as {count: number}).count; + const jaccardIndex = intersectingItems / uniqueIds; + + const onlyAItems = (uniqueCohortIds // cmp: https://observablehq.com/d/59236004518c5729 + .filter(aq.escape((d) => d[drawCht.label] !== undefined && d[remainingCht.label] === undefined)) + .count() // still a aq table + .object() as {count: number}).count; + const exclusiveInA = onlyAItems / uniqueIds; + + const onlyBItems = (uniqueCohortIds // cmp: https://observablehq.com/d/59236004518c5729 + .filter(aq.escape((d) => d[drawCht.label] === undefined && d[remainingCht.label] !== undefined)) + .count() // still a aq table + .object() as {count: number}).count; + const exclusiveInB = onlyBItems / uniqueIds; + + intersections.set(`${drawCht.id}-${remainingCht.id}`, { + intersection: jaccardIndex, + exclusiveInA, + exclusiveInB + }); if (jaccardIndex > maxJaccard) { maxJaccard = jaccardIndex; } } + i++; } let noOverlapCounter = 0; @@ -140,15 +159,25 @@ export class Characterize extends ATask { while (localChtCopy.length > 1) { const drawCht = localChtCopy.shift(); for (const remainingCht of localChtCopy) { - const jaccard = intersections.get(`${drawCht.id}-${remainingCht.id}`); - if (jaccard > 0) { + const {intersection, exclusiveInA, exclusiveInB} = intersections.get(`${drawCht.id}-${remainingCht.id}`); + if (intersection > 0) { container.insertAdjacentHTML('beforeend', ` -
    -
    -
    -
    -
    -
     ${Characterize.jaccardFormat(jaccard)}
    +
    +
    +
    +
    +
    +
    +
     ${Characterize.jaccardFormat(exclusiveInA)} are only in
    +
    +
    +
    +
     ${Characterize.jaccardFormat(intersection)} are in both
    +
    +
    +
    +
     ${Characterize.jaccardFormat(exclusiveInB)} are only in
    +
    `); diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 2c235e4..d8bae95 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -13,29 +13,40 @@ border-radius: $border-radius; opacity: 0.8; display: inline-block; - &:nth-child(2) { + + &.up { + transform: translate(0, -0.25em); + } + + &.left.down { // transformations don't stack, so combine into one rule transform: translate(-0.75em, 0.25em); } } - .cht-intersect { + .cht-overlap { + display: inline-flex; + flex-direction: column; + width: 500px; + } + + .cht-bar { display: inline-flex; - width: 40%; //don't want thae bars to be too long + // width: 40%; //don't want thae bars to be too long height: 1em; align-items: center; border-left: 2px solid $color-bar; - } - .cht-intersect-bar { - background: $color-bar; - height: 60%; - border-top-right-radius: $border-radius; - border-bottom-right-radius: $border-radius; - } + .cht-bar-bar { + background: $color-bar; + height: 60%; + border-top-right-radius: $border-radius; + border-bottom-right-radius: $border-radius; + } - .cht-intersect-label { - display: inline-block; - white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container + .cht-bar-label { + display: inline-block; + white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container + } } h1 { From 667d91e385f2ad18c609d93ddeba089f72f69cae Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 7 Jun 2022 09:27:06 +0200 Subject: [PATCH 15/60] show overlap with overlapping bars --- dist/Taskview/tasks/Characterize.js | 53 ++++++++------------ dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 22 ++------ src/Taskview/tasks/Characterize.ts | 49 ++++++++---------- src/scss/components/task/_characterize.scss | 22 ++------ 5 files changed, 51 insertions(+), 97 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 759e88d..2b6a68a 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -70,7 +70,7 @@ export class Characterize extends ATask { } showOverlap(container) { container.insertAdjacentHTML('beforeend', ` -

    Item Similarity of Cohorts

    +

    Overlap of Cohorts

    `); //in line to display "no overlap" note on the same line let localChtCopy = this.cohorts.slice(); const aqData = this.ids.flat(); @@ -116,36 +116,27 @@ export class Characterize extends ATask { container.insertAdjacentHTML('beforeend', `Cohorts do not overlap.`); } else { - localChtCopy = this.cohorts.slice(); - while (localChtCopy.length > 1) { - const drawCht = localChtCopy.shift(); - for (const remainingCht of localChtCopy) { - const { intersection, exclusiveInA, exclusiveInB } = intersections.get(`${drawCht.id}-${remainingCht.id}`); - if (intersection > 0) { - container.insertAdjacentHTML('beforeend', ` -
    -
    -
    -
    -
    -
    -
     ${Characterize.jaccardFormat(exclusiveInA)} are only in
    -
    -
    -
    -
     ${Characterize.jaccardFormat(intersection)} are in both
    -
    -
    -
    -
     ${Characterize.jaccardFormat(exclusiveInB)} are only in
    -
    -
    + const intersectArr = [...intersections] + .sort((cmp1, cmp2) => cmp2[1].intersection - cmp1[1].intersection); // sort by decreasing overlap + for (const [chtKey, { intersection, exclusiveInA, exclusiveInB }] of intersectArr) { + if (intersection > 0) { + const [chtA, chtB] = chtKey.split('-'); + const drawCht = this.cohorts.find((cht) => cht.id === chtA); + const remainingCht = this.cohorts.find((cht) => cht.id === chtB); + container.insertAdjacentHTML('beforeend', ` +
    +
    +
    +
    +
    +
    - `); - } - else { - noOverlapCounter++; - } +
     ${Characterize.jaccardFormat(intersection)}
    +
    + `); + } + else { + noOverlapCounter++; } } if (noOverlapCounter > 0) { @@ -192,7 +183,7 @@ export class Characterize extends ATask { return true; }) .map((attr) => 'gene' in attr ? attr.gene : attr.id); - const response = await this.postData(`http://localhost:8444/${endpoint}/`, { + const response = await this.postData(`http://localhost:9666/${endpoint}/`, { exclude: excludeAttributes, ids: this.ids, }); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 6ab1451..d9bf3ea 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index d8bae95..b9e1328 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -26,27 +26,13 @@ .cht-overlap { display: inline-flex; flex-direction: column; - width: 500px; + row-gap: 1px; + width: 50%; } .cht-bar { - display: inline-flex; - // width: 40%; //don't want thae bars to be too long - height: 1em; - align-items: center; - border-left: 2px solid $color-bar; - - .cht-bar-bar { - background: $color-bar; - height: 60%; - border-top-right-radius: $border-radius; - border-bottom-right-radius: $border-radius; - } - - .cht-bar-label { - display: inline-block; - white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container - } + height: 0.5em; + border-radius: $border-radius; } h1 { diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index b4e1257..6e53617 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -104,7 +104,7 @@ export class Characterize extends ATask { private showOverlap(container: HTMLDivElement) { container.insertAdjacentHTML('beforeend', ` -

    Item Similarity of Cohorts

    +

    Overlap of Cohorts

    `); //in line to display "no overlap" note on the same line let localChtCopy = this.cohorts.slice(); @@ -155,35 +155,26 @@ export class Characterize extends ATask { if (maxJaccard === 0) { // still zero --> no intersection container.insertAdjacentHTML('beforeend', `Cohorts do not overlap.`); } else { - localChtCopy = this.cohorts.slice(); - while (localChtCopy.length > 1) { - const drawCht = localChtCopy.shift(); - for (const remainingCht of localChtCopy) { - const {intersection, exclusiveInA, exclusiveInB} = intersections.get(`${drawCht.id}-${remainingCht.id}`); - if (intersection > 0) { - container.insertAdjacentHTML('beforeend', ` -
    -
    -
    -
    -
    -
    -
     ${Characterize.jaccardFormat(exclusiveInA)} are only in
    -
    -
    -
    -
     ${Characterize.jaccardFormat(intersection)} are in both
    -
    -
    -
    -
     ${Characterize.jaccardFormat(exclusiveInB)} are only in
    -
    -
    + const intersectArr = [...intersections] + .sort((cmp1, cmp2) => cmp2[1].intersection - cmp1[1].intersection); // sort by decreasing overlap + for (const [chtKey, {intersection, exclusiveInA, exclusiveInB}] of intersectArr) { + if (intersection > 0) { + const [chtA, chtB] = chtKey.split('-'); + const drawCht = this.cohorts.find((cht) => cht.id === chtA); + const remainingCht = this.cohorts.find((cht) => cht.id === chtB); + container.insertAdjacentHTML('beforeend', ` +
    +
    +
    +
    +
    +
    - `); - } else { - noOverlapCounter++; - } +
     ${Characterize.jaccardFormat(intersection)}
    +
    + `); + } else { + noOverlapCounter++; } } diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index d8bae95..b9e1328 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -26,27 +26,13 @@ .cht-overlap { display: inline-flex; flex-direction: column; - width: 500px; + row-gap: 1px; + width: 50%; } .cht-bar { - display: inline-flex; - // width: 40%; //don't want thae bars to be too long - height: 1em; - align-items: center; - border-left: 2px solid $color-bar; - - .cht-bar-bar { - background: $color-bar; - height: 60%; - border-top-right-radius: $border-radius; - border-bottom-right-radius: $border-radius; - } - - .cht-bar-label { - display: inline-block; - white-space: nowrap; // bar can be up 100% of the containers width, leaving no room for the next --> but the container is 50% wide at max, so we can let the text savely overflow the container - } + height: 0.5em; + border-radius: $border-radius; } h1 { From 171cd793ea45292daaef23288906c101e1764104 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 7 Jun 2022 09:27:17 +0200 Subject: [PATCH 16/60] change port --- src/Taskview/tasks/Characterize.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 6e53617..187b824 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -231,7 +231,7 @@ export class Characterize extends ATask { .map((attr) => 'gene' in attr ? (attr as GeneScoreAttribute).gene : attr.id); const response = await this.postData( - `http://localhost:8444/${endpoint}/`, { + `http://localhost:9666/${endpoint}/`, { exclude: excludeAttributes, ids: this.ids, }); From 9b2adfa91252c5a50707ce5e39482b6585e5ffa3 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 8 Jun 2022 09:21:17 +0200 Subject: [PATCH 17/60] Access kokiri via proxy --- dist/Taskview/tasks/Characterize.js | 2 +- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 2b6a68a..2102f16 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -183,7 +183,7 @@ export class Characterize extends ATask { return true; }) .map((attr) => 'gene' in attr ? attr.gene : attr.id); - const response = await this.postData(`http://localhost:9666/${endpoint}/`, { + const response = await this.postData(`http://localhost:8080/kokiri/${endpoint}/`, { exclude: excludeAttributes, ids: this.ids, }); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index d9bf3ea..40cad3e 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 187b824..aa2818d 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -231,7 +231,7 @@ export class Characterize extends ATask { .map((attr) => 'gene' in attr ? (attr as GeneScoreAttribute).gene : attr.id); const response = await this.postData( - `http://localhost:9666/${endpoint}/`, { + `http://localhost:8080/kokiri/${endpoint}/`, { exclude: excludeAttributes, ids: this.ids, }); From a213b2bc59d70d9ccaed04fcbe8175c842392b66 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 8 Jun 2022 09:40:42 +0200 Subject: [PATCH 18/60] remove localhost from url --- dist/Taskview/tasks/Characterize.d.ts | 2 +- dist/Taskview/tasks/Characterize.js | 9 +++++---- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 16 +++++++++------- 4 files changed, 16 insertions(+), 13 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index f568719..91330f1 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -33,5 +33,5 @@ export declare class Characterize extends ATask { setProgressDone(): void; fadeOutProgressBar(delay?: number): Promise; getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; - postData(url?: string, data?: {}): Promise; + postData(endpoint: string, data?: {}): Promise; } diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 2102f16..822af94 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -1,13 +1,13 @@ import * as aq from 'arquero'; -import * as LineUpJS from 'lineupjs'; import { format } from 'd3-format'; +import * as LineUpJS from 'lineupjs'; import tippy from 'tippy.js'; import { getCohortLabel } from '../../Cohort'; +import { colors } from '../../colors'; import { ServerColumnAttribute } from '../../data/Attribute'; import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; -import { colors } from '../../colors'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -183,7 +183,7 @@ export class Characterize extends ATask { return true; }) .map((attr) => 'gene' in attr ? attr.gene : attr.id); - const response = await this.postData(`http://localhost:8080/kokiri/${endpoint}/`, { + const response = await this.postData(endpoint, { exclude: excludeAttributes, ids: this.ids, }); @@ -309,7 +309,8 @@ export class Characterize extends ATask { return data; } // Example POST method implementation: - async postData(url = '', data = {}) { + async postData(endpoint, data = {}) { + const url = '/kokiri/' + endpoint + '/'; // Default options are marked with * const response = await fetch(url, { method: 'POST', diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 40cad3e..08fd72d 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index aa2818d..c29bd29 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,15 +1,15 @@ import * as aq from 'arquero'; -import * as LineUpJS from 'lineupjs'; import {format} from 'd3-format'; +import * as LineUpJS from 'lineupjs'; import tippy from 'tippy.js'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; -import {IAttribute, ServerColumnAttribute, GeneScoreAttribute} from '../../data/Attribute'; +import {colors} from '../../colors'; +import {GeneScoreAttribute, IAttribute, ServerColumnAttribute} from '../../data/Attribute'; import {Task} from '../../Tasks'; import {getAnimatedLoadingText} from '../../util'; import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; -import {colors} from '../../colors'; export class Characterize extends ATask { static readonly TREES = 500; @@ -167,8 +167,8 @@ export class Characterize extends ATask {
    -
    -
    +
    +
     ${Characterize.jaccardFormat(intersection)}
    @@ -231,7 +231,7 @@ export class Characterize extends ATask { .map((attr) => 'gene' in attr ? (attr as GeneScoreAttribute).gene : attr.id); const response = await this.postData( - `http://localhost:8080/kokiri/${endpoint}/`, { + endpoint, { exclude: excludeAttributes, ids: this.ids, }); @@ -367,7 +367,8 @@ export class Characterize extends ATask { } // Example POST method implementation: - async postData(url = '', data = {}) { + async postData(endpoint: string, data = {}) { + const url = '/kokiri/' + endpoint + '/'; // Default options are marked with * const response = await fetch(url, { method: 'POST', // *GET, POST, PUT, DELETE, etc. @@ -383,6 +384,7 @@ export class Characterize extends ATask { body: JSON.stringify(data), // body data type must match "Content-Type" header //TODO abortController }); + return response; } } From d95460c9ea25be0f0fd5a35da2e1a4799f37e70d Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 14 Jun 2022 12:00:02 +0200 Subject: [PATCH 19/60] Switch to Websockets --- dist/Taskview/tasks/Characterize.d.ts | 2 +- dist/Taskview/tasks/Characterize.js | 46 ++++++++++++++---------- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 48 ++++++++++++++----------- 4 files changed, 57 insertions(+), 41 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 91330f1..d10737e 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -13,7 +13,7 @@ export declare class Characterize extends ATask { hasOutput: boolean; private eventID; private ids; - private reader; + private ws; private progressBar; private lineup; private dataProv; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 822af94..f506a0c 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -183,25 +183,29 @@ export class Characterize extends ATask { return true; }) .map((attr) => 'gene' in attr ? attr.gene : attr.id); - const response = await this.postData(endpoint, { - exclude: excludeAttributes, - ids: this.ids, - }); - // start to read response stream - this.reader = response.body.getReader(); - const decoder = new TextDecoder('utf-8'); - let first = true; - while (true) { - const { value, done } = await this.reader.read(); //variable names are important for destructuring - if (done) { - console.log('the reader is done'); - this.setProgressDone(); - break; // if done, value is undefined --> skip the rest + const url = new URL(`/kokiri/${endpoint}/`, location.href); + url.protocol = url.protocol.replace('http', 'ws'); + console.log('url', url); + this.ws = new WebSocket(url); + this.ws.onopen = async () => { + const data = JSON.stringify({ + exclude: excludeAttributes, + ids: this.ids, + }); + console.log('Socket is open'); + try { + this.ws.send(data); } - const response = decoder.decode(value); - console.log('response', response); + catch { + console.error('error sending data'); + } + console.log('sent comparison data'); + }; + let first = true; + this.ws.onmessage = async (message) => { + console.log('response', message); + const responseData = JSON.parse(message.data); try { - const responseData = JSON.parse(response); console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { @@ -215,7 +219,11 @@ export class Characterize extends ATask { catch (e) { console.error('could not read JSON data', e); } - } + }; + this.ws.onclose = () => { + console.log('the socket is done'); + this.setProgressDone(); + }; } async createLineUp(data) { const builder = LineUpJS.builder(data); @@ -261,7 +269,7 @@ export class Characterize extends ATask { .querySelector(('a.run')) .addEventListener('click', () => { var _a; - (_a = this.reader) === null || _a === void 0 ? void 0 : _a.cancel(); + (_a = this.ws) === null || _a === void 0 ? void 0 : _a.close(); wrapper.querySelector('.progress-ctrl').remove(); this.progressBar.textContent = 'Stopped'; this.fadeOutProgressBar(); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 08fd72d..faff3f0 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index c29bd29..77af855 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -21,7 +21,7 @@ export class Characterize extends ATask { private eventID = 0; private ids: any[]; - private reader: ReadableStreamDefaultReader; + private ws: WebSocket; private progressBar: any; private lineup: LineUpJS.Taggle; @@ -230,29 +230,32 @@ export class Characterize extends ATask { }) .map((attr) => 'gene' in attr ? (attr as GeneScoreAttribute).gene : attr.id); - const response = await this.postData( - endpoint, { - exclude: excludeAttributes, - ids: this.ids, - }); - // start to read response stream - this.reader = response.body.getReader(); - const decoder = new TextDecoder('utf-8'); - let first = true; - while (true) { - const {value, done} = await this.reader.read(); //variable names are important for destructuring - if (done) { - console.log('the reader is done'); - this.setProgressDone(); - break; // if done, value is undefined --> skip the rest + const url = new URL(`/kokiri/${endpoint}/`, location.href); + url.protocol = url.protocol.replace('http', 'ws'); + console.log('url', url) + this.ws = new WebSocket(url) + this.ws.onopen = async () => { + const data = JSON.stringify({ // send as string, because sending JSON apparantly only works this way 🤷‍♀️ (see https://developer.mozilla.org/en-US/docs/Web/API/WebSockets_API/Writing_WebSocket_client_applications) + exclude: excludeAttributes, + ids: this.ids, + }) + console.log('Socket is open') + try { + this.ws.send(data) + } catch { + console.error('error sending data') } + console.log('sent comparison data') + }; - const response = decoder.decode(value); - console.log('response', response); + + let first = true; + this.ws.onmessage = async (message) => { + console.log('response', message); + const responseData = JSON.parse(message.data); try { - const responseData = JSON.parse(response); console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { @@ -265,6 +268,11 @@ export class Characterize extends ATask { console.error('could not read JSON data', e); } } + + this.ws.onclose = () => { + console.log('the socket is done'); + this.setProgressDone(); + } } async createLineUp(data) { @@ -314,7 +322,7 @@ export class Characterize extends ATask { wrapper .querySelector(('a.run')) .addEventListener('click', () => { - this.reader?.cancel(); + this.ws?.close(); wrapper.querySelector('.progress-ctrl').remove(); this.progressBar.textContent = 'Stopped'; this.fadeOutProgressBar(); From b0a780493bd07adce8782cd4bf2d9483247bc0af Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 15 Jun 2022 13:51:38 +0200 Subject: [PATCH 20/60] Add template files for custom lineup columns --- dist/Taskview/tasks/Characterize.d.ts | 7 + dist/Taskview/tasks/Characterize.js | 24 + dist/Taskview/tasks/Characterize.js.map | 2 +- .../LineUpDistributionColumn.d.ts | 125 ++++ .../Characterize/LineUpDistributionColumn.js | 334 ++++++++++ .../LineUpDistributionColumn.js.map | 1 + src/Taskview/tasks/Characterize.ts | 26 + .../Characterize/LineUpDistributionColumn.ts | 575 ++++++++++++++++++ 8 files changed, 1093 insertions(+), 1 deletion(-) create mode 100644 dist/Taskview/tasks/Characterize/LineUpDistributionColumn.d.ts create mode 100644 dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js create mode 100644 dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map create mode 100644 src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index d10737e..7986bc8 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -1,8 +1,10 @@ /// +import { ERenderMode, ICellRenderer, ICellRendererFactory } from 'lineupjs'; import { Cohort } from '../../Cohort'; import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; +import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; export declare class Characterize extends ATask { static readonly TREES = 500; static readonly jaccardFormat: (n: number | { @@ -35,3 +37,8 @@ export declare class Characterize extends ATask { getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; postData(endpoint: string, data?: {}): Promise; } +export declare class MyDistributionRenderer implements ICellRendererFactory { + readonly title: string; + canRender(col: LineUpDistributionColumn, mode: ERenderMode): boolean; + create(col: LineUpDistributionColumn): ICellRenderer; +} diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index f506a0c..41dffa8 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -1,6 +1,7 @@ import * as aq from 'arquero'; import { format } from 'd3-format'; import * as LineUpJS from 'lineupjs'; +import { ERenderMode, renderMissingDOM } from 'lineupjs'; import tippy from 'tippy.js'; import { getCohortLabel } from '../../Cohort'; import { colors } from '../../colors'; @@ -8,6 +9,7 @@ import { ServerColumnAttribute } from '../../data/Attribute'; import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; +import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -231,6 +233,9 @@ export class Characterize extends ATask { .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) + .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(50).build([])) + .registerRenderer("myDistributionRenderer", new MyDistributionRenderer()) + .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() .ranking(LineUpJS.buildRanking() .supportTypes() @@ -339,4 +344,23 @@ export class Characterize extends ATask { } Characterize.TREES = 500; Characterize.jaccardFormat = format('.1~%'); +export class MyDistributionRenderer { + constructor() { + this.title = "Distribution Chart"; + } + canRender(col, mode) { + return mode === ERenderMode.CELL; + } + create(col) { + return { + template: `
    blub
    `, + update: (n, d) => { + if (renderMissingDOM(n, col, d)) { + return; + } + console.log('Update'); + }, + }; + } +} //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index faff3f0..bbde99c 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.d.ts b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.d.ts new file mode 100644 index 0000000..87baee6 --- /dev/null +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.d.ts @@ -0,0 +1,125 @@ +import { Column, EAdvancedSortMethod, ECompareValueType, IAdvancedBoxPlotData, IColorMappingFunction, IDataRow, IKeyValue, IMapAbleDesc, IMapColumnDesc, IMappingFunction, INumberFilter, INumbersDesc, ITypeFactory, MapColumn, ValueColumn } from "lineupjs"; +import { IEventListener } from "lineupjs/build/src/internal"; +import { dirty, dirtyCaches, dirtyHeader, dirtyValues, groupRendererChanged, labelChanged, metaDataChanged, rendererTypeChanged, summaryRendererChanged, visibilityChanged, widthChanged } from "lineupjs/build/src/model/Column"; +import { dataLoaded } from "lineupjs/build/src/model/ValueColumn"; +/** + * emitted when the mapping property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function mappingChanged_NMC(previous: IMappingFunction, current: IMappingFunction): void; +/** + * emitted when the color mapping property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function colorMappingChanged_NMC(previous: IColorMappingFunction, current: IColorMappingFunction): void; +/** + * emitted when the sort method property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function sortMethodChanged_NMC(previous: EAdvancedSortMethod, current: EAdvancedSortMethod): void; +/** + * emitted when the filter property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function filterChanged_NMC(previous: INumberFilter | null, current: INumberFilter | null): void; +export declare type ILineUpDistributionColumnDesc = INumbersDesc & IMapColumnDesc; +export declare class LineUpDistributionColumn extends MapColumn { + static readonly EVENT_MAPPING_CHANGED = "mappingChanged"; + static readonly EVENT_COLOR_MAPPING_CHANGED = "colorMappingChanged"; + static readonly EVENT_SORTMETHOD_CHANGED = "sortMethodChanged"; + static readonly EVENT_FILTER_CHANGED = "filterChanged"; + private readonly numberFormat; + private sort; + private mapping; + private original; + private colorMapping; + /** + * currently active filter + * @type {{min: number, max: number}} + * @private + */ + private currentFilter; + private min; + private max; + constructor(id: string, desc: Readonly, factory: ITypeFactory); + getMin(): number; + getMax(): number; + getNumberFormat(): (n: number) => string; + private get_quartile; + private mean; + private get_advanced_value; + toCompareValue(row: IDataRow): number; + toCompareValueType(): ECompareValueType; + private getBoxPlotDataFromValueList; + getBoxPlotData(row: IDataRow): IAdvancedBoxPlotData | null; + getRawBoxPlotData(row: IDataRow): IAdvancedBoxPlotData | null; + getRange(): [string, string]; + getColorMapping(): IColorMappingFunction; + getNumber(row: IDataRow): number; + getRawNumber(row: IDataRow): number; + iterNumber(row: IDataRow): number[]; + iterRawNumber(row: IDataRow): number[]; + getValue(row: IDataRow): IKeyValue[]; + getRawValue(row: IDataRow): IKeyValue[]; + getExportValue(row: IDataRow, format: "text" | "json"): any; + getFormatedLabelArray(arr: any): string; + getLabels(row: IDataRow): { + key: string; + value: string; + }[]; + getSortMethod(): EAdvancedSortMethod; + setSortMethod(sort: EAdvancedSortMethod): void; + dump(toDescRef: (desc: any) => any): any; + restore(dump: any, factory: ITypeFactory): void; + protected createEventList(): string[]; + on(type: typeof LineUpDistributionColumn.EVENT_MAPPING_CHANGED, listener: typeof mappingChanged_NMC | null): this; + on(type: typeof LineUpDistributionColumn.EVENT_SORTMETHOD_CHANGED, listener: typeof sortMethodChanged_NMC | null): this; + on(type: typeof LineUpDistributionColumn.EVENT_FILTER_CHANGED, listener: typeof filterChanged_NMC | null): this; + on(type: typeof ValueColumn.EVENT_DATA_LOADED, listener: typeof dataLoaded | null): this; + on(type: typeof Column.EVENT_WIDTH_CHANGED, listener: typeof widthChanged | null): this; + on(type: typeof Column.EVENT_LABEL_CHANGED, listener: typeof labelChanged | null): this; + on(type: typeof Column.EVENT_METADATA_CHANGED, listener: typeof metaDataChanged | null): this; + on(type: typeof Column.EVENT_DIRTY, listener: typeof dirty | null): this; + on(type: typeof Column.EVENT_DIRTY_HEADER, listener: typeof dirtyHeader | null): this; + on(type: typeof Column.EVENT_DIRTY_VALUES, listener: typeof dirtyValues | null): this; + on(type: typeof Column.EVENT_DIRTY_CACHES, listener: typeof dirtyCaches | null): this; + on(type: typeof Column.EVENT_RENDERER_TYPE_CHANGED, listener: typeof rendererTypeChanged | null): this; + on(type: typeof Column.EVENT_GROUP_RENDERER_TYPE_CHANGED, listener: typeof groupRendererChanged | null): this; + on(type: typeof Column.EVENT_SUMMARY_RENDERER_TYPE_CHANGED, listener: typeof summaryRendererChanged | null): this; + on(type: typeof Column.EVENT_VISIBILITY_CHANGED, listener: typeof visibilityChanged | null): this; + on(type: string | string[], listener: IEventListener | null): this; + getOriginalMapping(): IMappingFunction; + getMapping(): IMappingFunction; + setMapping(mapping: IMappingFunction): void; + getColor(row: IDataRow): any; + isFiltered(): any; + getFilter(): INumberFilter; + setFilter(value: INumberFilter | null): void; + /** @internal */ + private isNumberIncluded; + /** + * filter the current row if any filter is set + * @param row + * @returns {boolean} + */ + filter(row: IDataRow): boolean; + clearFilter(): any; +} +export declare const DEFAULT_FORMATTER: (n: number | { + valueOf(): number; +}) => string; +export declare function noNumberFilter(): { + min: number; + max: number; + filterMissing: boolean; +}; +export declare function isEqualNumberFilter(a: INumberFilter, b: INumberFilter, delta?: number): boolean; +export declare function similar(a: number, b: number, delta?: number): boolean; +export declare function isUnknown(v?: number | null): boolean; +export declare function isDummyNumberFilter(filter: INumberFilter): boolean; +export declare function restoreMapping(desc: IMapAbleDesc, factory: ITypeFactory): IMappingFunction; +export declare function restoreNumberFilter(v: INumberFilter): INumberFilter; diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js new file mode 100644 index 0000000..496674a --- /dev/null +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js @@ -0,0 +1,334 @@ +var LineUpDistributionColumn_1; +import { __decorate } from "tslib"; +import { format } from 'd3-format'; +import { Column, dialogAddons, EAdvancedSortMethod, ECompareValueType, MapColumn, NumberColumn, ScaleMappingFunction, SortByDefault, toolbar } from "lineupjs"; +let LineUpDistributionColumn = LineUpDistributionColumn_1 = +//@ts-ignore +class LineUpDistributionColumn extends MapColumn { + constructor(id, desc, factory) { + super(id, desc); + this.numberFormat = DEFAULT_FORMATTER; + /** + * currently active filter + * @type {{min: number, max: number}} + * @private + */ + this.currentFilter = noNumberFilter(); + this.min = 0; + this.max = 1; + // this.mapping = restoreMapping(desc, factory); // TODO: check, if desc.range and desc.domain can be infered + this.mapping = new ScaleMappingFunction([desc["min"], desc["max"]], "linear", [0, 1]); + this.original = this.mapping.clone(); + this.sort = desc.sort || EAdvancedSortMethod.median; + this.colorMapping = factory.colorMappingFunction(desc.colorMapping || desc.color); + if (desc.numberFormat) { + this.numberFormat = format(desc.numberFormat); + } + //TODO: infer min and max if it is not given + this.min = desc["min"]; + this.max = desc["max"]; + } + getMin() { + return this.min; + } + getMax() { + return this.max; + } + getNumberFormat() { + return this.numberFormat; + } + // https://stackoverflow.com/questions/45309447/calculating-median-javascript + get_quartile(values, q = 0.5) { + // 1. quartile: q=0.25 | median: q=0.5 | 3. quartile: q=0.75 + if (values.length === 0) + return 0; + values.sort(function (a, b) { + return a - b; + }); + var half = Math.floor(values.length * q); + if (values.length % 2) + return values[half]; + return (values[half - 1] + values[half]) / 2.0; + } + // https://www.sitepoint.com/community/t/calculating-the-average-mean/7302/2 + mean(numbers) { + var total = 0, i; + for (i = 0; i < numbers.length; i += 1) { + total += numbers[i]; + } + return total / numbers.length; + } + get_advanced_value(method, value_list) { + switch (method) { + case EAdvancedSortMethod.min: + return Math.min(...value_list); + case EAdvancedSortMethod.max: + return Math.max(...value_list); + case EAdvancedSortMethod.mean: + return this.mean(value_list); + case EAdvancedSortMethod.median: + return this.get_quartile(value_list); + case EAdvancedSortMethod.q1: + return this.get_quartile(value_list, 1); + case EAdvancedSortMethod.q3: + return this.get_quartile(value_list, 3); + default: + return this.get_quartile(value_list); + } + } + toCompareValue(row) { + let data = this.getValue(row); + let value_list = data[0]["value"]; + const method = this.getSortMethod(); + return this.get_advanced_value(method, value_list); + } + toCompareValueType() { + return ECompareValueType.FLOAT; + } + getBoxPlotDataFromValueList(data) { + return { + mean: this.get_advanced_value(EAdvancedSortMethod.mean, data), + missing: 0, + count: data.length, + kdePoints: [], + max: this.get_advanced_value(EAdvancedSortMethod.max, data), + min: this.get_advanced_value(EAdvancedSortMethod.min, data), + median: this.get_advanced_value(EAdvancedSortMethod.median, data), + q1: this.get_advanced_value(EAdvancedSortMethod.q1, data), + q3: this.get_advanced_value(EAdvancedSortMethod.q3, data), + }; + } + getBoxPlotData(row) { + console.log("getBoxPlotData"); + const data = this.getValue(row)[0]["value"]; + if (data == null) { + return null; + } + return this.getBoxPlotDataFromValueList(data); + } + getRawBoxPlotData(row) { + console.log("getRawBoxPlotData"); + const data = this.getRawValue(row)[0]["value"]; + if (data == null) { + return null; + } + return this.getBoxPlotDataFromValueList(data); + } + getRange() { + console.log("getRange"); + return this.mapping.getRange(this.numberFormat); + } + getColorMapping() { + console.log("getColorMapping"); + return this.colorMapping.clone(); + } + getNumber(row) { + // console.log("getNumber") + return this.mapping.apply(this.toCompareValue(row)); + } + getRawNumber(row) { + // console.log("getRawNumber") + return this.toCompareValue(row); + } + iterNumber(row) { + // console.log("iterNumber") + const r = this.getValue(row); + // return r ? r.map((d) => d.value) : [NaN]; + // return r ? r[0]["value"] : [NaN]; + return [this.get_advanced_value(EAdvancedSortMethod.median, r[0]["value"])]; + } + iterRawNumber(row) { + // console.log("iterRawNumber") + const r = this.getRawValue(row); + // return r ? r.map((d) => d.value) : [NaN]; + // return r ? r[0]["value"] : [NaN]; + return [this.get_advanced_value(EAdvancedSortMethod.median, r[0]["value"])]; + } + getValue(row) { + const values = this.getRawValue(row); + if (values.length === 0) { + //@ts-ignore + return null; + } + //@ts-ignore + return values.map(({ key, value }) => { + return { + key, + value: value.length === 0 + ? null + : value.map((val) => this.mapping.apply(val)), + }; + }); + } + getRawValue(row) { + const r = super.getValue(row); + return r == null ? [] : r; + // const values = super.getValue(row); + // if(values.length === 0) + // return null; + // return values.map(({key, value}) => { + // return {key, value: value.length===0 ? null : value}; + // }); + } + getExportValue(row, format) { + return format === "json" + ? this.getRawValue(row) + : super.getExportValue(row, format); + } + getFormatedLabelArray(arr) { + return "[" + arr.map(item => this.numberFormat(item)).toString() + "]"; + } + getLabels(row) { + const v = this.getRawValue(row); + return v.map(({ key, value }) => ({ key, value: this.getFormatedLabelArray(value) })); + } + getSortMethod() { + return this.sort; + } + setSortMethod(sort) { + if (this.sort === sort) { + return; + } + this.fire([LineUpDistributionColumn_1.EVENT_SORTMETHOD_CHANGED], this.sort, (this.sort = sort)); + // sort by me if not already sorted by me + if (!this.isSortedByMe().asc) { + this.sortByMe(); + } + } + dump(toDescRef) { + const r = super.dump(toDescRef); + r.sortMethod = this.getSortMethod(); + r.filter = !isDummyNumberFilter(this.currentFilter) + ? this.currentFilter + : null; + r.map = this.mapping.toJSON(); + return r; + } + restore(dump, factory) { + super.restore(dump, factory); + if (dump.sortMethod) { + this.sort = dump.sortMethod; + } + if (dump.filter) { + this.currentFilter = restoreNumberFilter(dump.filter); + } + if (dump.map || dump.domain) { + this.mapping = restoreMapping(dump, factory); + } + } + createEventList() { + return super + .createEventList() + .concat([ + LineUpDistributionColumn_1.EVENT_MAPPING_CHANGED, + LineUpDistributionColumn_1.EVENT_SORTMETHOD_CHANGED, + LineUpDistributionColumn_1.EVENT_FILTER_CHANGED, + ]); + } + on(type, listener) { + return super.on(type, listener); + } + getOriginalMapping() { + return this.original.clone(); + } + getMapping() { + return this.mapping.clone(); + } + setMapping(mapping) { + if (this.mapping.eq(mapping)) { + return; + } + this.fire([ + LineUpDistributionColumn_1.EVENT_MAPPING_CHANGED, + Column.EVENT_DIRTY_VALUES, + Column.EVENT_DIRTY, + ], this.mapping.clone(), (this.mapping = mapping)); + } + getColor(row) { + return NumberColumn.prototype.getColor.call(this, row); + } + isFiltered() { + return NumberColumn.prototype.isFiltered.call(this); + } + getFilter() { + return NumberColumn.prototype.getFilter.call(this); + } + setFilter(value) { + NumberColumn.prototype.setFilter.call(this, value); + } + // filter(row: IDataRow) { + // return NumberColumn.prototype.filter.call(this, row); + // } + /** @internal */ + isNumberIncluded(filter, value) { + if (!filter) { + return true; + } + if (Number.isNaN(value)) { + return !filter.filterMissing; + } + return !((isFinite(filter.min) && value < filter.min) || + (isFinite(filter.max) && value > filter.max)); + } + /** + * filter the current row if any filter is set + * @param row + * @returns {boolean} + */ + // TODO: customize filter: max, min, median... + filter(row) { + // currently it checks, if the median is within the range + // const value = this.getRawNumber(row); + const value = this.get_advanced_value(EAdvancedSortMethod.median, this.getRawValue(row)[0]["value"]); + return this.isNumberIncluded(this.getFilter(), value); + } + clearFilter() { + return NumberColumn.prototype.clearFilter.call(this); + } +}; +LineUpDistributionColumn.EVENT_MAPPING_CHANGED = NumberColumn.EVENT_MAPPING_CHANGED; +LineUpDistributionColumn.EVENT_COLOR_MAPPING_CHANGED = NumberColumn.EVENT_COLOR_MAPPING_CHANGED; +LineUpDistributionColumn.EVENT_SORTMETHOD_CHANGED = NumberColumn.EVENT_SORTMETHOD_CHANGED; +LineUpDistributionColumn.EVENT_FILTER_CHANGED = NumberColumn.EVENT_FILTER_CHANGED; +LineUpDistributionColumn = LineUpDistributionColumn_1 = __decorate([ + toolbar("rename", "filterNumber", "sort", "sortBy"), + dialogAddons("sort", "sortNumbers"), + SortByDefault("descending") + //@ts-ignore +], LineUpDistributionColumn); +export { LineUpDistributionColumn }; +export const DEFAULT_FORMATTER = format(".3n"); +export function noNumberFilter() { + return { min: -Infinity, max: Infinity, filterMissing: false }; +} +export function isEqualNumberFilter(a, b, delta = 0.001) { + return (similar(a.min, b.min, delta) && + similar(a.max, b.max, delta) && + a.filterMissing === b.filterMissing); +} +export function similar(a, b, delta = 0.5) { + if (a === b) { + return true; + } + return Math.abs(a - b) < delta; +} +export function isUnknown(v) { + return v === null || v === undefined || isNaN(v); +} +export function isDummyNumberFilter(filter) { + return (!filter.filterMissing && !isFinite(filter.min) && !isFinite(filter.max)); +} +export function restoreMapping(desc, factory) { + if (desc.map) { + return factory.mappingFunction(desc.map); + } + return new ScaleMappingFunction(desc.domain || [0, 1], "linear", desc.range || [0, 1]); +} +export function restoreNumberFilter(v) { + return { + min: v.min != null && isFinite(v.min) ? v.min : -Infinity, + max: v.max != null && isFinite(v.max) ? v.max : +Infinity, + filterMissing: v.filterMissing, + }; +} +//# sourceMappingURL=LineUpDistributionColumn.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map new file mode 100644 index 0000000..7832a6f --- /dev/null +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 77af855..3eaff1b 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,6 +1,7 @@ import * as aq from 'arquero'; import {format} from 'd3-format'; import * as LineUpJS from 'lineupjs'; +import {ERenderMode, ICellRenderer, ICellRendererFactory, IDataRow, renderMissingDOM} from 'lineupjs'; import tippy from 'tippy.js'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; @@ -10,6 +11,7 @@ import {Task} from '../../Tasks'; import {getAnimatedLoadingText} from '../../util'; import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; +import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn'; export class Characterize extends ATask { static readonly TREES = 500; @@ -281,6 +283,9 @@ export class Characterize extends ATask { .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) + .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(50).build([])) + .registerRenderer("myDistributionRenderer", new MyDistributionRenderer()) + .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() .ranking(LineUpJS.buildRanking() .supportTypes() @@ -396,3 +401,24 @@ export class Characterize extends ATask { return response; } } + +export class MyDistributionRenderer implements ICellRendererFactory { + readonly title: string = "Distribution Chart"; + + canRender(col: LineUpDistributionColumn, mode: ERenderMode): boolean { + return mode === ERenderMode.CELL; + } + + create(col: LineUpDistributionColumn): ICellRenderer { + return { + template: `
    blub
    `, + update: (n: HTMLImageElement, d: IDataRow) => { + if (renderMissingDOM(n, col, d)) { + return; + } + + console.log('Update') + }, + }; + } +} \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts new file mode 100644 index 0000000..aefb12e --- /dev/null +++ b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts @@ -0,0 +1,575 @@ +import {format} from 'd3-format'; +import { + Column, + dialogAddons, + EAdvancedSortMethod, + ECompareValueType, + IAdvancedBoxPlotData, + IColorMappingFunction, + IDataRow, IKeyValue, IMapAbleDesc, IMapColumnDesc, + IMappingFunction, + INumberFilter, + INumbersDesc, + ITypeFactory, + MapColumn, + NumberColumn, + ScaleMappingFunction, + SortByDefault, + toolbar, + ValueColumn +} from "lineupjs"; +import { + IEventListener +} from "lineupjs/build/src/internal"; +import { + dirty, + dirtyCaches, + dirtyHeader, + dirtyValues, + groupRendererChanged, + labelChanged, + metaDataChanged, + rendererTypeChanged, + summaryRendererChanged, + visibilityChanged, + widthChanged +} from "lineupjs/build/src/model/Column"; +import {dataLoaded} from "lineupjs/build/src/model/ValueColumn"; + + +/** + * emitted when the mapping property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function mappingChanged_NMC( + previous: IMappingFunction, + current: IMappingFunction +): void; +/** + * emitted when the color mapping property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function colorMappingChanged_NMC( + previous: IColorMappingFunction, + current: IColorMappingFunction +): void; + +/** + * emitted when the sort method property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function sortMethodChanged_NMC( + previous: EAdvancedSortMethod, + current: EAdvancedSortMethod +): void; + +/** + * emitted when the filter property changes + * @asMemberOf NumberMapColumn + * @event + */ +export declare function filterChanged_NMC( + previous: INumberFilter | null, + current: INumberFilter | null +): void; + +export declare type ILineUpDistributionColumnDesc = INumbersDesc & IMapColumnDesc; + +@toolbar("rename", "filterNumber", "sort", "sortBy") +@dialogAddons("sort", "sortNumbers") +@SortByDefault("descending") +//@ts-ignore +export class LineUpDistributionColumn extends MapColumn { + static readonly EVENT_MAPPING_CHANGED = NumberColumn.EVENT_MAPPING_CHANGED; + static readonly EVENT_COLOR_MAPPING_CHANGED = + NumberColumn.EVENT_COLOR_MAPPING_CHANGED; + static readonly EVENT_SORTMETHOD_CHANGED = + NumberColumn.EVENT_SORTMETHOD_CHANGED; + static readonly EVENT_FILTER_CHANGED = NumberColumn.EVENT_FILTER_CHANGED; + + private readonly numberFormat: (n: number) => string = DEFAULT_FORMATTER; + + private sort: EAdvancedSortMethod; + private mapping: IMappingFunction; + private original: IMappingFunction; + private colorMapping: IColorMappingFunction; + /** + * currently active filter + * @type {{min: number, max: number}} + * @private + */ + private currentFilter: INumberFilter = noNumberFilter(); + + private min: number = 0; + private max: number = 1; + + constructor( + id: string, + desc: Readonly, + factory: ITypeFactory + ) { + super(id, desc); + // this.mapping = restoreMapping(desc, factory); // TODO: check, if desc.range and desc.domain can be infered + this.mapping = new ScaleMappingFunction( + [desc["min"], desc["max"]], + "linear", + [0, 1] + ); + this.original = this.mapping.clone(); + this.sort = desc.sort || EAdvancedSortMethod.median; + this.colorMapping = factory.colorMappingFunction( + desc.colorMapping || desc.color + ); + + if (desc.numberFormat) { + this.numberFormat = format(desc.numberFormat); + } + + //TODO: infer min and max if it is not given + this.min = desc["min"]; + this.max = desc["max"]; + } + + getMin() { + return this.min; + } + + getMax() { + return this.max; + } + + getNumberFormat() { + return this.numberFormat; + } + + // https://stackoverflow.com/questions/45309447/calculating-median-javascript + private get_quartile(values, q = 0.5) { + // 1. quartile: q=0.25 | median: q=0.5 | 3. quartile: q=0.75 + if (values.length === 0) return 0; + + values.sort(function (a, b) { + return a - b; + }); + + var half = Math.floor(values.length * q); + + if (values.length % 2) return values[half]; + + return (values[half - 1] + values[half]) / 2.0; + } + + // https://www.sitepoint.com/community/t/calculating-the-average-mean/7302/2 + private mean(numbers) { + var total = 0, + i; + for (i = 0; i < numbers.length; i += 1) { + total += numbers[i]; + } + return total / numbers.length; + } + + private get_advanced_value( + method: EAdvancedSortMethod, + value_list: number[] + ): number { + switch (method) { + case EAdvancedSortMethod.min: + return Math.min(...value_list); + case EAdvancedSortMethod.max: + return Math.max(...value_list); + case EAdvancedSortMethod.mean: + return this.mean(value_list); + case EAdvancedSortMethod.median: + return this.get_quartile(value_list); + case EAdvancedSortMethod.q1: + return this.get_quartile(value_list, 1); + case EAdvancedSortMethod.q3: + return this.get_quartile(value_list, 3); + default: + return this.get_quartile(value_list); + } + } + + toCompareValue(row: IDataRow): number { + let data = this.getValue(row); + let value_list = data[0]["value"]; + const method = this.getSortMethod(); + return this.get_advanced_value(method, value_list); + } + + toCompareValueType() { + return ECompareValueType.FLOAT; + } + + private getBoxPlotDataFromValueList( + data: number[] + ): IAdvancedBoxPlotData | null { + return { + mean: this.get_advanced_value(EAdvancedSortMethod.mean, data), + missing: 0, + count: data.length, + kdePoints: [], + max: this.get_advanced_value(EAdvancedSortMethod.max, data), + min: this.get_advanced_value(EAdvancedSortMethod.min, data), + median: this.get_advanced_value(EAdvancedSortMethod.median, data), + q1: this.get_advanced_value(EAdvancedSortMethod.q1, data), + q3: this.get_advanced_value(EAdvancedSortMethod.q3, data), + }; + } + + getBoxPlotData(row: IDataRow): IAdvancedBoxPlotData | null { + console.log("getBoxPlotData"); + const data = this.getValue(row)[0]["value"]; + if (data == null) { + return null; + } + return this.getBoxPlotDataFromValueList(data); + } + + getRawBoxPlotData(row: IDataRow): IAdvancedBoxPlotData | null { + console.log("getRawBoxPlotData"); + const data = this.getRawValue(row)[0]["value"]; + if (data == null) { + return null; + } + return this.getBoxPlotDataFromValueList(data); + } + + getRange() { + console.log("getRange"); + return this.mapping.getRange(this.numberFormat); + } + + getColorMapping() { + console.log("getColorMapping"); + return this.colorMapping.clone(); + } + + getNumber(row: IDataRow): number { + // console.log("getNumber") + return this.mapping.apply(this.toCompareValue(row)); + } + + getRawNumber(row: IDataRow): number { + // console.log("getRawNumber") + return this.toCompareValue(row); + } + + iterNumber(row: IDataRow) { + // console.log("iterNumber") + const r = this.getValue(row); + // return r ? r.map((d) => d.value) : [NaN]; + // return r ? r[0]["value"] : [NaN]; + return [this.get_advanced_value(EAdvancedSortMethod.median, r[0]["value"])]; + } + + iterRawNumber(row: IDataRow) { + // console.log("iterRawNumber") + const r = this.getRawValue(row); + // return r ? r.map((d) => d.value) : [NaN]; + // return r ? r[0]["value"] : [NaN]; + return [this.get_advanced_value(EAdvancedSortMethod.median, r[0]["value"])]; + } + + getValue(row: IDataRow): IKeyValue[] { + const values = this.getRawValue(row); + + if (values.length === 0) { + //@ts-ignore + return null; + } + + //@ts-ignore + return values.map(({key, value}) => { + return { + key, + value: + value.length === 0 + ? null + : value.map((val) => this.mapping.apply(val)), + }; + }); + } + + getRawValue(row: IDataRow): IKeyValue[] { + const r = super.getValue(row); + return r == null ? [] : r; + // const values = super.getValue(row); + + // if(values.length === 0) + // return null; + + // return values.map(({key, value}) => { + // return {key, value: value.length===0 ? null : value}; + // }); + } + + getExportValue(row: IDataRow, format: "text" | "json"): any { + return format === "json" + ? this.getRawValue(row) + : super.getExportValue(row, format); + } + + getFormatedLabelArray(arr): string { + return "[" + arr.map(item => this.numberFormat(item)).toString() + "]"; + } + + getLabels(row: IDataRow) { + const v = this.getRawValue(row); + return v.map(({key, value}) => ({key, value: this.getFormatedLabelArray(value)})); + } + + getSortMethod() { + return this.sort; + } + + setSortMethod(sort: EAdvancedSortMethod) { + if (this.sort === sort) { + return; + } + this.fire( + [LineUpDistributionColumn.EVENT_SORTMETHOD_CHANGED], + this.sort, + (this.sort = sort) + ); + // sort by me if not already sorted by me + if (!this.isSortedByMe().asc) { + this.sortByMe(); + } + } + + dump(toDescRef: (desc: any) => any): any { + const r = super.dump(toDescRef); + r.sortMethod = this.getSortMethod(); + r.filter = !isDummyNumberFilter(this.currentFilter) + ? this.currentFilter + : null; + r.map = this.mapping.toJSON(); + return r; + } + + restore(dump: any, factory: ITypeFactory) { + super.restore(dump, factory); + if (dump.sortMethod) { + this.sort = dump.sortMethod; + } + if (dump.filter) { + this.currentFilter = restoreNumberFilter(dump.filter); + } + if (dump.map || dump.domain) { + this.mapping = restoreMapping(dump, factory); + } + } + + protected createEventList() { + return super + .createEventList() + .concat([ + LineUpDistributionColumn.EVENT_MAPPING_CHANGED, + LineUpDistributionColumn.EVENT_SORTMETHOD_CHANGED, + LineUpDistributionColumn.EVENT_FILTER_CHANGED, + ]); + } + + on( + type: typeof LineUpDistributionColumn.EVENT_MAPPING_CHANGED, + listener: typeof mappingChanged_NMC | null + ): this; + on( + type: typeof LineUpDistributionColumn.EVENT_SORTMETHOD_CHANGED, + listener: typeof sortMethodChanged_NMC | null + ): this; + on( + type: typeof LineUpDistributionColumn.EVENT_FILTER_CHANGED, + listener: typeof filterChanged_NMC | null + ): this; + on( + type: typeof ValueColumn.EVENT_DATA_LOADED, + listener: typeof dataLoaded | null + ): this; + on( + type: typeof Column.EVENT_WIDTH_CHANGED, + listener: typeof widthChanged | null + ): this; + on( + type: typeof Column.EVENT_LABEL_CHANGED, + listener: typeof labelChanged | null + ): this; + on( + type: typeof Column.EVENT_METADATA_CHANGED, + listener: typeof metaDataChanged | null + ): this; + on(type: typeof Column.EVENT_DIRTY, listener: typeof dirty | null): this; + on( + type: typeof Column.EVENT_DIRTY_HEADER, + listener: typeof dirtyHeader | null + ): this; + on( + type: typeof Column.EVENT_DIRTY_VALUES, + listener: typeof dirtyValues | null + ): this; + on( + type: typeof Column.EVENT_DIRTY_CACHES, + listener: typeof dirtyCaches | null + ): this; + on( + type: typeof Column.EVENT_RENDERER_TYPE_CHANGED, + listener: typeof rendererTypeChanged | null + ): this; + on( + type: typeof Column.EVENT_GROUP_RENDERER_TYPE_CHANGED, + listener: typeof groupRendererChanged | null + ): this; + on( + type: typeof Column.EVENT_SUMMARY_RENDERER_TYPE_CHANGED, + listener: typeof summaryRendererChanged | null + ): this; + on( + type: typeof Column.EVENT_VISIBILITY_CHANGED, + listener: typeof visibilityChanged | null + ): this; + on(type: string | string[], listener: IEventListener | null): this; // required for correct typings in *.d.ts + on(type: string | string[], listener: IEventListener | null): this { + return super.on(type as any, listener); + } + + getOriginalMapping() { + return this.original.clone(); + } + + getMapping() { + return this.mapping.clone(); + } + + setMapping(mapping: IMappingFunction) { + if (this.mapping.eq(mapping)) { + return; + } + this.fire( + [ + LineUpDistributionColumn.EVENT_MAPPING_CHANGED, + Column.EVENT_DIRTY_VALUES, + Column.EVENT_DIRTY, + ], + this.mapping.clone(), + (this.mapping = mapping) + ); + } + + getColor(row: IDataRow) { + return NumberColumn.prototype.getColor.call(this, row); + } + + isFiltered() { + return NumberColumn.prototype.isFiltered.call(this); + } + + getFilter(): INumberFilter { + return NumberColumn.prototype.getFilter.call(this); + } + + setFilter(value: INumberFilter | null) { + NumberColumn.prototype.setFilter.call(this, value); + } + + // filter(row: IDataRow) { + // return NumberColumn.prototype.filter.call(this, row); + // } + + /** @internal */ + private isNumberIncluded(filter: INumberFilter | null, value: number) { + if (!filter) { + return true; + } + if (Number.isNaN(value)) { + return !filter.filterMissing; + } + return !( + (isFinite(filter.min) && value < filter.min) || + (isFinite(filter.max) && value > filter.max) + ); + } + + /** + * filter the current row if any filter is set + * @param row + * @returns {boolean} + */ + // TODO: customize filter: max, min, median... + filter(row: IDataRow) { + // currently it checks, if the median is within the range + // const value = this.getRawNumber(row); + const value = this.get_advanced_value( + EAdvancedSortMethod.median, + this.getRawValue(row)[0]["value"] + ); + + return this.isNumberIncluded(this.getFilter(), value); + } + + clearFilter() { + return NumberColumn.prototype.clearFilter.call(this); + } +} + + + + + +export const DEFAULT_FORMATTER = format(".3n"); + +export function noNumberFilter() { + return {min: -Infinity, max: Infinity, filterMissing: false}; +} + +export function isEqualNumberFilter( + a: INumberFilter, + b: INumberFilter, + delta = 0.001 +) { + return ( + similar(a.min, b.min, delta) && + similar(a.max, b.max, delta) && + a.filterMissing === b.filterMissing + ); +} +export function similar(a: number, b: number, delta = 0.5) { + if (a === b) { + return true; + } + return Math.abs(a - b) < delta; +} +export function isUnknown(v?: number | null) { + return v === null || v === undefined || isNaN(v); +} + +export function isDummyNumberFilter(filter: INumberFilter) { + return ( + !filter.filterMissing && !isFinite(filter.min) && !isFinite(filter.max) + ); +} + +export function restoreMapping( + desc: IMapAbleDesc, + factory: ITypeFactory +): IMappingFunction { + if (desc.map) { + return factory.mappingFunction(desc.map); + } + return new ScaleMappingFunction( + desc.domain || [0, 1], + "linear", + desc.range || [0, 1] + ); +} + +export function restoreNumberFilter(v: INumberFilter): INumberFilter { + return { + min: v.min != null && isFinite(v.min) ? v.min : -Infinity, + max: v.max != null && isFinite(v.max) ? v.max : +Infinity, + filterMissing: v.filterMissing, + }; +} From 9f1fb001f12bf4ca24eb0bd29f24f2ff7fcc04c8 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 19 Jul 2022 16:36:41 +0200 Subject: [PATCH 21/60] show embedding and accuracy --- dist/Taskview/tasks/Characterize.d.ts | 3 +- dist/Taskview/tasks/Characterize.js | 58 +++++++++++++----- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 2 +- src/Taskview/tasks/Characterize.ts | 62 +++++++++++++++----- src/scss/components/task/_characterize.scss | 2 +- 6 files changed, 96 insertions(+), 33 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index d10737e..0fd79e7 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -4,7 +4,7 @@ import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; export declare class Characterize extends ATask { - static readonly TREES = 500; + static readonly TREES = 200; static readonly jaccardFormat: (n: number | { valueOf(): number; }) => string; @@ -19,6 +19,7 @@ export declare class Characterize extends ATask { private dataProv; private cohorts; private definingAttributes; + private chart; supports(attributes: IAttribute[], cohorts: ICohort[]): boolean; showSearchBar(): boolean; show(columnHeader: HTMLDivElement, container: HTMLDivElement, attributes: IAttribute[], cohorts: ICohort[]): Promise; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index f506a0c..5d5edfc 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -2,6 +2,7 @@ import * as aq from 'arquero'; import { format } from 'd3-format'; import * as LineUpJS from 'lineupjs'; import tippy from 'tippy.js'; +import vegaEmbed from 'vega-embed'; import { getCohortLabel } from '../../Cohort'; import { colors } from '../../colors'; import { ServerColumnAttribute } from '../../data/Attribute'; @@ -54,14 +55,18 @@ export class Characterize extends ATask {
    +
    +
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { - if (this.lineup) { - this.lineup.destroy(); - } + var _a, _b; + (_a = this.lineup) === null || _a === void 0 ? void 0 : _a.destroy(); this.$container.querySelector('.lineup-container').innerHTML = ''; + (_b = this.chart) === null || _b === void 0 ? void 0 : _b.finalize(); + this.$container.querySelector('.chart-container').innerHTML = ''; + this.$container.querySelector('.accuracy-container').innerHTML = ''; this.addProgressBar(); this.compare(`cmp_${btn.id}`); })); @@ -205,19 +210,44 @@ export class Characterize extends ATask { this.ws.onmessage = async (message) => { console.log('response', message); const responseData = JSON.parse(message.data); - try { - console.log(responseData.trees); - this.setProgress(responseData.trees); - if (first) { - await this.createLineUp(responseData.importances); // await so its ready for the next response - first = false; + if (responseData.trees) { + try { + console.log(responseData.trees); + this.setProgress(responseData.trees); + if (first) { + await this.createLineUp(responseData.importances); // await so its ready for the next response + first = false; + } + else { + this.updateLineUp(responseData.importances); + } + this.$container.querySelector('.accuracy-container').innerHTML = `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; } - else { - this.updateLineUp(responseData.importances); + catch (e) { + console.error('could not read JSON data', e); } } - catch (e) { - console.error('could not read JSON data', e); + else if (responseData.embedding) { + console.log('create plot'); + const result = await vegaEmbed(this.$container.querySelector('.chart-container'), { + "$schema": "https://vega.github.io/schema/vega-lite/v5.json", + "title": "Classifier", + "data": { + "values": responseData.embedding + }, + "width": 500, + "height": 500, + "mark": { "type": "point" }, + "encoding": { + "x": { "field": "x", "type": "quantitative", axis: null }, + "y": { "field": "y", "type": "quantitative", axis: null }, + "color": { "field": "cht", "type": "nominal", legend: null } + }, + config: { + range: { category: this.cohorts.map((cht) => cht.colorTaskView) } + } + }, { actions: false, renderer: 'svg' }); + this.chart = result.view; } }; this.ws.onclose = () => { @@ -337,6 +367,6 @@ export class Characterize extends ATask { return response; } } -Characterize.TREES = 500; +Characterize.TREES = 200; Characterize.jaccardFormat = format('.1~%'); //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index faff3f0..7ef04ed 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index b9e1328..0ce553a 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto auto 1fr; // 1fr for lineup + grid-template-rows: auto auto auto auto 1fr auto; // 1fr for lineup row-gap: 1em; .cht-icon { diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 77af855..b8cc1c1 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -2,6 +2,8 @@ import * as aq from 'arquero'; import {format} from 'd3-format'; import * as LineUpJS from 'lineupjs'; import tippy from 'tippy.js'; +import {View as VegaView} from 'vega'; +import vegaEmbed from 'vega-embed'; import {Cohort, getCohortLabel} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; import {colors} from '../../colors'; @@ -12,7 +14,7 @@ import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; export class Characterize extends ATask { - static readonly TREES = 500; + static readonly TREES = 200; static readonly jaccardFormat = format('.1~%'); public label = `Characterize`; @@ -28,6 +30,7 @@ export class Characterize extends ATask { private dataProv: LineUpJS.LocalDataProvider; private cohorts: Cohort[]; private definingAttributes: IAttribute[]; + private chart: VegaView; supports(attributes: IAttribute[], cohorts: ICohort[]) { @@ -85,15 +88,18 @@ export class Characterize extends ATask {
    +
    +
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { - if (this.lineup) { - this.lineup.destroy(); - } + this.lineup?.destroy(); this.$container.querySelector('.lineup-container').innerHTML = ''; + this.chart?.finalize(); + this.$container.querySelector('.chart-container').innerHTML = ''; + this.$container.querySelector('.accuracy-container').innerHTML = ''; this.addProgressBar(); this.compare(`cmp_${btn.id}`); })); @@ -255,19 +261,45 @@ export class Characterize extends ATask { console.log('response', message); const responseData = JSON.parse(message.data); - try { - console.log(responseData.trees); - this.setProgress(responseData.trees); - if (first) { - await this.createLineUp(responseData.importances); // await so its ready for the next response - first = false; - } else { - this.updateLineUp(responseData.importances); + if(responseData.trees) { + try { + console.log(responseData.trees); + this.setProgress(responseData.trees); + if (first) { + await this.createLineUp(responseData.importances); // await so its ready for the next response + first = false; + } else { + this.updateLineUp(responseData.importances); + } + + this.$container.querySelector('.accuracy-container').innerHTML = `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; + + } catch (e) { + console.error('could not read JSON data', e); } - } catch (e) { - console.error('could not read JSON data', e); + } else if (responseData.embedding) { + console.log('create plot') + const result = await vegaEmbed(this.$container.querySelector('.chart-container') as HTMLDivElement, { + "$schema": "https://vega.github.io/schema/vega-lite/v5.json", + "title": "Classifier", + "data": { + "values": responseData.embedding + }, + "width": 500, + "height": 500, + "mark": {"type": "point"}, + "encoding": { + "x": { "field": "x", "type": "quantitative", axis: null }, + "y": { "field": "y", "type": "quantitative", axis: null }, + "color": {"field": "cht", "type": "nominal", legend: null} + }, + config: { + range: {category: this.cohorts.map((cht) => cht.colorTaskView)} + } + }, {actions: false, renderer: 'svg'}); + this.chart = result.view; } - } + } this.ws.onclose = () => { console.log('the socket is done'); diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index b9e1328..0ce553a 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto auto 1fr; // 1fr for lineup + grid-template-rows: auto auto auto auto 1fr auto; // 1fr for lineup row-gap: 1em; .cht-icon { From 4e4be1854b69facf6510c08cabc6a55dcb5f3347 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 20 Jul 2022 15:05:10 +0200 Subject: [PATCH 22/60] support multiple charts --- dist/Taskview/tasks/Characterize.js | 32 ++++++++++++++++------- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 34 +++++++++++++++++-------- 3 files changed, 48 insertions(+), 20 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 5d5edfc..706464f 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -64,7 +64,8 @@ export class Characterize extends ATask { var _a, _b; (_a = this.lineup) === null || _a === void 0 ? void 0 : _a.destroy(); this.$container.querySelector('.lineup-container').innerHTML = ''; - (_b = this.chart) === null || _b === void 0 ? void 0 : _b.finalize(); + (_b = this.chart) === null || _b === void 0 ? void 0 : _b.forEach((view) => view.finalize()); + this.chart = []; this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; this.addProgressBar(); @@ -221,7 +222,8 @@ export class Characterize extends ATask { else { this.updateLineUp(responseData.importances); } - this.$container.querySelector('.accuracy-container').innerHTML = `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; + this.$container.querySelector('.accuracy-container').innerHTML = + `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)} (using 8 attributes)`; } catch (e) { console.error('could not read JSON data', e); @@ -229,25 +231,37 @@ export class Characterize extends ATask { } else if (responseData.embedding) { console.log('create plot'); - const result = await vegaEmbed(this.$container.querySelector('.chart-container'), { + const vegaContainer = this.$container + .querySelector('.chart-container') + .insertAdjacentElement('beforeend', document.createElement('div')); + const result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", - "title": "Classifier", + "title": `${responseData.data} Data Embedding`, "data": { "values": responseData.embedding }, - "width": 500, - "height": 500, + "transform": [ + { "calculate": "'#'+datum.cht", "as": "chts" } + ], + "width": 400, + "height": 400, "mark": { "type": "point" }, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, "y": { "field": "y", "type": "quantitative", axis: null }, - "color": { "field": "cht", "type": "nominal", legend: null } + "color": { "field": "chts", "type": "nominal" }, + "opacity": { "condition": { "param": "cohort", "value": 0.9 }, "value": 0.01 } }, + "params": [{ + "name": "cohort", + "select": { "type": "point", "fields": ["chts"] }, + "bind": "legend" + }], config: { range: { category: this.cohorts.map((cht) => cht.colorTaskView) } } }, { actions: false, renderer: 'svg' }); - this.chart = result.view; + this.chart.push(result.view); } }; this.ws.onclose = () => { @@ -367,6 +381,6 @@ export class Characterize extends ATask { return response; } } -Characterize.TREES = 200; +Characterize.TREES = 500; Characterize.jaccardFormat = format('.1~%'); //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 7ef04ed..c7b2dac 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index b8cc1c1..e2dc5be 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -14,7 +14,7 @@ import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; export class Characterize extends ATask { - static readonly TREES = 200; + static readonly TREES = 500; static readonly jaccardFormat = format('.1~%'); public label = `Characterize`; @@ -30,7 +30,7 @@ export class Characterize extends ATask { private dataProv: LineUpJS.LocalDataProvider; private cohorts: Cohort[]; private definingAttributes: IAttribute[]; - private chart: VegaView; + private chart: VegaView[]; supports(attributes: IAttribute[], cohorts: ICohort[]) { @@ -97,7 +97,8 @@ export class Characterize extends ATask { this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { this.lineup?.destroy(); this.$container.querySelector('.lineup-container').innerHTML = ''; - this.chart?.finalize(); + this.chart?.forEach((view) => view.finalize()); + this.chart = []; this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; this.addProgressBar(); @@ -272,32 +273,45 @@ export class Characterize extends ATask { this.updateLineUp(responseData.importances); } - this.$container.querySelector('.accuracy-container').innerHTML = `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; + this.$container.querySelector('.accuracy-container').innerHTML = + `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)} (using 8 attributes)`; } catch (e) { console.error('could not read JSON data', e); } } else if (responseData.embedding) { console.log('create plot') - const result = await vegaEmbed(this.$container.querySelector('.chart-container') as HTMLDivElement, { + const vegaContainer = this.$container + .querySelector('.chart-container') + .insertAdjacentElement('beforeend', document.createElement('div')) as HTMLDivElement; + const result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", - "title": "Classifier", + "title": `${responseData.data} Data Embedding`, "data": { "values": responseData.embedding }, - "width": 500, - "height": 500, + "transform": [ + {"calculate": "'#'+datum.cht", "as": "chts"} + ], + "width": 400, + "height": 400, "mark": {"type": "point"}, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, "y": { "field": "y", "type": "quantitative", axis: null }, - "color": {"field": "cht", "type": "nominal", legend: null} + "color": {"field": "chts", "type": "nominal"}, + "opacity": { "condition": {"param": "cohort", "value": 0.9}, "value": 0.01 } }, + "params": [{ + "name": "cohort", + "select": {"type": "point", "fields": ["chts"]}, + "bind": "legend" + }], config: { range: {category: this.cohorts.map((cht) => cht.colorTaskView)} } }, {actions: false, renderer: 'svg'}); - this.chart = result.view; + this.chart.push(result.view); } } From 8ac8f2f78aa2b08035f1bb7f8eedaa5bf8057560 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 20 Jul 2022 15:05:31 +0200 Subject: [PATCH 23/60] add d.ts --- dist/Taskview/tasks/Characterize.d.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 0fd79e7..50ef82e 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -4,7 +4,7 @@ import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; export declare class Characterize extends ATask { - static readonly TREES = 200; + static readonly TREES = 500; static readonly jaccardFormat: (n: number | { valueOf(): number; }) => string; From 4869a6dcb213ba4a2515936f5972fef49abd7519 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 20 Jul 2022 15:25:15 +0200 Subject: [PATCH 24/60] adapt plot size --- dist/Taskview/tasks/Characterize.js | 4 ++-- src/Taskview/tasks/Characterize.ts | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 706464f..43c04aa 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -243,8 +243,8 @@ export class Characterize extends ATask { "transform": [ { "calculate": "'#'+datum.cht", "as": "chts" } ], - "width": 400, - "height": 400, + "width": 700, + "height": 500, "mark": { "type": "point" }, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index e2dc5be..1bf348b 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -293,8 +293,8 @@ export class Characterize extends ATask { "transform": [ {"calculate": "'#'+datum.cht", "as": "chts"} ], - "width": 400, - "height": 400, + "width": 700, + "height": 500, "mark": {"type": "point"}, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, From 2620ba0632e4b9ef70ff1a6ee2176afbe03e2dfb Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 20 Jul 2022 15:28:38 +0200 Subject: [PATCH 25/60] fix label --- dist/Taskview/tasks/Characterize.js | 2 +- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 43c04aa..c96d0a9 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -223,7 +223,7 @@ export class Characterize extends ATask { this.updateLineUp(responseData.importances); } this.$container.querySelector('.accuracy-container').innerHTML = - `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)} (using 8 attributes)`; + `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; } catch (e) { console.error('could not read JSON data', e); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index c7b2dac..b23f332 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 1bf348b..7946668 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -274,7 +274,7 @@ export class Characterize extends ATask { } this.$container.querySelector('.accuracy-container').innerHTML = - `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)} (using 8 attributes)`; + `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; } catch (e) { console.error('could not read JSON data', e); @@ -292,7 +292,7 @@ export class Characterize extends ATask { }, "transform": [ {"calculate": "'#'+datum.cht", "as": "chts"} - ], + ], "width": 700, "height": 500, "mark": {"type": "point"}, From cdf103fe9fe29137a96aa6b18b12342adf35e9bb Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 20 Jul 2022 16:33:18 +0200 Subject: [PATCH 26/60] hide category column if not needed --- dist/Taskview/tasks/Characterize.d.ts | 2 +- dist/Taskview/tasks/Characterize.js | 15 +++++++++++---- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 18 ++++++++++++++---- 4 files changed, 27 insertions(+), 10 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 50ef82e..01a88f6 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -27,7 +27,7 @@ export declare class Characterize extends ATask { private showOverlap; setDefiningAttributeTooltip(hintText: HTMLElement): void; private compare; - createLineUp(data: any): Promise; + createLineUp(data: any, showCategoryColumn?: boolean): Promise; updateLineUp(importances: any): void; addProgressBar(): void; setProgress(iteration: number, done?: boolean): void; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index c96d0a9..c14191d 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -216,7 +216,8 @@ export class Characterize extends ATask { console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { - await this.createLineUp(responseData.importances); // await so its ready for the next response + const showCategoryColumn = endpoint === 'cmp_meta'; + await this.createLineUp(responseData.importances, showCategoryColumn); // await so its ready for the next response first = false; } else { @@ -269,11 +270,17 @@ export class Characterize extends ATask { this.setProgressDone(); }; } - async createLineUp(data) { + async createLineUp(data, showCategoryColumn = true) { const builder = LineUpJS.builder(data); + const categoryCol = LineUpJS.buildStringColumn('category').label('Category').width(200); + if (!showCategoryColumn) { + categoryCol.hidden(); + } this.lineup = builder - .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) - .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) + .column(showCategoryColumn ? + LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200) : + LineUpJS.buildStringColumn('attribute').label('Attribute').width(200)) + .column(categoryCol) .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) .deriveColors() .ranking(LineUpJS.buildRanking() diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index b23f332..d106d6d 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 7946668..fc663bc 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -267,7 +267,8 @@ export class Characterize extends ATask { console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { - await this.createLineUp(responseData.importances); // await so its ready for the next response + const showCategoryColumn = endpoint === 'cmp_meta'; + await this.createLineUp(responseData.importances, showCategoryColumn); // await so its ready for the next response first = false; } else { this.updateLineUp(responseData.importances); @@ -321,11 +322,20 @@ export class Characterize extends ATask { } } - async createLineUp(data) { + async createLineUp(data, showCategoryColumn=true) { const builder = LineUpJS.builder(data); + const categoryCol = LineUpJS.buildStringColumn('category').label('Category').width(200) + if (!showCategoryColumn) { + categoryCol.hidden(); + } + this.lineup = builder - .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200)) - .column(LineUpJS.buildStringColumn('category').label('Category').width(200)) + .column( + showCategoryColumn ? + LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200) : + LineUpJS.buildStringColumn('attribute').label('Attribute').width(200) + ) + .column(categoryCol) .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) .deriveColors() .ranking(LineUpJS.buildRanking() From e7fd3dbd378e35098f1dcb3e7b307b458714a157 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 21 Jul 2022 09:58:11 +0200 Subject: [PATCH 27/60] use d3v7 and d3v3 imports remove depenencies to d3 add dependency to tdp_core --- dist/CohortRepresentations.js | 5 +++-- dist/CohortRepresentations.js.map | 2 +- dist/Taskview/SearchBar.js | 2 +- dist/Taskview/SearchBar.js.map | 2 +- dist/Taskview/SearchColumn.js | 2 +- dist/Taskview/SearchColumn.js.map | 2 +- dist/Taskview/columns/AColumn.js | 2 +- dist/Taskview/columns/AColumn.js.map | 2 +- dist/Taskview/columns/AttributeColumn.js | 2 +- dist/Taskview/columns/AttributeColumn.js.map | 2 +- dist/Taskview/columns/CohortColumn.js | 2 +- dist/Taskview/columns/CohortColumn.js.map | 2 +- dist/Taskview/columns/NumberColumn.js | 2 +- dist/Taskview/columns/NumberColumn.js.map | 2 +- dist/Taskview/tasks/ATask.d.ts | 2 +- dist/Taskview/tasks/ATask.js | 2 +- dist/Taskview/tasks/ATask.js.map | 2 +- dist/Taskview/tasks/Compare.js | 12 ++++++------ dist/Taskview/tasks/Compare.js.map | 2 +- dist/Taskview/tasks/Details.js | 2 +- dist/Taskview/tasks/Details.js.map | 2 +- dist/Taskview/tasks/Filter.d.ts | 2 +- dist/Taskview/tasks/Prevalence.js | 4 +--- dist/Taskview/tasks/Prevalence.js.map | 2 +- dist/Taskview/visualizations/AVegaVisualization.js | 3 +-- .../visualizations/AVegaVisualization.js.map | 2 +- dist/Taskview/visualizations/DensityPlot.js | 3 +-- dist/Taskview/visualizations/DensityPlot.js.map | 2 +- dist/Taskview/visualizations/GroupedBoxplot.js | 3 +-- dist/Taskview/visualizations/GroupedBoxplot.js.map | 2 +- .../visualizations/MultiAttributeVisualization.js | 3 +-- .../MultiAttributeVisualization.js.map | 2 +- dist/Taskview/visualizations/Scatterplot.js | 2 +- dist/Taskview/visualizations/Scatterplot.js.map | 2 +- dist/app.js | 2 +- dist/app.js.map | 2 +- dist/util.d.ts | 2 +- dist/util.js | 2 +- dist/util.js.map | 2 +- dist/utilLabels.js | 2 +- dist/utilLabels.js.map | 2 +- package.json | 5 +---- src/CohortRepresentations.ts | 5 +++-- src/Taskview/SearchBar.ts | 2 +- src/Taskview/SearchColumn.ts | 2 +- src/Taskview/columns/AColumn.ts | 2 +- src/Taskview/columns/AttributeColumn.ts | 2 +- src/Taskview/columns/CohortColumn.ts | 2 +- src/Taskview/columns/NumberColumn.ts | 2 +- src/Taskview/tasks/ATask.ts | 2 +- src/Taskview/tasks/Compare.ts | 12 ++++++------ src/Taskview/tasks/Details.ts | 2 +- src/Taskview/tasks/Filter.ts | 2 +- src/Taskview/tasks/Prevalence.ts | 4 +--- src/Taskview/visualizations/AVegaVisualization.ts | 3 +-- src/Taskview/visualizations/DensityPlot.ts | 3 +-- src/Taskview/visualizations/GroupedBoxplot.ts | 3 +-- src/Taskview/visualizations/KaplanMeierPlot.ts | 2 +- .../visualizations/MultiAttributeVisualization.ts | 3 +-- src/Taskview/visualizations/Scatterplot.ts | 2 +- src/app.ts | 2 +- src/util.ts | 2 +- src/utilLabels.ts | 2 +- 63 files changed, 77 insertions(+), 90 deletions(-) diff --git a/dist/CohortRepresentations.js b/dist/CohortRepresentations.js index db23aff..187a132 100644 --- a/dist/CohortRepresentations.js +++ b/dist/CohortRepresentations.js @@ -1,4 +1,4 @@ -import d3 from 'd3'; +import { hsl } from 'd3v7'; import tippy from 'tippy.js'; import { getRootCohort } from './cohortview'; import { log } from './util'; @@ -233,7 +233,8 @@ export class RectCohortRep { this._representation.style.backgroundColor = color; this._repClone.style.backgroundColor = color; // font color = white if color is too dark - if (color !== null && color !== 'transparent' && d3.hsl(color).l < 0.6) { //transparent has lightness of zero + console.log("color", hsl(color).l); + if (color !== null && color !== 'transparent' && hsl(color).l < 0.6) { //transparent has lightness of zero this._representation.style.color = 'white'; this._repClone.style.color = 'white'; this._removeButton.style.color = 'white'; diff --git a/dist/CohortRepresentations.js.map b/dist/CohortRepresentations.js.map index f6cb5ff..eefd8dc 100644 --- a/dist/CohortRepresentations.js.map +++ b/dist/CohortRepresentations.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/SearchBar.js b/dist/Taskview/SearchBar.js index bc8bfeb..e86bebd 100644 --- a/dist/Taskview/SearchBar.js +++ b/dist/Taskview/SearchBar.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import { RestBaseUtils } from 'tdp_core'; import { dataTypes, depletion } from 'tdp_publicdb'; import { colors } from '../colors'; diff --git a/dist/Taskview/SearchBar.js.map b/dist/Taskview/SearchBar.js.map index 0fa5646..79900e0 100644 --- a/dist/Taskview/SearchBar.js.map +++ b/dist/Taskview/SearchBar.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/Taskview/SearchColumn.js b/dist/Taskview/SearchColumn.js index 1adf740..67d8060 100644 --- a/dist/Taskview/SearchColumn.js +++ b/dist/Taskview/SearchColumn.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import * as $ from 'jquery'; import tippy from 'tippy.js'; import { toAttribute } from '../data/Attribute'; diff --git a/dist/Taskview/SearchColumn.js.map b/dist/Taskview/SearchColumn.js.map index 3f01e16..5d69051 100644 --- a/dist/Taskview/SearchColumn.js.map +++ b/dist/Taskview/SearchColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/columns/AColumn.js b/dist/Taskview/columns/AColumn.js index c3f81b6..6c4bdb2 100644 --- a/dist/Taskview/columns/AColumn.js +++ b/dist/Taskview/columns/AColumn.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import { EMPTY_COHORT_ID, LOADER_COHORT_ID } from '../../Cohort'; import { colors } from '../../colors'; import { createSearchBarTooltip } from '../../Tooltip'; diff --git a/dist/Taskview/columns/AColumn.js.map b/dist/Taskview/columns/AColumn.js.map index ec1bae2..a1df94c 100644 --- a/dist/Taskview/columns/AColumn.js.map +++ b/dist/Taskview/columns/AColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/columns/AttributeColumn.js b/dist/Taskview/columns/AttributeColumn.js index 85932c3..a1d6c2a 100644 --- a/dist/Taskview/columns/AttributeColumn.js +++ b/dist/Taskview/columns/AttributeColumn.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import vegaEmbed from 'vega-embed'; import { colors } from '../../colors'; import { NumRangeOperators } from '../../rest'; diff --git a/dist/Taskview/columns/AttributeColumn.js.map b/dist/Taskview/columns/AttributeColumn.js.map index 8b9516d..b10e2c3 100644 --- a/dist/Taskview/columns/AttributeColumn.js.map +++ b/dist/Taskview/columns/AttributeColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/Taskview/columns/CohortColumn.js b/dist/Taskview/columns/CohortColumn.js index 8afb8f6..f34f0e1 100644 --- a/dist/Taskview/columns/CohortColumn.js +++ b/dist/Taskview/columns/CohortColumn.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import { OnboardingManager } from '../../OnboardingManager'; import { SortType } from '../../util'; import { ColumnSortEvent } from '../../utilCustomEvents'; diff --git a/dist/Taskview/columns/CohortColumn.js.map b/dist/Taskview/columns/CohortColumn.js.map index e0ba32b..4feb3ea 100644 --- a/dist/Taskview/columns/CohortColumn.js.map +++ b/dist/Taskview/columns/CohortColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/columns/NumberColumn.js b/dist/Taskview/columns/NumberColumn.js index e4c8090..c869a41 100644 --- a/dist/Taskview/columns/NumberColumn.js +++ b/dist/Taskview/columns/NumberColumn.js @@ -1,4 +1,4 @@ -import { format as d3Format } from 'd3-format'; +import { format as d3Format } from 'd3v7'; import { ADataColumn } from './AColumn'; export default class NumberColumn extends ADataColumn { constructor($container) { diff --git a/dist/Taskview/columns/NumberColumn.js.map b/dist/Taskview/columns/NumberColumn.js.map index 9cbc681..dd044ee 100644 --- a/dist/Taskview/columns/NumberColumn.js.map +++ b/dist/Taskview/columns/NumberColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/Taskview/tasks/ATask.d.ts b/dist/Taskview/tasks/ATask.d.ts index aef2c59..1767a2f 100644 --- a/dist/Taskview/tasks/ATask.d.ts +++ b/dist/Taskview/tasks/ATask.d.ts @@ -1,4 +1,4 @@ -import { Selection } from 'd3-selection'; +import { Selection } from 'd3v7'; import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; export declare const TASK_CLOSE_EVENT_TYPE = "task:close"; diff --git a/dist/Taskview/tasks/ATask.js b/dist/Taskview/tasks/ATask.js index fb01bd3..bacc2e3 100644 --- a/dist/Taskview/tasks/ATask.js +++ b/dist/Taskview/tasks/ATask.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import { OnboardingManager } from '../../OnboardingManager'; export const TASK_CLOSE_EVENT_TYPE = 'task:close'; export class TaskCloseEvent extends CustomEvent { diff --git a/dist/Taskview/tasks/ATask.js.map b/dist/Taskview/tasks/ATask.js.map index 966c437..dd19f86 100644 --- a/dist/Taskview/tasks/ATask.js.map +++ b/dist/Taskview/tasks/ATask.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Compare.js b/dist/Taskview/tasks/Compare.js index 5dcd5aa..d0a7285 100644 --- a/dist/Taskview/tasks/Compare.js +++ b/dist/Taskview/tasks/Compare.js @@ -3,8 +3,8 @@ * Copyright (c) The Caleydo Team. All rights reserved. * Licensed under the new BSD license, available at http://caleydo.org/license **************************************************************************** */ -import * as d3 from 'd3'; -import { select } from 'd3-selection'; +import { hsl, scaleLinear, select } from 'd3v7'; +import * as d3v3 from 'd3v3'; import { MethodManager, SCOPE, Type, WorkerManager } from 'tourdino'; import { log } from '../../util'; import { ATask } from './ATask'; @@ -83,7 +83,7 @@ export class Compare extends ATask { const parent = select(this).node().parentNode; //parent span-element select(parent).style('background-color', (d) => d.colorTaskView); let color = '#333333'; - if (d && d.colorTaskView && 'transparent' !== d.colorTaskView && d3.hsl(d.colorTaskView).l < 0.5) { //transparent has lightness of zero + if (d && d.colorTaskView && 'transparent' !== d.colorTaskView && hsl(d.colorTaskView).l < 0.5) { //transparent has lightness of zero color = 'white'; } select(parent.parentNode).style('color', color) @@ -398,7 +398,7 @@ export class Compare extends ATask { if (measure.visualization) { const visualization = measure.visualization; if (cellData.setParameters) { - const d3v3Details = d3.select(details.node()); + const d3v3Details = d3v3.select(details.node()); visualization.generateVisualization(d3v3Details, cellData.setParameters, cellData.score); } } @@ -579,7 +579,7 @@ const insertLegend = (parentElement) => { }; export function textColor4Background(backgroundColor) { let color = '#333333'; - if ('transparent' !== backgroundColor && d3.hsl(backgroundColor).l < 0.5) { //transparent has lightness of zero + if ('transparent' !== backgroundColor && hsl(backgroundColor).l < 0.5) { //transparent has lightness of zero color = 'white'; } return color; @@ -589,7 +589,7 @@ export function score2color(score) { let foreground = '#333333'; //kinda black if (score <= 0.05) { // log.debug('bg color cahnge') - const calcColor = d3.scale.linear().domain([0, 0.05]).range(['#000000', '#FFFFFF']); + const calcColor = scaleLinear().domain([0, 0.05]).range(['#000000', '#FFFFFF']); background = calcColor(score).toString(); foreground = textColor4Background(background); } diff --git a/dist/Taskview/tasks/Compare.js.map b/dist/Taskview/tasks/Compare.js.map index 3474a91..93eba4a 100644 --- a/dist/Taskview/tasks/Compare.js.map +++ b/dist/Taskview/tasks/Compare.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Details.js b/dist/Taskview/tasks/Details.js index f60ec52..1e32700 100644 --- a/dist/Taskview/tasks/Details.js +++ b/dist/Taskview/tasks/Details.js @@ -1,5 +1,5 @@ import * as aq from 'arquero'; -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import * as LineUpJS from 'lineupjs'; import { colors } from '../../colors'; import { getCohortData } from '../../rest'; diff --git a/dist/Taskview/tasks/Details.js.map b/dist/Taskview/tasks/Details.js.map index 0728409..3792ca4 100644 --- a/dist/Taskview/tasks/Details.js.map +++ b/dist/Taskview/tasks/Details.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Filter.d.ts b/dist/Taskview/tasks/Filter.d.ts index 63c475e..9ee1c8a 100644 --- a/dist/Taskview/tasks/Filter.d.ts +++ b/dist/Taskview/tasks/Filter.d.ts @@ -1,4 +1,4 @@ -import { Selection } from 'd3-selection'; +import { Selection } from 'd3v7'; import { ICohort } from '../../CohortInterfaces'; import { IAttribute } from '../../data/Attribute'; import { AVegaVisualization } from '../visualizations/AVegaVisualization'; diff --git a/dist/Taskview/tasks/Prevalence.js b/dist/Taskview/tasks/Prevalence.js index 3516128..e4386df 100644 --- a/dist/Taskview/tasks/Prevalence.js +++ b/dist/Taskview/tasks/Prevalence.js @@ -1,6 +1,4 @@ -import { format } from 'd3-format'; -import { select } from 'd3-selection'; -import { transition } from 'd3-transition'; +import { format, select, transition } from 'd3v7'; import tippy from 'tippy.js'; import { getRootCohort } from '../../cohortview'; import { colors } from '../../colors'; diff --git a/dist/Taskview/tasks/Prevalence.js.map b/dist/Taskview/tasks/Prevalence.js.map index afbb2b8..01eda46 100644 --- a/dist/Taskview/tasks/Prevalence.js.map +++ b/dist/Taskview/tasks/Prevalence.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/visualizations/AVegaVisualization.js b/dist/Taskview/visualizations/AVegaVisualization.js index c6bc09d..6bce1d6 100644 --- a/dist/Taskview/visualizations/AVegaVisualization.js +++ b/dist/Taskview/visualizations/AVegaVisualization.js @@ -1,5 +1,4 @@ -import { format } from 'd3-format'; -import { select } from 'd3-selection'; +import { format, select } from 'd3v7'; import { cloneDeep } from 'lodash'; import tippy from 'tippy.js'; import vegaEmbed from 'vega-embed'; diff --git a/dist/Taskview/visualizations/AVegaVisualization.js.map b/dist/Taskview/visualizations/AVegaVisualization.js.map index 12faa56..8f45f5f 100644 --- a/dist/Taskview/visualizations/AVegaVisualization.js.map +++ b/dist/Taskview/visualizations/AVegaVisualization.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/visualizations/DensityPlot.js b/dist/Taskview/visualizations/DensityPlot.js index 20df981..22b266c 100644 --- a/dist/Taskview/visualizations/DensityPlot.js +++ b/dist/Taskview/visualizations/DensityPlot.js @@ -1,5 +1,4 @@ -import { format } from 'd3-format'; -import { select } from 'd3-selection'; +import { format, select } from 'd3v7'; import log from 'loglevel'; import { AVegaVisualization, SingleAttributeVisualization } from './AVegaVisualization'; import { DATA_LABEL } from './constants'; diff --git a/dist/Taskview/visualizations/DensityPlot.js.map b/dist/Taskview/visualizations/DensityPlot.js.map index 41b14d0..5e3e21f 100644 --- a/dist/Taskview/visualizations/DensityPlot.js.map +++ b/dist/Taskview/visualizations/DensityPlot.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/visualizations/GroupedBoxplot.js b/dist/Taskview/visualizations/GroupedBoxplot.js index 7f5768c..0f59a55 100644 --- a/dist/Taskview/visualizations/GroupedBoxplot.js +++ b/dist/Taskview/visualizations/GroupedBoxplot.js @@ -1,5 +1,4 @@ -import { format } from 'd3-format'; -import { select } from 'd3-selection'; +import { format, select } from 'd3v7'; import log from 'loglevel'; import { NumRangeOperators } from '../../rest'; import { FilterEvent, SplitEvent } from '../../utilCustomEvents'; diff --git a/dist/Taskview/visualizations/GroupedBoxplot.js.map b/dist/Taskview/visualizations/GroupedBoxplot.js.map index b6660d7..f0023eb 100644 --- a/dist/Taskview/visualizations/GroupedBoxplot.js.map +++ b/dist/Taskview/visualizations/GroupedBoxplot.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/visualizations/MultiAttributeVisualization.js b/dist/Taskview/visualizations/MultiAttributeVisualization.js index 6efe2ed..b317b01 100644 --- a/dist/Taskview/visualizations/MultiAttributeVisualization.js +++ b/dist/Taskview/visualizations/MultiAttributeVisualization.js @@ -1,6 +1,5 @@ import * as aq from 'arquero'; -import { format } from 'd3-format'; -import { select } from 'd3-selection'; +import { format, select } from 'd3v7'; import tippy from 'tippy.js'; import vegaEmbed from 'vega-embed'; import { getCohortLabel } from '../../Cohort'; diff --git a/dist/Taskview/visualizations/MultiAttributeVisualization.js.map b/dist/Taskview/visualizations/MultiAttributeVisualization.js.map index ef8d595..402ed43 100644 --- a/dist/Taskview/visualizations/MultiAttributeVisualization.js.map +++ b/dist/Taskview/visualizations/MultiAttributeVisualization.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/Taskview/visualizations/Scatterplot.js b/dist/Taskview/visualizations/Scatterplot.js index c66fa18..39935a0 100644 --- a/dist/Taskview/visualizations/Scatterplot.js +++ b/dist/Taskview/visualizations/Scatterplot.js @@ -1,5 +1,5 @@ import * as Comlink from 'comlink'; -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import { ServerColumnAttribute } from '../../data/Attribute'; import { NumRangeOperators } from '../../rest'; import { inRange } from '../../util'; diff --git a/dist/Taskview/visualizations/Scatterplot.js.map b/dist/Taskview/visualizations/Scatterplot.js.map index b638f92..cf10280 100644 --- a/dist/Taskview/visualizations/Scatterplot.js.map +++ b/dist/Taskview/visualizations/Scatterplot.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/app.js b/dist/app.js index 1c14b9e..51c6d75 100644 --- a/dist/app.js +++ b/dist/app.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import SplitGrid from 'split-grid'; import { AppContext, ATDPApplication, NotificationHandler, ObjectRefUtils, RestBaseUtils } from 'tdp_core'; import { cellline, tissue } from 'tdp_publicdb'; diff --git a/dist/app.js.map b/dist/app.js.map index 3eb4a69..4bf2aed 100644 --- a/dist/app.js.map +++ b/dist/app.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/util.d.ts b/dist/util.d.ts index 32f5824..30b49e3 100644 --- a/dist/util.d.ts +++ b/dist/util.d.ts @@ -1,4 +1,4 @@ -import { Selection } from 'd3-selection'; +import { Selection } from 'd3v7'; import * as logger from 'loglevel'; import { ICohort } from './CohortInterfaces'; import { IAttribute } from './data/Attribute'; diff --git a/dist/util.js b/dist/util.js index 3af72fb..b92bf6a 100644 --- a/dist/util.js +++ b/dist/util.js @@ -1,4 +1,4 @@ -import { select } from 'd3-selection'; +import { select } from 'd3v7'; import * as logger from 'loglevel'; import { NotificationHandler } from 'tdp_core'; logger.setDefaultLevel(logger.levels.INFO); diff --git a/dist/util.js.map b/dist/util.js.map index c67b5d3..cbdb42a 100644 --- a/dist/util.js.map +++ b/dist/util.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/utilLabels.js b/dist/utilLabels.js index 77d44b5..3179fdf 100644 --- a/dist/utilLabels.js +++ b/dist/utilLabels.js @@ -1,4 +1,4 @@ -import { format } from 'd3-format'; +import { format } from 'd3v7'; import { isEqualsList, isNumRangeFilter, NumRangeOperators } from './rest'; export function niceName(label) { return label.split('_').map((l) => l[0].toUpperCase() + l.slice(1)).join(' '); diff --git a/dist/utilLabels.js.map b/dist/utilLabels.js.map index cf3190c..4b021b5 100644 --- a/dist/utilLabels.js.map +++ b/dist/utilLabels.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/package.json b/package.json index f60ddfe..10c4cae 100644 --- a/package.json +++ b/package.json @@ -66,10 +66,6 @@ "canvas-confetti": "^1.4.0", "clone": "^2.1.2", "comlink": "^4.2.0", - "d3-array": "^3.1.4", - "d3-format": "^3.1.0", - "d3-selection": "^3.0.0", - "d3-transition": "^3.0.1", "jquery": "^3.5.0", "lineupjs": "4.6.0", "lodash.merge": "^4.x", @@ -79,6 +75,7 @@ "react-dom": "^16.13.0", "react-router-dom": "^5.2.0", "split-grid": "^1.0.9", + "tdp_core": "git+ssh://git@github.com:datavisyn/tdp_core#mp/add_d3v7", "tdp_publicdb": "git+ssh://git@github.com:caleydo/tdp_publicdb#develop", "tippy.js": "^6.2.6", "tourdino": "git+ssh://git@github.com:caleydo/tourdino#develop", diff --git a/src/CohortRepresentations.ts b/src/CohortRepresentations.ts index e2c6f7f..ee9aae1 100644 --- a/src/CohortRepresentations.ts +++ b/src/CohortRepresentations.ts @@ -1,4 +1,4 @@ -import d3 from 'd3'; +import {hsl} from 'd3v7'; import tippy from 'tippy.js'; import {Cohort} from './Cohort'; import {IElement, IRectCohortRep} from './CohortInterfaces'; @@ -286,7 +286,8 @@ export class RectCohortRep implements IRectCohortRep { this._representation.style.backgroundColor = color; this._repClone.style.backgroundColor = color; // font color = white if color is too dark - if (color !== null && color !== 'transparent' && d3.hsl(color).l < 0.6) { //transparent has lightness of zero + console.log("color", hsl(color).l); + if (color !== null && color !== 'transparent' && hsl(color).l < 0.6) { //transparent has lightness of zero this._representation.style.color = 'white'; this._repClone.style.color = 'white'; this._removeButton.style.color = 'white'; diff --git a/src/Taskview/SearchBar.ts b/src/Taskview/SearchBar.ts index fdb118a..28bfba1 100644 --- a/src/Taskview/SearchBar.ts +++ b/src/Taskview/SearchBar.ts @@ -1,4 +1,4 @@ -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import {IdTextPair, IServerColumn, RestBaseUtils} from 'tdp_core'; import {dataTypes, depletion, IDataSubtypeConfig, IDataTypeConfig} from 'tdp_publicdb'; import {colors} from '../colors'; diff --git a/src/Taskview/SearchColumn.ts b/src/Taskview/SearchColumn.ts index 3dfb098..e8bf1c8 100644 --- a/src/Taskview/SearchColumn.ts +++ b/src/Taskview/SearchColumn.ts @@ -1,4 +1,4 @@ -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import * as $ from 'jquery'; import tippy from 'tippy.js'; import {Cohort} from '../Cohort'; diff --git a/src/Taskview/columns/AColumn.ts b/src/Taskview/columns/AColumn.ts index 185c08f..1919476 100644 --- a/src/Taskview/columns/AColumn.ts +++ b/src/Taskview/columns/AColumn.ts @@ -1,4 +1,4 @@ -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import {Cohort, EMPTY_COHORT_ID, LOADER_COHORT_ID} from '../../Cohort'; import {colors} from '../../colors'; import {createSearchBarTooltip} from '../../Tooltip'; diff --git a/src/Taskview/columns/AttributeColumn.ts b/src/Taskview/columns/AttributeColumn.ts index 7b8262f..123f91e 100644 --- a/src/Taskview/columns/AttributeColumn.ts +++ b/src/Taskview/columns/AttributeColumn.ts @@ -1,4 +1,4 @@ -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import vegaEmbed from 'vega-embed'; import {TopLevelSpec as VegaLiteSpec} from 'vega-lite'; import {Cohort} from '../../Cohort'; diff --git a/src/Taskview/columns/CohortColumn.ts b/src/Taskview/columns/CohortColumn.ts index b2f91ae..12aef4f 100644 --- a/src/Taskview/columns/CohortColumn.ts +++ b/src/Taskview/columns/CohortColumn.ts @@ -1,4 +1,4 @@ -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import {Cohort} from '../../Cohort'; import {OnboardingManager} from '../../OnboardingManager'; import {SortType} from '../../util'; diff --git a/src/Taskview/columns/NumberColumn.ts b/src/Taskview/columns/NumberColumn.ts index 1d79104..b29908a 100644 --- a/src/Taskview/columns/NumberColumn.ts +++ b/src/Taskview/columns/NumberColumn.ts @@ -1,4 +1,4 @@ -import {format as d3Format} from 'd3-format'; +import {format as d3Format} from 'd3v7'; import {Cohort} from '../../Cohort'; import {ADataColumn} from './AColumn'; diff --git a/src/Taskview/tasks/ATask.ts b/src/Taskview/tasks/ATask.ts index c62a13e..f96a950 100644 --- a/src/Taskview/tasks/ATask.ts +++ b/src/Taskview/tasks/ATask.ts @@ -1,4 +1,4 @@ -import {select, Selection} from 'd3-selection'; +import {select, Selection} from 'd3v7'; import {ICohort} from '../../CohortInterfaces'; import {IAttribute} from '../../data/Attribute'; import {OnboardingManager} from '../../OnboardingManager'; diff --git a/src/Taskview/tasks/Compare.ts b/src/Taskview/tasks/Compare.ts index 3c5b3e6..d60aa31 100644 --- a/src/Taskview/tasks/Compare.ts +++ b/src/Taskview/tasks/Compare.ts @@ -5,8 +5,8 @@ **************************************************************************** */ -import * as d3 from 'd3'; -import {select, Selection} from 'd3-selection'; +import {hsl, scaleLinear, select, Selection} from 'd3v7'; +import * as d3v3 from 'd3v3'; import {IMeasureResult, IMeasureVisualization, ISetParameters, ISimilarityMeasure, MethodManager, SCOPE, Type, WorkerManager} from 'tourdino'; import {Cohort} from '../../Cohort'; import {Attribute, IAttribute} from '../../data/Attribute'; @@ -101,7 +101,7 @@ export class Compare extends ATask { const parent = select(this).node().parentNode as HTMLElement; //parent span-element select(parent).style('background-color', (d) => (d as Cohort).colorTaskView); let color = '#333333'; - if (d && d.colorTaskView && 'transparent' !== d.colorTaskView && d3.hsl(d.colorTaskView).l < 0.5) { //transparent has lightness of zero + if (d && d.colorTaskView && 'transparent' !== d.colorTaskView && hsl(d.colorTaskView).l < 0.5) { //transparent has lightness of zero color = 'white'; } select(parent.parentNode as HTMLElement).style('color', color) @@ -465,7 +465,7 @@ export class Compare extends ATask { if (measure.visualization) { const visualization: IMeasureVisualization = measure.visualization; if (cellData.setParameters) { - const d3v3Details = d3.select(details.node()); + const d3v3Details = d3v3.select(details.node()); visualization.generateVisualization(d3v3Details, cellData.setParameters, cellData.score); } } @@ -695,7 +695,7 @@ interface IHighlightData { export function textColor4Background(backgroundColor: string) { let color = '#333333'; - if ('transparent' !== backgroundColor && d3.hsl(backgroundColor).l < 0.5) { //transparent has lightness of zero + if ('transparent' !== backgroundColor && hsl(backgroundColor).l < 0.5) { //transparent has lightness of zero color = 'white'; } @@ -709,7 +709,7 @@ export function score2color(score: number): {background: string, foreground: str if (score <= 0.05) { // log.debug('bg color cahnge') - const calcColor = d3.scale.linear().domain([0, 0.05]).range(['#000000', '#FFFFFF']); + const calcColor = scaleLinear().domain([0, 0.05]).range(['#000000', '#FFFFFF']); background = calcColor(score).toString(); foreground = textColor4Background(background); diff --git a/src/Taskview/tasks/Details.ts b/src/Taskview/tasks/Details.ts index 949bf4b..929d11a 100644 --- a/src/Taskview/tasks/Details.ts +++ b/src/Taskview/tasks/Details.ts @@ -1,5 +1,5 @@ import * as aq from 'arquero'; -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import * as LineUpJS from 'lineupjs'; import {Cohort} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; diff --git a/src/Taskview/tasks/Filter.ts b/src/Taskview/tasks/Filter.ts index 1b32008..31757bc 100644 --- a/src/Taskview/tasks/Filter.ts +++ b/src/Taskview/tasks/Filter.ts @@ -1,5 +1,5 @@ -import {Selection} from 'd3-selection'; +import {Selection} from 'd3v7'; import {ICohort} from '../../CohortInterfaces'; import {IAttribute} from '../../data/Attribute'; import {getAnimatedLoadingText, log} from '../../util'; diff --git a/src/Taskview/tasks/Prevalence.ts b/src/Taskview/tasks/Prevalence.ts index 856a444..91d3269 100644 --- a/src/Taskview/tasks/Prevalence.ts +++ b/src/Taskview/tasks/Prevalence.ts @@ -1,6 +1,4 @@ -import {format} from 'd3-format'; -import {select} from 'd3-selection'; -import {transition} from 'd3-transition'; +import {format, select, transition} from 'd3v7'; import tippy from 'tippy.js'; import {Cohort, IBloodlineElement} from '../../Cohort'; import {ICohort} from '../../CohortInterfaces'; diff --git a/src/Taskview/visualizations/AVegaVisualization.ts b/src/Taskview/visualizations/AVegaVisualization.ts index 5beaaf1..bb6725f 100644 --- a/src/Taskview/visualizations/AVegaVisualization.ts +++ b/src/Taskview/visualizations/AVegaVisualization.ts @@ -1,5 +1,4 @@ -import {format} from 'd3-format'; -import {select} from 'd3-selection'; +import {format, select} from 'd3v7'; import {cloneDeep} from 'lodash'; import tippy from 'tippy.js'; import {View as VegaView} from 'vega'; diff --git a/src/Taskview/visualizations/DensityPlot.ts b/src/Taskview/visualizations/DensityPlot.ts index 14b0eab..883181d 100644 --- a/src/Taskview/visualizations/DensityPlot.ts +++ b/src/Taskview/visualizations/DensityPlot.ts @@ -1,5 +1,4 @@ -import {format} from 'd3-format'; -import {select} from 'd3-selection'; +import {format, select} from 'd3v7'; import log from 'loglevel'; import {Spec as VegaSpec} from 'vega'; import {TopLevelSpec as VegaLiteSpec} from 'vega-lite'; diff --git a/src/Taskview/visualizations/GroupedBoxplot.ts b/src/Taskview/visualizations/GroupedBoxplot.ts index dc2af61..9c6a9ec 100644 --- a/src/Taskview/visualizations/GroupedBoxplot.ts +++ b/src/Taskview/visualizations/GroupedBoxplot.ts @@ -1,5 +1,4 @@ -import {format} from 'd3-format'; -import {select} from 'd3-selection'; +import {format, select} from 'd3v7'; import log from 'loglevel'; import {Spec as VegaSpec} from 'vega'; import {TopLevelSpec as VegaLiteSpec} from 'vega-lite'; diff --git a/src/Taskview/visualizations/KaplanMeierPlot.ts b/src/Taskview/visualizations/KaplanMeierPlot.ts index d57601f..35f7097 100644 --- a/src/Taskview/visualizations/KaplanMeierPlot.ts +++ b/src/Taskview/visualizations/KaplanMeierPlot.ts @@ -1,5 +1,5 @@ import log from 'loglevel'; -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import {TopLevelSpec as VegaLiteSpec} from 'vega-lite'; import {Spec as VegaSpec, None} from 'vega'; import {IdValuePair, ServerColumnAttribute} from '../../data/Attribute'; diff --git a/src/Taskview/visualizations/MultiAttributeVisualization.ts b/src/Taskview/visualizations/MultiAttributeVisualization.ts index 4bfcd75..a3f2569 100644 --- a/src/Taskview/visualizations/MultiAttributeVisualization.ts +++ b/src/Taskview/visualizations/MultiAttributeVisualization.ts @@ -1,6 +1,5 @@ import * as aq from 'arquero'; -import {format} from 'd3-format'; -import {select} from 'd3-selection'; +import {format, select} from 'd3v7'; import tippy from 'tippy.js'; import vegaEmbed from 'vega-embed'; import {TopLevelSpec as VegaLiteSpec} from 'vega-lite'; diff --git a/src/Taskview/visualizations/Scatterplot.ts b/src/Taskview/visualizations/Scatterplot.ts index c03af0d..35db688 100644 --- a/src/Taskview/visualizations/Scatterplot.ts +++ b/src/Taskview/visualizations/Scatterplot.ts @@ -1,5 +1,5 @@ import * as Comlink from 'comlink'; -import {select} from 'd3-selection'; +import {select} from 'd3v7'; import {Spec as VegaSpec} from 'vega'; import {TopLevelSpec as VegaLiteSpec} from 'vega-lite'; import {Cohort} from '../../Cohort'; diff --git a/src/app.ts b/src/app.ts index 5012194..e3abbaf 100644 --- a/src/app.ts +++ b/src/app.ts @@ -1,4 +1,4 @@ -import {select, Selection} from 'd3-selection'; +import {select, Selection} from 'd3v7'; import SplitGrid from 'split-grid'; import {AppContext, ATDPApplication, CLUEGraphManager, IDatabaseViewDesc, IObjectRef, IServerColumn, ITDPOptions, NotificationHandler, ObjectRefUtils, ProvenanceGraph, RestBaseUtils} from 'tdp_core'; import {cellline, tissue} from 'tdp_publicdb'; diff --git a/src/util.ts b/src/util.ts index 70e1018..d7b2be0 100644 --- a/src/util.ts +++ b/src/util.ts @@ -1,4 +1,4 @@ -import {select, Selection} from 'd3-selection'; +import {select, Selection} from 'd3v7'; import * as logger from 'loglevel'; import {NotificationHandler} from 'tdp_core'; import {ICohort} from './CohortInterfaces'; diff --git a/src/utilLabels.ts b/src/utilLabels.ts index fa61854..52d573c 100644 --- a/src/utilLabels.ts +++ b/src/utilLabels.ts @@ -1,4 +1,4 @@ -import {format} from 'd3-format'; +import {format} from 'd3v7'; import {IEqualsList, INumRange, isEqualsList, isNumRangeFilter, NumRangeOperators} from './rest'; export function niceName(label: string): string { From 0f01c7d3b5857d0c5e1bf17e5415515b7f15349d Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 21 Jul 2022 10:03:00 +0200 Subject: [PATCH 28/60] remove console log --- dist/CohortRepresentations.js | 1 - dist/CohortRepresentations.js.map | 2 +- src/CohortRepresentations.ts | 1 - 3 files changed, 1 insertion(+), 3 deletions(-) diff --git a/dist/CohortRepresentations.js b/dist/CohortRepresentations.js index 187a132..0f6057c 100644 --- a/dist/CohortRepresentations.js +++ b/dist/CohortRepresentations.js @@ -233,7 +233,6 @@ export class RectCohortRep { this._representation.style.backgroundColor = color; this._repClone.style.backgroundColor = color; // font color = white if color is too dark - console.log("color", hsl(color).l); if (color !== null && color !== 'transparent' && hsl(color).l < 0.6) { //transparent has lightness of zero this._representation.style.color = 'white'; this._repClone.style.color = 'white'; diff --git a/dist/CohortRepresentations.js.map b/dist/CohortRepresentations.js.map index eefd8dc..93f1fb6 100644 --- a/dist/CohortRepresentations.js.map +++ b/dist/CohortRepresentations.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/CohortRepresentations.ts b/src/CohortRepresentations.ts index ee9aae1..e763abb 100644 --- a/src/CohortRepresentations.ts +++ b/src/CohortRepresentations.ts @@ -286,7 +286,6 @@ export class RectCohortRep implements IRectCohortRep { this._representation.style.backgroundColor = color; this._repClone.style.backgroundColor = color; // font color = white if color is too dark - console.log("color", hsl(color).l); if (color !== null && color !== 'transparent' && hsl(color).l < 0.6) { //transparent has lightness of zero this._representation.style.color = 'white'; this._repClone.style.color = 'white'; From a16e3b06089ad181bb2d7a53c5d9d42af8caf387 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Mon, 25 Jul 2022 08:46:09 +0200 Subject: [PATCH 29/60] Update layout, add parameters and OOB error --- dist/Taskview/tasks/Characterize.d.ts | 1 + dist/Taskview/tasks/Characterize.js | 43 +++++++++++++++---- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 8 +++- src/Taskview/tasks/Characterize.ts | 44 ++++++++++++++++---- src/scss/components/task/_characterize.scss | 8 +++- 6 files changed, 87 insertions(+), 19 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 01a88f6..061b298 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -31,6 +31,7 @@ export declare class Characterize extends ATask { updateLineUp(importances: any): void; addProgressBar(): void; setProgress(iteration: number, done?: boolean): void; + setProgressIndefinite(): void; setProgressDone(): void; fadeOutProgressBar(delay?: number): Promise; getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index c14191d..b71b88c 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -52,13 +52,26 @@ export class Characterize extends ATask { Exclude the cohorts' defining attributes +
    + + + 40 + +   + + + + 5 +
    -
    -
    +
    +
    +
    +
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { var _a, _b; @@ -189,6 +202,8 @@ export class Characterize extends ATask { return true; }) .map((attr) => 'gene' in attr ? attr.gene : attr.id); + const maxDepth = parseInt(this.$container.querySelector('input#max-depth').value); + const minGroupSize = parseInt(this.$container.querySelector('input#min-group-size').value); const url = new URL(`/kokiri/${endpoint}/`, location.href); url.protocol = url.protocol.replace('http', 'ws'); console.log('url', url); @@ -196,6 +211,9 @@ export class Characterize extends ATask { this.ws.onopen = async () => { const data = JSON.stringify({ exclude: excludeAttributes, + n_estimators: Characterize.TREES, + max_depth: maxDepth, + min_samples_leaf: minGroupSize, ids: this.ids, }); console.log('Socket is open'); @@ -224,7 +242,11 @@ export class Characterize extends ATask { this.updateLineUp(responseData.importances); } this.$container.querySelector('.accuracy-container').innerHTML = - `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; + ` +

    Accuracy:

    ${Characterize.jaccardFormat(responseData.accuracy)} +

    OOB Error:

    ${Characterize.jaccardFormat(responseData.oobError)} + + `; } catch (e) { console.error('could not read JSON data', e); @@ -233,8 +255,7 @@ export class Characterize extends ATask { else if (responseData.embedding) { console.log('create plot'); const vegaContainer = this.$container - .querySelector('.chart-container') - .insertAdjacentElement('beforeend', document.createElement('div')); + .querySelector('.chart-container'); const result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "title": `${responseData.data} Data Embedding`, @@ -244,8 +265,8 @@ export class Characterize extends ATask { "transform": [ { "calculate": "'#'+datum.cht", "as": "chts" } ], - "width": 700, - "height": 500, + "width": "container", + "height": "container", "mark": { "type": "point" }, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, @@ -289,6 +310,7 @@ export class Characterize extends ATask { .sortBy('Importance', 'desc') // .groupBy('Attribute') .groupSortBy('Importance', 'desc')) + .sidePanel(false) .buildTaggle(this.$container.querySelector('.lineup-container')); this.dataProv = this.lineup.data; const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... @@ -330,9 +352,14 @@ export class Characterize extends ATask { this.progressBar.textContent = `${iteration}/${Characterize.TREES}`; this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; if (iteration === Characterize.TREES) { - this.setProgressDone(); + this.setProgressIndefinite(); } } + setProgressIndefinite() { + this.progressBar.textContent = 'Summarizing'; + this.progressBar.classList.toggle('progress-bar-animated', true); + this.progressBar.classList.toggle('progress-bar-striped', true); + } setProgressDone() { this.progressBar.textContent = 'Done'; this.fadeOutProgressBar(); diff --git a/dist/Taskview/tasks/Characterize.js.map 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 0ce553a..9a1405c 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto auto auto 1fr auto; // 1fr for lineup + grid-template-rows: auto auto auto auto minmax(500px, 1fr); row-gap: 1em; .cht-icon { @@ -38,4 +38,10 @@ h1 { font-size: 1.1em; } + + .classifier-result { + display: grid; + grid-template-columns: 1fr 1fr; + grid-template-rows: 1fr; + } } \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index fc663bc..0f9e44a 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -85,13 +85,26 @@ export class Characterize extends ATask { Exclude the cohorts' defining attributes +
    + + + 40 + +   + + + + 5 +
    -
    -
    +
    +
    +
    +
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { @@ -237,6 +250,8 @@ export class Characterize extends ATask { }) .map((attr) => 'gene' in attr ? (attr as GeneScoreAttribute).gene : attr.id); + const maxDepth = parseInt((this.$container.querySelector('input#max-depth') as HTMLInputElement).value); + const minGroupSize = parseInt((this.$container.querySelector('input#min-group-size') as HTMLInputElement).value); const url = new URL(`/kokiri/${endpoint}/`, location.href); url.protocol = url.protocol.replace('http', 'ws'); @@ -245,6 +260,9 @@ export class Characterize extends ATask { this.ws.onopen = async () => { const data = JSON.stringify({ // send as string, because sending JSON apparantly only works this way 🤷‍♀️ (see https://developer.mozilla.org/en-US/docs/Web/API/WebSockets_API/Writing_WebSocket_client_applications) exclude: excludeAttributes, + n_estimators: Characterize.TREES, + max_depth: maxDepth, + min_samples_leaf: minGroupSize, ids: this.ids, }) console.log('Socket is open') @@ -275,7 +293,11 @@ export class Characterize extends ATask { } this.$container.querySelector('.accuracy-container').innerHTML = - `

    Cohort Separability:

    ${Characterize.jaccardFormat(responseData.accuracy)}`; + ` +

    Accuracy:

    ${Characterize.jaccardFormat(responseData.accuracy)} +

    OOB Error:

    ${Characterize.jaccardFormat(responseData.oobError)} + + `; } catch (e) { console.error('could not read JSON data', e); @@ -283,8 +305,7 @@ export class Characterize extends ATask { } else if (responseData.embedding) { console.log('create plot') const vegaContainer = this.$container - .querySelector('.chart-container') - .insertAdjacentElement('beforeend', document.createElement('div')) as HTMLDivElement; + .querySelector('.chart-container') as HTMLDivElement; const result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "title": `${responseData.data} Data Embedding`, @@ -294,8 +315,8 @@ export class Characterize extends ATask { "transform": [ {"calculate": "'#'+datum.cht", "as": "chts"} ], - "width": 700, - "height": 500, + "width": "container", + "height": "container", "mark": {"type": "point"}, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, @@ -345,6 +366,7 @@ export class Characterize extends ATask { // .groupBy('Attribute') .groupSortBy('Importance', 'desc') ) + .sidePanel(false) .buildTaggle(this.$container.querySelector('.lineup-container')); this.dataProv = this.lineup.data as LineUpJS.LocalDataProvider; @@ -390,10 +412,16 @@ export class Characterize extends ATask { this.progressBar.style.width = `${100 * iteration / Characterize.TREES}%`; if (iteration === Characterize.TREES) { - this.setProgressDone(); + this.setProgressIndefinite(); } } + setProgressIndefinite() { + this.progressBar.textContent = 'Summarizing'; + this.progressBar.classList.toggle('progress-bar-animated', true); + this.progressBar.classList.toggle('progress-bar-striped', true); + } + setProgressDone() { this.progressBar.textContent = 'Done'; this.fadeOutProgressBar(); diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 0ce553a..9a1405c 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto auto auto 1fr auto; // 1fr for lineup + grid-template-rows: auto auto auto auto minmax(500px, 1fr); row-gap: 1em; .cht-icon { @@ -38,4 +38,10 @@ h1 { font-size: 1.1em; } + + .classifier-result { + display: grid; + grid-template-columns: 1fr 1fr; + grid-template-rows: 1fr; + } } \ No newline at end of file From 4f04144ee79fb0045e87b141a25e67ea27743823 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Mon, 25 Jul 2022 11:22:20 +0200 Subject: [PATCH 30/60] Make inputs more compact --- dist/Taskview/tasks/Characterize.js | 21 +++++++++++---------- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 21 +++++++++++---------- 3 files changed, 23 insertions(+), 21 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index b71b88c..e5f7910 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -52,17 +52,18 @@ export class Characterize extends ATask { Exclude the cohorts' defining attributes -
    - - - 40 -   +   - - - 5 -
    + + + 50 + +   + + + + 1
    @@ -244,7 +245,7 @@ export class Characterize extends ATask { this.$container.querySelector('.accuracy-container').innerHTML = `

    Accuracy:

    ${Characterize.jaccardFormat(responseData.accuracy)} -

    OOB Error:

    ${Characterize.jaccardFormat(responseData.oobError)} +

    OOB Score:

    ${Characterize.jaccardFormat(responseData.oobError)} `; } diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 4e42dcd..164eff9 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 0f9e44a..60ba6d8 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -85,17 +85,18 @@ export class Characterize extends ATask { Exclude the cohorts' defining attributes -
    - - - 40 -   +   - - - 5 -
    + + + 50 + +   + + + + 1
    @@ -295,7 +296,7 @@ export class Characterize extends ATask { this.$container.querySelector('.accuracy-container').innerHTML = `

    Accuracy:

    ${Characterize.jaccardFormat(responseData.accuracy)} -

    OOB Error:

    ${Characterize.jaccardFormat(responseData.oobError)} +

    OOB Score:

    ${Characterize.jaccardFormat(responseData.oobError)} `; From 1bed6c3f7a2623d3893ab93ab31ea501afd9bbe6 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 26 Jul 2022 14:35:24 +0200 Subject: [PATCH 31/60] update code such that lineup updates --- .../Characterize/LineUpDistributionColumn.js | 29 +++++++++-------- .../LineUpDistributionColumn.js.map | 2 +- .../Characterize/LineUpDistributionColumn.ts | 31 ++++++++----------- 3 files changed, 28 insertions(+), 34 deletions(-) diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js index 496674a..2124a74 100644 --- a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js @@ -151,24 +151,21 @@ class LineUpDistributionColumn extends MapColumn { return null; } //@ts-ignore - return values.map(({ key, value }) => { - return { - key, - value: value.length === 0 - ? null - : value.map((val) => this.mapping.apply(val)), - }; - }); + return values.map((d) => d.value); + // //@ts-ignore + // return values.map(({key, value}) => { + // return { + // key, + // value: + // value.length === 0 + // ? null + // : value.map((val) => this.mapping.apply(val)), + // }; + // }); } getRawValue(row) { const r = super.getValue(row); return r == null ? [] : r; - // const values = super.getValue(row); - // if(values.length === 0) - // return null; - // return values.map(({key, value}) => { - // return {key, value: value.length===0 ? null : value}; - // }); } getExportValue(row, format) { return format === "json" @@ -279,7 +276,9 @@ class LineUpDistributionColumn extends MapColumn { filter(row) { // currently it checks, if the median is within the range // const value = this.getRawNumber(row); - const value = this.get_advanced_value(EAdvancedSortMethod.median, this.getRawValue(row)[0]["value"]); + const value = this.get_advanced_value(EAdvancedSortMethod.median, + //@ts-ignore + this.getRawValue(row).map((v) => v.value)); return this.isNumberIncluded(this.getFilter(), value); } clearFilter() { diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map index 7832a6f..39053b4 100644 --- a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts index aefb12e..9a39160 100644 --- a/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts +++ b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts @@ -283,28 +283,22 @@ export class LineUpDistributionColumn extends MapColumn { } //@ts-ignore - return values.map(({key, value}) => { - return { - key, - value: - value.length === 0 - ? null - : value.map((val) => this.mapping.apply(val)), - }; - }); + return values.map((d) => d.value); + // //@ts-ignore + // return values.map(({key, value}) => { + // return { + // key, + // value: + // value.length === 0 + // ? null + // : value.map((val) => this.mapping.apply(val)), + // }; + // }); } getRawValue(row: IDataRow): IKeyValue[] { const r = super.getValue(row); return r == null ? [] : r; - // const values = super.getValue(row); - - // if(values.length === 0) - // return null; - - // return values.map(({key, value}) => { - // return {key, value: value.length===0 ? null : value}; - // }); } getExportValue(row: IDataRow, format: "text" | "json"): any { @@ -504,7 +498,8 @@ export class LineUpDistributionColumn extends MapColumn { // const value = this.getRawNumber(row); const value = this.get_advanced_value( EAdvancedSortMethod.median, - this.getRawValue(row)[0]["value"] + //@ts-ignore + this.getRawValue(row).map((v) => v.value) ); return this.isNumberIncluded(this.getFilter(), value); From afa59274e3c557227591997ef6a1d1fd44802bb3 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 26 Jul 2022 14:35:34 +0200 Subject: [PATCH 32/60] wider lineup for testing --- dist/scss/components/task/_characterize.scss | 2 +- src/scss/components/task/_characterize.scss | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 9a1405c..6a3cdde 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -41,7 +41,7 @@ .classifier-result { display: grid; - grid-template-columns: 1fr 1fr; + grid-template-columns: 5fr 1fr; grid-template-rows: 1fr; } } \ No newline at end of file diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 9a1405c..6a3cdde 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -41,7 +41,7 @@ .classifier-result { display: grid; - grid-template-columns: 1fr 1fr; + grid-template-columns: 5fr 1fr; grid-template-rows: 1fr; } } \ No newline at end of file From a56924a782476a7686530131f28d56997b83e0c0 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 26 Jul 2022 14:35:49 +0200 Subject: [PATCH 33/60] show loading animation til distributions are visible --- dist/Taskview/tasks/Characterize.d.ts | 4 +- dist/Taskview/tasks/Characterize.js | 59 ++++++++++++++++++++--- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 64 ++++++++++++++++++++++--- 4 files changed, 114 insertions(+), 15 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 465a08f..83fcc87 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -6,7 +6,7 @@ import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; export declare class Characterize extends ATask { - static readonly TREES = 500; + static readonly TREES = 200; static readonly jaccardFormat: (n: number | { valueOf(): number; }) => string; @@ -41,6 +41,8 @@ export declare class Characterize extends ATask { } export declare class MyDistributionRenderer implements ICellRendererFactory { readonly title: string; + static readonly WIDTH = 200; + static readonly HEIGHT = 50; canRender(col: LineUpDistributionColumn, mode: ERenderMode): boolean; create(col: LineUpDistributionColumn): ICellRenderer; } diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 582acd6..2b1bfab 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -2,6 +2,8 @@ import * as aq from 'arquero'; import { format } from 'd3-format'; import * as LineUpJS from 'lineupjs'; import { ERenderMode, renderMissingDOM } from 'lineupjs'; +// import * as d3 from 'd3'; +import { select } from 'd3-selection'; import tippy from 'tippy.js'; import vegaEmbed from 'vega-embed'; import { getCohortLabel } from '../../Cohort'; @@ -230,8 +232,8 @@ export class Characterize extends ATask { }; let first = true; this.ws.onmessage = async (message) => { - console.log('response', message); const responseData = JSON.parse(message.data); + console.log('response', responseData); if (responseData.trees) { try { console.log(responseData.trees); @@ -301,12 +303,12 @@ export class Characterize extends ATask { categoryCol.hidden(); } this.lineup = builder + .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) .column(showCategoryColumn ? LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200) : LineUpJS.buildStringColumn('attribute').label('Attribute').width(200)) .column(categoryCol) - .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) - .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(50).build([])) + .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([])) .registerRenderer("myDistributionRenderer", new MyDistributionRenderer()) .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() @@ -317,6 +319,7 @@ export class Characterize extends ATask { // .groupBy('Attribute') .groupSortBy('Importance', 'desc')) .sidePanel(false) + .rowHeight(50) .buildTaggle(this.$container.querySelector('.lineup-container')); this.dataProv = this.lineup.data; const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... @@ -421,7 +424,7 @@ export class Characterize extends ATask { return response; } } -Characterize.TREES = 500; +Characterize.TREES = 200; Characterize.jaccardFormat = format('.1~%'); export class MyDistributionRenderer { constructor() { @@ -432,14 +435,58 @@ export class MyDistributionRenderer { } create(col) { return { - template: `
    blub
    `, + template: `
    + + + + + + + + + + + + + + + + +
    `, update: (n, d) => { + var _a; if (renderMissingDOM(n, col, d)) { return; } - console.log('Update'); + const data = (_a = d.v) === null || _a === void 0 ? void 0 : _a.distribution; + if (d.v.random !== false) { + console.log('remove loader'); + select(n).selectAll('#loading').remove(); + // const chart = select(n).select('#chart g') + // X axis + // var x = d3.scaleBand() + // .range([ 0, MyDistributionRenderer.WIDTH ]) + // .domain(data.map(function(d) { return d.Country; })) + // .padding(0.2); + // // Add Y axis + // var y = d3.scaleLinear() + // .domain([0, 13000]) + // .range([ MyDistributionRenderer.HEIGHT, 0]); + // // Bars + // chart.selectAll("mybar") + // .data(data) + // .enter() + // .append("rect") + // .attr("x", function(d) { return x(d.Country); }) + // .attr("y", function(d) { return y(d.Value); }) + // .attr("width", x.bandwidth()) + // .attr("height", function(d) { return MyDistributionRenderer.HEIGHT - y(d.Value); }) + // .attr("fill", "#69b3a2") + } }, }; } } +MyDistributionRenderer.WIDTH = 200; +MyDistributionRenderer.HEIGHT = 50; //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index f8a7f64..5f8ad2b 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index c2e7c44..b2698b5 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -2,6 +2,8 @@ import * as aq from 'arquero'; import {format} from 'd3-format'; import * as LineUpJS from 'lineupjs'; import {ERenderMode, ICellRenderer, ICellRendererFactory, IDataRow, renderMissingDOM} from 'lineupjs'; +// import * as d3 from 'd3'; +import {select} from 'd3-selection'; import tippy from 'tippy.js'; import {View as VegaView} from 'vega'; import vegaEmbed from 'vega-embed'; @@ -16,7 +18,7 @@ import {ATask} from './ATask'; import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn'; export class Characterize extends ATask { - static readonly TREES = 500; + static readonly TREES = 200; static readonly jaccardFormat = format('.1~%'); public label = `Characterize`; @@ -280,8 +282,8 @@ export class Characterize extends ATask { let first = true; this.ws.onmessage = async (message) => { - console.log('response', message); const responseData = JSON.parse(message.data); + console.log('response', responseData); if(responseData.trees) { try { @@ -354,14 +356,14 @@ export class Characterize extends ATask { } this.lineup = builder + .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) .column( showCategoryColumn ? LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200) : LineUpJS.buildStringColumn('attribute').label('Attribute').width(200) ) .column(categoryCol) - .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) - .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(50).build([])) + .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([])) .registerRenderer("myDistributionRenderer", new MyDistributionRenderer()) .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() @@ -373,6 +375,7 @@ export class Characterize extends ATask { .groupSortBy('Importance', 'desc') ) .sidePanel(false) + .rowHeight(50) .buildTaggle(this.$container.querySelector('.lineup-container')); this.dataProv = this.lineup.data as LineUpJS.LocalDataProvider; @@ -489,6 +492,8 @@ export class Characterize extends ATask { export class MyDistributionRenderer implements ICellRendererFactory { readonly title: string = "Distribution Chart"; + static readonly WIDTH=200; + static readonly HEIGHT=50; canRender(col: LineUpDistributionColumn, mode: ERenderMode): boolean { return mode === ERenderMode.CELL; @@ -496,13 +501,58 @@ export class MyDistributionRenderer implements ICellRendererFactory { create(col: LineUpDistributionColumn): ICellRenderer { return { - template: `
    blub
    `, + template: `
    + + + + + + + + + + + + + + + + +
    `, update: (n: HTMLImageElement, d: IDataRow) => { if (renderMissingDOM(n, col, d)) { return; - } - console.log('Update') + } + const data = d.v?.distribution; + if (d.v.random !== false) { + console.log('remove loader'); + select(n).selectAll('#loading').remove(); + + // const chart = select(n).select('#chart g') + // X axis + // var x = d3.scaleBand() + // .range([ 0, MyDistributionRenderer.WIDTH ]) + // .domain(data.map(function(d) { return d.Country; })) + // .padding(0.2); + + + // // Add Y axis + // var y = d3.scaleLinear() + // .domain([0, 13000]) + // .range([ MyDistributionRenderer.HEIGHT, 0]); + + // // Bars + // chart.selectAll("mybar") + // .data(data) + // .enter() + // .append("rect") + // .attr("x", function(d) { return x(d.Country); }) + // .attr("y", function(d) { return y(d.Value); }) + // .attr("width", x.bandwidth()) + // .attr("height", function(d) { return MyDistributionRenderer.HEIGHT - y(d.Value); }) + // .attr("fill", "#69b3a2") + } }, }; } From 90d27567a9b6eebecf020f0c03001826e6fede8f Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 26 Jul 2022 20:50:20 +0200 Subject: [PATCH 34/60] add distribution column --- dist/Taskview/tasks/Characterize.d.ts | 4 +- dist/Taskview/tasks/Characterize.js | 80 ++++++++++------- dist/Taskview/tasks/Characterize.js.map | 2 +- .../Characterize/LineUpDistributionColumn.js | 3 +- .../LineUpDistributionColumn.js.map | 2 +- dist/scss/components/task/_characterize.scss | 2 +- src/Taskview/tasks/Characterize.ts | 88 +++++++++++-------- .../Characterize/LineUpDistributionColumn.ts | 3 +- src/scss/components/task/_characterize.scss | 2 +- 9 files changed, 108 insertions(+), 78 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 83fcc87..d5ab6f7 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -40,9 +40,11 @@ export declare class Characterize extends ATask { postData(endpoint: string, data?: {}): Promise; } export declare class MyDistributionRenderer implements ICellRendererFactory { + private cohorts; readonly title: string; static readonly WIDTH = 200; - static readonly HEIGHT = 50; + static readonly HEIGHT = 40; + constructor(cohorts: Cohort[]); canRender(col: LineUpDistributionColumn, mode: ERenderMode): boolean; create(col: LineUpDistributionColumn): ICellRenderer; } diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 2b1bfab..83b4da3 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -2,8 +2,7 @@ import * as aq from 'arquero'; import { format } from 'd3-format'; import * as LineUpJS from 'lineupjs'; import { ERenderMode, renderMissingDOM } from 'lineupjs'; -// import * as d3 from 'd3'; -import { select } from 'd3-selection'; +import * as d3 from 'd3v7'; import tippy from 'tippy.js'; import vegaEmbed from 'vega-embed'; import { getCohortLabel } from '../../Cohort'; @@ -303,13 +302,13 @@ export class Characterize extends ATask { categoryCol.hidden(); } this.lineup = builder - .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) + .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150).colorMapping(colors.barColor)) .column(showCategoryColumn ? - LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200) : + LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150) : LineUpJS.buildStringColumn('attribute').label('Attribute').width(200)) .column(categoryCol) .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([])) - .registerRenderer("myDistributionRenderer", new MyDistributionRenderer()) + .registerRenderer("myDistributionRenderer", new MyDistributionRenderer(this.cohorts)) .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() .ranking(LineUpJS.buildRanking() @@ -427,7 +426,8 @@ export class Characterize extends ATask { Characterize.TREES = 200; Characterize.jaccardFormat = format('.1~%'); export class MyDistributionRenderer { - constructor() { + constructor(cohorts) { + this.cohorts = cohorts; this.title = "Distribution Chart"; } canRender(col, mode) { @@ -437,13 +437,13 @@ export class MyDistributionRenderer { return { template: `
    - + - + - + @@ -451,6 +451,10 @@ export class MyDistributionRenderer { + + + +
    `, update: (n, d) => { @@ -459,34 +463,44 @@ export class MyDistributionRenderer { return; } const data = (_a = d.v) === null || _a === void 0 ? void 0 : _a.distribution; - if (d.v.random !== false) { - console.log('remove loader'); - select(n).selectAll('#loading').remove(); - // const chart = select(n).select('#chart g') - // X axis - // var x = d3.scaleBand() - // .range([ 0, MyDistributionRenderer.WIDTH ]) - // .domain(data.map(function(d) { return d.Country; })) - // .padding(0.2); - // // Add Y axis - // var y = d3.scaleLinear() - // .domain([0, 13000]) - // .range([ MyDistributionRenderer.HEIGHT, 0]); - // // Bars - // chart.selectAll("mybar") - // .data(data) - // .enter() - // .append("rect") - // .attr("x", function(d) { return x(d.Country); }) - // .attr("y", function(d) { return y(d.Value); }) - // .attr("width", x.bandwidth()) - // .attr("height", function(d) { return MyDistributionRenderer.HEIGHT - y(d.Value); }) - // .attr("fill", "#69b3a2") + if (data && d.v.random === false) { + d3.select(n).selectAll('#loading').remove(); + d3.select(n).select('.xaxis path').attr('stroke', colors.barColor); + const chart = d3.select(n).select('#chart g'); + if (d.v.type === 'cat') { + console.log(`OK: ${d.v.attribute}`); + // X axis + var x = d3.scaleBand() + .range([0, MyDistributionRenderer.WIDTH]) + .domain(data.map(function (d) { return d.cht; })) + .padding(0.2); + // Add Y axis + var y = d3.scaleLinear() + .domain([0, 1]) + .range([MyDistributionRenderer.HEIGHT, 0]); + // Bars + chart.selectAll("rect") + .data(data) + .enter() + .append("rect") + .attr("x", (d) => x(d.cht)) + .attr("y", (d) => y(d.value)) + .attr("width", x.bandwidth()) + .attr("height", function (d) { return MyDistributionRenderer.HEIGHT - y(d.value); }) + .attr("fill", (d, i) => this.cohorts[i].colorTaskView) + .exit().remove(); + } + else { + console.log(`type of ${d.v.attribute} is ${d.v.type}`); + } + } + else { + console.log(`${d.v.attribute} is random`); } }, }; } } MyDistributionRenderer.WIDTH = 200; -MyDistributionRenderer.HEIGHT = 50; +MyDistributionRenderer.HEIGHT = 40; //# sourceMappingURL=Characterize.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 5f8ad2b..4e40e75 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js index 2124a74..9b54e8b 100644 --- a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js @@ -142,7 +142,8 @@ class LineUpDistributionColumn extends MapColumn { const r = this.getRawValue(row); // return r ? r.map((d) => d.value) : [NaN]; // return r ? r[0]["value"] : [NaN]; - return [this.get_advanced_value(EAdvancedSortMethod.median, r[0]["value"])]; + //@ts-ignore + return [this.get_advanced_value(EAdvancedSortMethod.median, r.map((d) => d["value"]))]; } getValue(row) { const values = this.getRawValue(row); diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map index 39053b4..11566bb 100644 --- a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 6a3cdde..55525b8 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -41,7 +41,7 @@ .classifier-result { display: grid; - grid-template-columns: 5fr 1fr; + grid-template-columns: 2fr 1fr; grid-template-rows: 1fr; } } \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index b2698b5..59cbec0 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -2,8 +2,7 @@ import * as aq from 'arquero'; import {format} from 'd3-format'; import * as LineUpJS from 'lineupjs'; import {ERenderMode, ICellRenderer, ICellRendererFactory, IDataRow, renderMissingDOM} from 'lineupjs'; -// import * as d3 from 'd3'; -import {select} from 'd3-selection'; +import * as d3 from 'd3v7'; import tippy from 'tippy.js'; import {View as VegaView} from 'vega'; import vegaEmbed from 'vega-embed'; @@ -356,15 +355,15 @@ export class Characterize extends ATask { } this.lineup = builder - .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150)) + .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150).colorMapping(colors.barColor)) .column( showCategoryColumn ? - LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(200) : + LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150) : LineUpJS.buildStringColumn('attribute').label('Attribute').width(200) ) .column(categoryCol) .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([])) - .registerRenderer("myDistributionRenderer", new MyDistributionRenderer()) + .registerRenderer("myDistributionRenderer", new MyDistributionRenderer(this.cohorts)) .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() .ranking(LineUpJS.buildRanking() @@ -493,7 +492,9 @@ export class Characterize extends ATask { export class MyDistributionRenderer implements ICellRendererFactory { readonly title: string = "Distribution Chart"; static readonly WIDTH=200; - static readonly HEIGHT=50; + static readonly HEIGHT=40; + + constructor(private cohorts: Cohort[]) {} canRender(col: LineUpDistributionColumn, mode: ERenderMode): boolean { return mode === ERenderMode.CELL; @@ -503,13 +504,13 @@ export class MyDistributionRenderer implements ICellRendererFactory { return { template: `
    - + - + - + @@ -517,41 +518,52 @@ export class MyDistributionRenderer implements ICellRendererFactory { + + + +
    `, update: (n: HTMLImageElement, d: IDataRow) => { if (renderMissingDOM(n, col, d)) { return; - } - const data = d.v?.distribution; - if (d.v.random !== false) { - console.log('remove loader'); - select(n).selectAll('#loading').remove(); - - // const chart = select(n).select('#chart g') - // X axis - // var x = d3.scaleBand() - // .range([ 0, MyDistributionRenderer.WIDTH ]) - // .domain(data.map(function(d) { return d.Country; })) - // .padding(0.2); - - - // // Add Y axis - // var y = d3.scaleLinear() - // .domain([0, 13000]) - // .range([ MyDistributionRenderer.HEIGHT, 0]); - - // // Bars - // chart.selectAll("mybar") - // .data(data) - // .enter() - // .append("rect") - // .attr("x", function(d) { return x(d.Country); }) - // .attr("y", function(d) { return y(d.Value); }) - // .attr("width", x.bandwidth()) - // .attr("height", function(d) { return MyDistributionRenderer.HEIGHT - y(d.Value); }) - // .attr("fill", "#69b3a2") + + const data = d.v?.distribution as Array<{cht: string, value: number}>; + if (data && d.v.random === false) { + d3.select(n).selectAll('#loading').remove(); + d3.select(n).select('.xaxis path').attr('stroke', colors.barColor); + + const chart = d3.select(n).select('#chart g') + if (d.v.type === 'cat') { + console.log(`OK: ${d.v.attribute}`); + // X axis + var x = d3.scaleBand() + .range([ 0, MyDistributionRenderer.WIDTH ]) + .domain(data.map(function(d) { return d.cht; })) + .padding(0.2); + + // Add Y axis + var y = d3.scaleLinear() + .domain([0, 1]) + .range([ MyDistributionRenderer.HEIGHT, 0]); + + // Bars + chart.selectAll("rect") + .data(data) + .enter() + .append("rect") + .attr("x", (d) => x(d.cht)) + .attr("y", (d) => y(d.value)) + .attr("width", x.bandwidth()) + .attr("height", function(d) { return MyDistributionRenderer.HEIGHT - y(d.value); }) + .attr("fill", (d, i) => this.cohorts[i].colorTaskView) + .exit().remove(); + } else { + console.log(`type of ${d.v.attribute} is ${d.v.type}`); + } + } else { + console.log(`${d.v.attribute} is random`); } }, }; diff --git a/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts index 9a39160..4a9006b 100644 --- a/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts +++ b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts @@ -271,7 +271,8 @@ export class LineUpDistributionColumn extends MapColumn { const r = this.getRawValue(row); // return r ? r.map((d) => d.value) : [NaN]; // return r ? r[0]["value"] : [NaN]; - return [this.get_advanced_value(EAdvancedSortMethod.median, r[0]["value"])]; + //@ts-ignore + return [this.get_advanced_value(EAdvancedSortMethod.median, r.map((d) => d["value"]))]; } getValue(row: IDataRow): IKeyValue[] { diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 6a3cdde..55525b8 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -41,7 +41,7 @@ .classifier-result { display: grid; - grid-template-columns: 5fr 1fr; + grid-template-columns: 2fr 1fr; grid-template-rows: 1fr; } } \ No newline at end of file From 578264f523699a490c69c2446ca4eef7484f8e27 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 27 Jul 2022 07:47:01 +0200 Subject: [PATCH 35/60] increase precision of importance column --- dist/Taskview/tasks/Characterize.js | 9 +++++++-- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 17 +++++++++++++---- 3 files changed, 21 insertions(+), 7 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 83b4da3..08baf01 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -302,12 +302,17 @@ export class Characterize extends ATask { categoryCol.hidden(); } this.lineup = builder - .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150).colorMapping(colors.barColor)) + .column(LineUpJS.buildNumberColumn('importance', [0, 1]) + .label('Importance') + .width(150) + .colorMapping(colors.barColor) + .numberFormat('.3f')) .column(showCategoryColumn ? LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150) : LineUpJS.buildStringColumn('attribute').label('Attribute').width(200)) .column(categoryCol) - .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([])) + .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution') + .renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([])) .registerRenderer("myDistributionRenderer", new MyDistributionRenderer(this.cohorts)) .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 4e40e75..d3a8a55 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 59cbec0..3aa4784 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -355,16 +355,25 @@ export class Characterize extends ATask { } this.lineup = builder - .column(LineUpJS.buildNumberColumn('importance', [0, 1]).label('Importance').width(150).colorMapping(colors.barColor)) + .column( + LineUpJS.buildNumberColumn('importance', [0, 1]) + .label('Importance') + .width(150) + .colorMapping(colors.barColor) + .numberFormat('.3f') + ) .column( showCategoryColumn ? LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150) : LineUpJS.buildStringColumn('attribute').label('Attribute').width(200) ) .column(categoryCol) - .column(LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution').renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([])) - .registerRenderer("myDistributionRenderer", new MyDistributionRenderer(this.cohorts)) - .registerColumnType("myDistributionColumn", LineUpDistributionColumn) + .column( + LineUpJS.buildColumn("myDistributionColumn", 'distribution').label('Distribution') + .renderer("myDistributionRenderer", "myDistributionRenderer").width(200).build([]) + ) + .registerRenderer("myDistributionRenderer", new MyDistributionRenderer(this.cohorts)) + .registerColumnType("myDistributionColumn", LineUpDistributionColumn) .deriveColors() .ranking(LineUpJS.buildRanking() .supportTypes() From 3bd2e5766018370e4fc0cc356c24292bc6db6a45 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 27 Jul 2022 07:58:17 +0200 Subject: [PATCH 36/60] try different filters --- dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js | 3 ++- .../tasks/Characterize/LineUpDistributionColumn.js.map | 2 +- src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js index 9b54e8b..d038aaf 100644 --- a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js @@ -299,7 +299,8 @@ LineUpDistributionColumn = LineUpDistributionColumn_1 = __decorate([ export { LineUpDistributionColumn }; export const DEFAULT_FORMATTER = format(".3n"); export function noNumberFilter() { - return { min: -Infinity, max: Infinity, filterMissing: false }; + // return {min: Number.NEGATIVE_INFINITY, max: Number.POSITIVE_INFINITY, filterMissing: false } + return { min: Number.NaN, max: Number.NaN, filterMissing: false }; } export function isEqualNumberFilter(a, b, delta = 0.001) { return (similar(a.min, b.min, delta) && diff --git a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map index 11566bb..55826e1 100644 --- a/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map +++ b/dist/Taskview/tasks/Characterize/LineUpDistributionColumn.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts index 4a9006b..f74d004 100644 --- a/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts +++ b/src/Taskview/tasks/Characterize/LineUpDistributionColumn.ts @@ -518,7 +518,8 @@ export class LineUpDistributionColumn extends MapColumn { export const DEFAULT_FORMATTER = format(".3n"); export function noNumberFilter() { - return {min: -Infinity, max: Infinity, filterMissing: false}; + // return {min: Number.NEGATIVE_INFINITY, max: Number.POSITIVE_INFINITY, filterMissing: false } + return {min: Number.NaN, max: Number.NaN, filterMissing: false}; } export function isEqualNumberFilter( From 52e8df1eacbbe0cec69492b4ddbbe1ec01e2fa92 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 28 Jul 2022 17:12:43 +0200 Subject: [PATCH 37/60] do 300 Trees --- src/Taskview/tasks/Characterize.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 3aa4784..3a80879 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -17,7 +17,7 @@ import {ATask} from './ATask'; import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn'; export class Characterize extends ATask { - static readonly TREES = 200; + static readonly TREES = 300; static readonly jaccardFormat = format('.1~%'); public label = `Characterize`; From 22d90c5324ff920a04d03f67c2dccf99b0ad1fce Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 28 Jul 2022 17:13:01 +0200 Subject: [PATCH 38/60] update layout and add confusions --- dist/Taskview/tasks/Characterize.d.ts | 3 +- dist/Taskview/tasks/Characterize.js | 83 ++++++++++++++++++-- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 4 +- src/Taskview/tasks/Characterize.ts | 83 ++++++++++++++++++-- src/scss/components/task/_characterize.scss | 4 +- 6 files changed, 162 insertions(+), 17 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index d5ab6f7..abc5678 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -6,7 +6,7 @@ import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; export declare class Characterize extends ATask { - static readonly TREES = 200; + static readonly TREES = 300; static readonly jaccardFormat: (n: number | { valueOf(): number; }) => string; @@ -29,6 +29,7 @@ export declare class Characterize extends ATask { private showOverlap; setDefiningAttributeTooltip(hintText: HTMLElement): void; private compare; + updateConfusionMatrix(responseData: any): Promise; createLineUp(data: any, showCategoryColumn?: boolean): Promise; updateLineUp(importances: any): void; addProgressBar(): void; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 08baf01..e17d7a5 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -73,18 +73,23 @@ export class Characterize extends ATask {
    -
    +
    +
    +
    +
    +
    Items ranked by predicition probability
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { var _a, _b; (_a = this.lineup) === null || _a === void 0 ? void 0 : _a.destroy(); - this.$container.querySelector('.lineup-container').innerHTML = ''; + this.$container.querySelector('.attribute-ranking').innerHTML = ''; (_b = this.chart) === null || _b === void 0 ? void 0 : _b.forEach((view) => view.finalize()); this.chart = []; this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; + this.$container.querySelector('.cohort-confusion').innerHTML = ''; this.addProgressBar(); this.compare(`cmp_${btn.id}`); })); @@ -251,6 +256,7 @@ export class Characterize extends ATask {

    OOB Score:

    ${Characterize.jaccardFormat(responseData.oobError)} `; + this.updateConfusionMatrix(responseData); } catch (e) { console.error('could not read JSON data', e); @@ -262,7 +268,7 @@ export class Characterize extends ATask { .querySelector('.chart-container'); const result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", - "title": `${responseData.data} Data Embedding`, + "title": `Cohort Certainty`, "data": { "values": responseData.embedding }, @@ -271,7 +277,7 @@ export class Characterize extends ATask { ], "width": "container", "height": "container", - "mark": { "type": "point" }, + "mark": { "type": "point", "filled": true }, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, "y": { "field": "y", "type": "quantitative", axis: null }, @@ -288,6 +294,7 @@ export class Characterize extends ATask { } }, { actions: false, renderer: 'svg' }); this.chart.push(result.view); + console.log('scatter', result.spec); } }; this.ws.onclose = () => { @@ -295,6 +302,70 @@ export class Characterize extends ATask { this.setProgressDone(); }; } + async updateConfusionMatrix(responseData) { + // confusionMatrix by Sklearn + // data structure: + // Each row of of the confusionMatrix is for one cohort + // first column of first row: samples of first cohort classified as first cohort + // 2nd column of first row: samples of first cohort classified as second cohort + // and so on + // + // i.e., sum of first row equals items in first cohort + // sum of first column equals items classified as first cohort + const confPlotData = []; + for (const [row, target_cht] of this.cohorts.entries()) { + for (const [column, predicted_cht] of this.cohorts.entries()) { + const shareOfPredicted = responseData.confusionMatrix[row][column]; + confPlotData.push({ + target: target_cht.label, + predict: predicted_cht.label, + correct: row === column, + share: shareOfPredicted + }); + } + } + this.$container.querySelector('.cohort-confusion').innerHTML = ''; + let vegaContainer = this.$container.querySelector('.cohort-confusion').insertAdjacentElement('beforeend', document.createElement('div')); + let result = await vegaEmbed(vegaContainer, { + "$schema": "https://vega.github.io/schema/vega-lite/v5.json", + "data": { "values": confPlotData }, + "height": 200, + width: 400, + "encoding": { + "x": { + "field": "share", "type": "quantitative", + "title": "Predictions", + "stack": true, + "axis": { "format": ".1%" } + } + }, + "layer": [{ + "mark": { "type": "bar", "tooltip": true, }, + "encoding": { + "color": { "field": "predict", legend: null }, + "y": { "field": "target", "title": null }, + "order": { "field": "share", "type": "quantitative", "sort": "descending" }, + "opacity": { + "condition": { "test": { "field": "correct", "equal": true }, "value": 1 }, + "value": 0.5 + } + } + }, + { + "data": { "values": [{ "val": 1 }] }, + "mark": { "type": "rule", "strokeDash": [2] }, + "encoding": { + "x": { "field": "val" } + } + } + ], + config: { + range: { category: this.cohorts.map((cht) => cht.colorTaskView) } + } + }, { actions: false, renderer: 'svg' }); + // this.chart.push(result.view); + console.log('conf', result.spec); + } async createLineUp(data, showCategoryColumn = true) { const builder = LineUpJS.builder(data); const categoryCol = LineUpJS.buildStringColumn('category').label('Category').width(200); @@ -324,7 +395,7 @@ export class Characterize extends ATask { .groupSortBy('Importance', 'desc')) .sidePanel(false) .rowHeight(50) - .buildTaggle(this.$container.querySelector('.lineup-container')); + .buildTaggle(this.$container.querySelector('.attribute-ranking')); this.dataProv = this.lineup.data; const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... children[children.length - 1].setFilter({ @@ -428,7 +499,7 @@ export class Characterize extends ATask { return response; } } -Characterize.TREES = 200; +Characterize.TREES = 300; Characterize.jaccardFormat = format('.1~%'); export class MyDistributionRenderer { constructor(cohorts) { diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index d3a8a55..6d588c9 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 55525b8..6249668 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto auto auto minmax(500px, 1fr); + grid-template-rows: auto auto auto auto minmax(400px, 1fr) minmax(400px, 1fr); row-gap: 1em; .cht-icon { @@ -39,7 +39,7 @@ font-size: 1.1em; } - .classifier-result { + .classifier-result, .probabilities { display: grid; grid-template-columns: 2fr 1fr; grid-template-rows: 1fr; diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 3a80879..970ec69 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -106,18 +106,23 @@ export class Characterize extends ATask {
    -
    +
    +
    +
    +
    +
    Items ranked by predicition probability
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { this.lineup?.destroy(); - this.$container.querySelector('.lineup-container').innerHTML = ''; + this.$container.querySelector('.attribute-ranking').innerHTML = ''; this.chart?.forEach((view) => view.finalize()); this.chart = []; this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; + this.$container.querySelector('.cohort-confusion').innerHTML = ''; this.addProgressBar(); this.compare(`cmp_${btn.id}`); })); @@ -303,6 +308,8 @@ export class Characterize extends ATask { `; + this.updateConfusionMatrix(responseData); + } catch (e) { console.error('could not read JSON data', e); } @@ -312,7 +319,7 @@ export class Characterize extends ATask { .querySelector('.chart-container') as HTMLDivElement; const result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", - "title": `${responseData.data} Data Embedding`, + "title": `Cohort Certainty`, "data": { "values": responseData.embedding }, @@ -321,7 +328,7 @@ export class Characterize extends ATask { ], "width": "container", "height": "container", - "mark": {"type": "point"}, + "mark": {"type": "point", "filled": true}, "encoding": { "x": { "field": "x", "type": "quantitative", axis: null }, "y": { "field": "y", "type": "quantitative", axis: null }, @@ -338,6 +345,7 @@ export class Characterize extends ATask { } }, {actions: false, renderer: 'svg'}); this.chart.push(result.view); + console.log('scatter', result.spec); } } @@ -347,6 +355,71 @@ export class Characterize extends ATask { } } + async updateConfusionMatrix(responseData: any) { + // confusionMatrix by Sklearn + // data structure: + // Each row of of the confusionMatrix is for one cohort + // first column of first row: samples of first cohort classified as first cohort + // 2nd column of first row: samples of first cohort classified as second cohort + // and so on + // + // i.e., sum of first row equals items in first cohort + // sum of first column equals items classified as first cohort + const confPlotData = []; + for (const [row,target_cht] of this.cohorts.entries()) { + for (const [column, predicted_cht] of this.cohorts.entries()) { + const shareOfPredicted = responseData.confusionMatrix[row][column]; + confPlotData.push({ + target: target_cht.label, + predict: predicted_cht.label, + correct: row===column, + share: shareOfPredicted + }); + } + } + this.$container.querySelector('.cohort-confusion').innerHTML = ''; + let vegaContainer = this.$container.querySelector('.cohort-confusion').insertAdjacentElement('beforeend', document.createElement('div')) as HTMLDivElement; + let result = await vegaEmbed(vegaContainer, { + "$schema": "https://vega.github.io/schema/vega-lite/v5.json", + "data": {"values": confPlotData}, + "height": 200, + width: 400, + "encoding": { + "x": { + "field": "share", "type": "quantitative", + "title": "Predictions", + "stack": true, + "axis": {"format": ".1%"} + } + }, + "layer": [{ + "mark": {"type": "bar", "tooltip": true, }, + "encoding": { + "color": {"field": "predict", legend: null}, + "y": {"field": "target", "title": null}, + "order": {"field": "share", "type": "quantitative", "sort": "descending"}, + "opacity": { + "condition": {"test": {"field": "correct", "equal":true}, "value": 1}, + "value": 0.5 + } + } + }, + { + "data": {"values": [{"val": 1}]}, + "mark": {"type": "rule", "strokeDash": [2]}, + "encoding": { + "x": { "field": "val"} + } + } + ], + config: { + range: {category: this.cohorts.map((cht) => cht.colorTaskView)} + } + }, {actions: false, renderer: 'svg'}); + // this.chart.push(result.view); + console.log('conf', result.spec); + } + async createLineUp(data, showCategoryColumn=true) { const builder = LineUpJS.builder(data); const categoryCol = LineUpJS.buildStringColumn('category').label('Category').width(200) @@ -384,7 +457,7 @@ export class Characterize extends ATask { ) .sidePanel(false) .rowHeight(50) - .buildTaggle(this.$container.querySelector('.lineup-container')); + .buildTaggle(this.$container.querySelector('.attribute-ranking')); this.dataProv = this.lineup.data as LineUpJS.LocalDataProvider; diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 55525b8..6249668 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -4,7 +4,7 @@ height: 100%; display: grid; grid-template-columns: 1fr; - grid-template-rows: auto auto auto auto minmax(500px, 1fr); + grid-template-rows: auto auto auto auto minmax(400px, 1fr) minmax(400px, 1fr); row-gap: 1em; .cht-icon { @@ -39,7 +39,7 @@ font-size: 1.1em; } - .classifier-result { + .classifier-result, .probabilities { display: grid; grid-template-columns: 2fr 1fr; grid-template-rows: 1fr; From c56e3996e1fd0f1a1bc367564a1b46c5f353e323 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 3 Aug 2022 11:47:35 +0200 Subject: [PATCH 39/60] switch to flex layout --- dist/Taskview/tasks/Characterize.d.ts | 2 +- dist/Taskview/tasks/Characterize.js | 31 +++++++++---------- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 20 +++++++++--- src/Taskview/tasks/Characterize.ts | 32 +++++++++----------- src/scss/components/task/_characterize.scss | 20 +++++++++--- 6 files changed, 64 insertions(+), 43 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index abc5678..3b2e9fc 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -7,7 +7,7 @@ import { ATask } from './ATask'; import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; export declare class Characterize extends ATask { static readonly TREES = 300; - static readonly jaccardFormat: (n: number | { + static readonly formatPercent: (n: number | { valueOf(): number; }) => string; label: string; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index e17d7a5..a5d216d 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -54,13 +54,14 @@ export class Characterize extends ATask {

    Cohort Differences

    +   Exclude the cohorts' defining attributes   - - 50 + + 100   @@ -70,14 +71,17 @@ export class Characterize extends ATask {
    -
    -
    +
    +
    +
    +
    +
    -
    Items ranked by predicition probability
    +
    TODO: Items ranked by predicition probability
    `; @@ -152,14 +156,14 @@ export class Characterize extends ATask { const drawCht = this.cohorts.find((cht) => cht.id === chtA); const remainingCht = this.cohorts.find((cht) => cht.id === chtB); container.insertAdjacentHTML('beforeend', ` -
    +
    -
     ${Characterize.jaccardFormat(intersection)}
    +
     ${Characterize.formatPercent(intersection)}
    `); } @@ -250,12 +254,7 @@ export class Characterize extends ATask { else { this.updateLineUp(responseData.importances); } - this.$container.querySelector('.accuracy-container').innerHTML = - ` -

    Accuracy:

    ${Characterize.jaccardFormat(responseData.accuracy)} -

    OOB Score:

    ${Characterize.jaccardFormat(responseData.oobError)} - - `; + this.$container.querySelector('.accuracy-container').innerHTML = `

    Differentiation: ${Characterize.formatPercent(responseData.oobError)}

    `; this.updateConfusionMatrix(responseData); } catch (e) { @@ -329,7 +328,7 @@ export class Characterize extends ATask { let result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "data": { "values": confPlotData }, - "height": 200, + height: { step: 30 }, width: 400, "encoding": { "x": { @@ -500,7 +499,7 @@ export class Characterize extends ATask { } } Characterize.TREES = 300; -Characterize.jaccardFormat = format('.1~%'); +Characterize.formatPercent = format('.1~%'); export class MyDistributionRenderer { constructor(cohorts) { this.cohorts = cohorts; @@ -511,7 +510,7 @@ export class MyDistributionRenderer { } create(col) { return { - template: `
    + template: `
    diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 6d588c9..eb972c5 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 6249668..ac3a9e6 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -2,10 +2,9 @@ $border-radius: 0.2em; height: 100%; - display: grid; - grid-template-columns: 1fr; - grid-template-rows: auto auto auto auto minmax(400px, 1fr) minmax(400px, 1fr); - row-gap: 1em; + display: flex; + flex-direction: column; + gap: 1em; .cht-icon { width: 1.5em; @@ -34,14 +33,27 @@ height: 0.5em; border-radius: $border-radius; } + .cht-bar-label { + font-weight: 500; + } h1 { font-size: 1.1em; } + h2 { + font-size: 1em; + } + .classifier-result, .probabilities { display: grid; grid-template-columns: 2fr 1fr; grid-template-rows: 1fr; } + + .center { + display: flex; + justify-content: center; + align-items: center; + } } \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 970ec69..a84e84e 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -18,7 +18,7 @@ import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn' export class Characterize extends ATask { static readonly TREES = 300; - static readonly jaccardFormat = format('.1~%'); + static readonly formatPercent = format('.1~%'); public label = `Characterize`; public id = `characterize`; @@ -87,13 +87,14 @@ export class Characterize extends ATask {

    Cohort Differences

    +   Exclude the cohorts' defining attributes   - - 50 + + 100   @@ -103,14 +104,17 @@ export class Characterize extends ATask {
    -
    -
    +
    +
    +
    +
    +
    -
    Items ranked by predicition probability
    +
    TODO: Items ranked by predicition probability
    `; @@ -192,14 +196,14 @@ export class Characterize extends ATask { const drawCht = this.cohorts.find((cht) => cht.id === chtA); const remainingCht = this.cohorts.find((cht) => cht.id === chtB); container.insertAdjacentHTML('beforeend', ` -
    +
    -
     ${Characterize.jaccardFormat(intersection)}
    +
     ${Characterize.formatPercent(intersection)}
    `); } else { @@ -301,13 +305,7 @@ export class Characterize extends ATask { this.updateLineUp(responseData.importances); } - this.$container.querySelector('.accuracy-container').innerHTML = - ` -

    Accuracy:

    ${Characterize.jaccardFormat(responseData.accuracy)} -

    OOB Score:

    ${Characterize.jaccardFormat(responseData.oobError)} - - `; - + this.$container.querySelector('.accuracy-container').innerHTML = `

    Differentiation: ${Characterize.formatPercent(responseData.oobError)}

    `; this.updateConfusionMatrix(responseData); } catch (e) { @@ -382,7 +380,7 @@ export class Characterize extends ATask { let result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "data": {"values": confPlotData}, - "height": 200, + height: {step: 30}, width: 400, "encoding": { "x": { @@ -584,7 +582,7 @@ export class MyDistributionRenderer implements ICellRendererFactory { create(col: LineUpDistributionColumn): ICellRenderer { return { - template: `
    + template: `
    diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 6249668..ac3a9e6 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -2,10 +2,9 @@ $border-radius: 0.2em; height: 100%; - display: grid; - grid-template-columns: 1fr; - grid-template-rows: auto auto auto auto minmax(400px, 1fr) minmax(400px, 1fr); - row-gap: 1em; + display: flex; + flex-direction: column; + gap: 1em; .cht-icon { width: 1.5em; @@ -34,14 +33,27 @@ height: 0.5em; border-radius: $border-radius; } + .cht-bar-label { + font-weight: 500; + } h1 { font-size: 1.1em; } + h2 { + font-size: 1em; + } + .classifier-result, .probabilities { display: grid; grid-template-columns: 2fr 1fr; grid-template-rows: 1fr; } + + .center { + display: flex; + justify-content: center; + align-items: center; + } } \ No newline at end of file From c6d0894cbe756d21316686146914ec6d903c11a0 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 3 Aug 2022 12:15:22 +0200 Subject: [PATCH 40/60] add scatterplot heatmap grow/shrink layout --- dist/Taskview/tasks/Characterize.js | 39 +- dist/Taskview/tasks/Characterize.js.map | 2 +- .../Characterize/ProbabilityScatterplot.d.ts | 7 + .../Characterize/ProbabilityScatterplot.js | 345 +++++++++++++++++ .../ProbabilityScatterplot.js.map | 1 + dist/scss/components/task/_characterize.scss | 9 + src/Taskview/tasks/Characterize.ts | 41 +-- .../Characterize/ProbabilityScatterplot.ts | 346 ++++++++++++++++++ src/scss/components/task/_characterize.scss | 9 + 9 files changed, 738 insertions(+), 61 deletions(-) create mode 100644 dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts create mode 100644 dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js create mode 100644 dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map create mode 100644 src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index a5d216d..8f55434 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -12,6 +12,7 @@ import { getAnimatedLoadingText } from '../../util'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; +import { ProbabilityScatterplot } from './Characterize/ProbabilityScatterplot'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -72,15 +73,15 @@ export class Characterize extends ATask {
    -
    +
    -
    +
    -
    +
    TODO: Items ranked by predicition probability
    @@ -94,6 +95,7 @@ export class Characterize extends ATask { this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; this.$container.querySelector('.cohort-confusion').innerHTML = ''; + this.$container.querySelectorAll('.resizeable').forEach((elem) => elem.classList.remove('filled')); this.addProgressBar(); this.compare(`cmp_${btn.id}`); })); @@ -247,6 +249,7 @@ export class Characterize extends ATask { console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { + this.$container.querySelectorAll('.resizeable').forEach((elem) => elem.classList.add('filled')); const showCategoryColumn = endpoint === 'cmp_meta'; await this.createLineUp(responseData.importances, showCategoryColumn); // await so its ready for the next response first = false; @@ -265,33 +268,8 @@ export class Characterize extends ATask { console.log('create plot'); const vegaContainer = this.$container .querySelector('.chart-container'); - const result = await vegaEmbed(vegaContainer, { - "$schema": "https://vega.github.io/schema/vega-lite/v5.json", - "title": `Cohort Certainty`, - "data": { - "values": responseData.embedding - }, - "transform": [ - { "calculate": "'#'+datum.cht", "as": "chts" } - ], - "width": "container", - "height": "container", - "mark": { "type": "point", "filled": true }, - "encoding": { - "x": { "field": "x", "type": "quantitative", axis: null }, - "y": { "field": "y", "type": "quantitative", axis: null }, - "color": { "field": "chts", "type": "nominal" }, - "opacity": { "condition": { "param": "cohort", "value": 0.9 }, "value": 0.01 } - }, - "params": [{ - "name": "cohort", - "select": { "type": "point", "fields": ["chts"] }, - "bind": "legend" - }], - config: { - range: { category: this.cohorts.map((cht) => cht.colorTaskView) } - } - }, { actions: false, renderer: 'svg' }); + const scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); + const result = await vegaEmbed(vegaContainer, scatterplot.getSpec(), { actions: false, renderer: 'svg' }); this.chart.push(result.view); console.log('scatter', result.spec); } @@ -328,6 +306,7 @@ export class Characterize extends ATask { let result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "data": { "values": confPlotData }, + padding: 20, height: { step: 30 }, width: 400, "encoding": { diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index eb972c5..3f5141e 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts new file mode 100644 index 0000000..1319e8b --- /dev/null +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts @@ -0,0 +1,7 @@ +import { Spec as VegaSpec } from 'vega'; +export declare class ProbabilityScatterplot { + private data; + private cohorts; + constructor(data: any, cohorts: any); + getSpec(): VegaSpec; +} diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js new file mode 100644 index 0000000..68e2b22 --- /dev/null +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js @@ -0,0 +1,345 @@ +export class ProbabilityScatterplot { + constructor(data, cohorts) { + this.data = data; + this.cohorts = cohorts; + } + getSpec() { + return { + "$schema": "https://vega.github.io/schema/vega/v5.json", + "scales": [ + { + "name": "x", + "type": "linear", + "round": true, + "nice": true, + "zero": true, + "domain": { + "fields": [ + { + "signal": "[bin_x_bins.start, bin_x_bins.stop]" + }, + { "data": "source", "field": "x" } + ] + }, + "domainRaw": { "signal": "zoom[\"x\"]" }, + "range": "width" + }, + { + "name": "y", + "type": "linear", + "round": true, + "nice": true, + "zero": true, + "domain": { + "fields": [ + { + "signal": "[bin_y_bins.start, bin_y_bins.stop]" + }, + { "data": "source", "field": "y" } + ] + }, + "domainRaw": { "signal": "zoom[\"y\"]" }, + "range": "height" + }, + { + "name": "color", + "type": "ordinal", + "domain": { + "data": "source", + "field": "cht" + }, + "range": this.cohorts.map(c => c.colorTaskView) + }, + { + "name": "prob", + "type": "linear", + "round": false, + "nice": false, + "zero": true, + "domain": { "data": "sampled_prob", "field": "max_max_prob" }, + "range": [0, 1], + "reverse": false + }, + { + "name": "density", + "type": "linear", + "zero": true, + "domain": [0, 1], + "range": ["#fff", "#666"], + "reverse": false + } + ], + "marks": [ + { + "type": "image", + "from": { "data": "sampled_density" }, + "encode": { + "update": { + "x": { "value": 0 }, + "y": { "value": 0 }, + "width": { "signal": "width" }, + "height": { "signal": "height" }, + "aspect": { "value": false }, + "smooth": { "value": true } + } + }, + "transform": [ + { + "type": "heatmap", + "field": "datum.grid", + "resolve": "shared", + "color": { "expr": "scale('color', warn(datum.datum.max_cht))" } + } + ] + }, + { + "name": "marks", + "type": "symbol", + "from": { "data": "source" }, + "encode": { + "update": { + "x": { "scale": "x", "field": "x" }, + "y": { "scale": "y", "field": "y" }, + "fill": { "scale": "color", "field": "cht" }, + "opacity": { "value": 0.7 }, + "size": { "value": 15 } + } + } + }, + { + // invisible heatmap over everything else for regional tooltips + "type": "rect", + "style": ["rect"], + "from": { "data": "sampled_prob" }, + "encode": { + "update": { + "x": { "scale": "x", "field": "bin_x", "offset": 0.5 }, + "x2": { "scale": "x", "field": "bin_x_end", "offset": 0.5 }, + "y": { "scale": "y", "field": "bin_y", "offset": 0.5 }, + "y2": { "scale": "y", "field": "bin_y_end", "offset": 0.5 }, + "tooltip": { + "signal": "{\"cht\": datum[\"max_cht\"], \"prob\": format(datum[\"max_max_prob\"], \".0%\")}" + }, + "opacity": { "value": 0 } + } + } + } + ], + "data": [ + { + "name": "source", + "values": this.data + }, + { + "name": "sampled_prob", + "source": "source", + "transform": [ + { "type": "extent", "field": "x", "signal": "bin_x_extent" }, + { + "type": "bin", + "field": "x", + "as": ["bin_x", "bin_x_end"], + "signal": "bin_x_bins", + "extent": { "signal": "bin_x_extent" }, + "maxbins": 60, + "nice": false + }, + { "type": "extent", "field": "y", "signal": "bin_y_extent" }, + { + "type": "bin", + "field": "y", + "as": ["bin_y", "bin_y_end"], + "signal": "bin_y_bins", + "extent": { "signal": "bin_y_extent" }, + "maxbins": 60, + "nice": false + }, + { + "type": "aggregate", + "groupby": ["bin_x", "bin_x_end", "bin_y", "bin_y_end"], + "ops": ["argmax"], + "fields": ["max_prob"], + "as": ["max"], + "drop": false + }, + { + "type": "formula", + "expr": "datum.max.cht", + "as": "max_cht" + }, + { + "type": "formula", + "expr": "datum.max.max_prob", + "as": "max_max_prob" + }, + { + "type": "formula", + "expr": "(datum.bin_x + datum.bin_x_end)/2", + "as": "x_sampled" + }, + { + "type": "formula", + "expr": "(datum.bin_y + datum.bin_y_end)/2", + "as": "y_sampled" + } + ] + }, + { + "name": "sampled_density", + "source": "sampled_prob", + "transform": [ + { + "type": "kde2d", + "groupby": ["max_cht"], + "size": [{ "signal": "width" }, { "signal": "height" }], + "x": { "expr": "scale('x', datum.x_sampled)" }, + "y": { "expr": "scale('y', datum.y_sampled)" }, + "weight": { "expr": "scale('prob', datum.max_max_prob)" }, + "bandwidth": [10, 10], + "cellSize": 4 + }, + { + "type": "heatmap", + "field": "grid", + "color": { "expr": "scale('density', datum.$value / datum.$max)" }, + "opacity": 0.9 + } + ] + }, + { "name": "zoom_store" } + ], "signals": [ + { + "name": "width", + "init": "isFinite(containerSize()[0]) ? containerSize()[0] : 200", + "on": [ + { + "update": "isFinite(containerSize()[0]) ? containerSize()[0] : 200", + "events": "window:resize" + } + ] + }, + { + "name": "height", + "init": "isFinite(containerSize()[1]) ? containerSize()[1] : 200", + "on": [ + { + "update": "isFinite(containerSize()[1]) ? containerSize()[1] : 200", + "events": "window:resize" + } + ] + }, + { + "name": "unit", + "value": {}, + "on": [ + { "events": "mousemove", "update": "isTuple(group()) ? group() : unit" } + ] + }, + { "name": "zoom", "update": "vlSelectionResolve(\"zoom_store\", \"union\")" }, + { + "name": "zoom_x", + "on": [ + { "events": [{ "source": "view", "type": "dblclick" }], "update": "null" }, + { + "events": { "signal": "zoom_translate_delta" }, + "update": "panLinear(zoom_translate_anchor.extent_x, -zoom_translate_delta.x / width)" + }, + { + "events": { "signal": "zoom_zoom_delta" }, + "update": "zoomLinear(domain(\"x\"), zoom_zoom_anchor.x, zoom_zoom_delta)" + } + ] + }, + { + "name": "zoom_y", + "on": [ + { "events": [{ "source": "view", "type": "dblclick" }], "update": "null" }, + { + "events": { "signal": "zoom_translate_delta" }, + "update": "panLinear(zoom_translate_anchor.extent_y, zoom_translate_delta.y / height)" + }, + { + "events": { "signal": "zoom_zoom_delta" }, + "update": "zoomLinear(domain(\"y\"), zoom_zoom_anchor.y, zoom_zoom_delta)" + } + ] + }, + { + "name": "zoom_tuple", + "on": [ + { + "events": [{ "signal": "zoom_x || zoom_y" }], + "update": "zoom_x && zoom_y ? {unit: \"layer_1\", fields: zoom_tuple_fields, values: [zoom_x,zoom_y]} : null" + } + ] + }, + { + "name": "zoom_tuple_fields", + "value": [ + { "field": "x", "channel": "x", "type": "R" }, + { "field": "y", "channel": "y", "type": "R" } + ] + }, + { + "name": "zoom_translate_anchor", + "value": {}, + "on": [ + { + "events": [{ "source": "scope", "type": "mousedown" }], + "update": "{x: x(unit), y: y(unit), extent_x: domain(\"x\"), extent_y: domain(\"y\")}" + } + ] + }, + { + "name": "zoom_translate_delta", + "value": {}, + "on": [ + { + "events": [ + { + "source": "window", + "type": "mousemove", + "consume": true, + "between": [ + { "source": "scope", "type": "mousedown" }, + { "source": "window", "type": "mouseup" } + ] + } + ], + "update": "{x: zoom_translate_anchor.x - x(unit), y: zoom_translate_anchor.y - y(unit)}" + } + ] + }, + { + "name": "zoom_zoom_anchor", + "on": [ + { + "events": [{ "source": "scope", "type": "wheel", "consume": true }], + "update": "{x: invert(\"x\", x(unit)), y: invert(\"y\", y(unit))}" + } + ] + }, + { + "name": "zoom_zoom_delta", + "on": [ + { + "events": [{ "source": "scope", "type": "wheel", "consume": true }], + "force": true, + "update": "pow(1.001, event.deltaY * pow(16, event.deltaMode))" + } + ] + }, + { + "name": "zoom_modify", + "on": [ + { + "events": { "signal": "zoom_tuple" }, + "update": "modify(\"zoom_store\", zoom_tuple, true)" + } + ] + } + ], + }; + } +} +//# sourceMappingURL=ProbabilityScatterplot.js.map \ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map new file mode 100644 index 0000000..6cce237 --- /dev/null +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index ac3a9e6..bbeddd0 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -56,4 +56,13 @@ justify-content: center; align-items: center; } + + .resizeable { + flex-grow: 1; + flex-shrink: 1; + + &.filled { + flex-basis: 400px; + } + } } \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index a84e84e..33c0f27 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -15,6 +15,7 @@ import {getAnimatedLoadingText} from '../../util'; import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn'; +import {ProbabilityScatterplot} from './Characterize/ProbabilityScatterplot'; export class Characterize extends ATask { static readonly TREES = 300; @@ -105,15 +106,15 @@ export class Characterize extends ATask {
    -
    +
    -
    +
    -
    +
    TODO: Items ranked by predicition probability
    @@ -127,6 +128,8 @@ export class Characterize extends ATask { this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; this.$container.querySelector('.cohort-confusion').innerHTML = ''; + + this.$container.querySelectorAll('.resizeable').forEach((elem) => elem.classList.remove('filled')); this.addProgressBar(); this.compare(`cmp_${btn.id}`); })); @@ -298,6 +301,7 @@ export class Characterize extends ATask { console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { + this.$container.querySelectorAll('.resizeable').forEach((elem) => elem.classList.add('filled')); const showCategoryColumn = endpoint === 'cmp_meta'; await this.createLineUp(responseData.importances, showCategoryColumn); // await so its ready for the next response first = false; @@ -315,33 +319,9 @@ export class Characterize extends ATask { console.log('create plot') const vegaContainer = this.$container .querySelector('.chart-container') as HTMLDivElement; - const result = await vegaEmbed(vegaContainer, { - "$schema": "https://vega.github.io/schema/vega-lite/v5.json", - "title": `Cohort Certainty`, - "data": { - "values": responseData.embedding - }, - "transform": [ - {"calculate": "'#'+datum.cht", "as": "chts"} - ], - "width": "container", - "height": "container", - "mark": {"type": "point", "filled": true}, - "encoding": { - "x": { "field": "x", "type": "quantitative", axis: null }, - "y": { "field": "y", "type": "quantitative", axis: null }, - "color": {"field": "chts", "type": "nominal"}, - "opacity": { "condition": {"param": "cohort", "value": 0.9}, "value": 0.01 } - }, - "params": [{ - "name": "cohort", - "select": {"type": "point", "fields": ["chts"]}, - "bind": "legend" - }], - config: { - range: {category: this.cohorts.map((cht) => cht.colorTaskView)} - } - }, {actions: false, renderer: 'svg'}); + + const scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); + const result = await vegaEmbed(vegaContainer, scatterplot.getSpec(), {actions: false, renderer: 'svg'}); this.chart.push(result.view); console.log('scatter', result.spec); } @@ -380,6 +360,7 @@ export class Characterize extends ATask { let result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "data": {"values": confPlotData}, + padding: 20, height: {step: 30}, width: 400, "encoding": { diff --git a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts new file mode 100644 index 0000000..ad0f769 --- /dev/null +++ b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts @@ -0,0 +1,346 @@ +import {Spec as VegaSpec} from 'vega'; + +export class ProbabilityScatterplot{ + constructor(private data, private cohorts) { + + } + + public getSpec(): VegaSpec { + return { + "$schema": "https://vega.github.io/schema/vega/v5.json", + "scales": [ + { + "name": "x", + "type": "linear", + "round": true, + "nice": true, + "zero": true, + "domain": { + "fields": [ + { + "signal": "[bin_x_bins.start, bin_x_bins.stop]" + }, + {"data": "source", "field": "x"} + ] + }, + "domainRaw": {"signal": "zoom[\"x\"]"}, + "range": "width" + }, + { + "name": "y", + "type": "linear", + "round": true, + "nice": true, + "zero": true, + "domain": { + "fields": [ + { + "signal": "[bin_y_bins.start, bin_y_bins.stop]" + }, + {"data": "source", "field": "y"} + ] + }, + "domainRaw": {"signal": "zoom[\"y\"]"}, + "range": "height" + }, + { + "name": "color", + "type": "ordinal", + "domain": { + "data": "source", + "field": "cht" + }, + "range": this.cohorts.map(c => c.colorTaskView) + }, + { + "name": "prob", + "type": "linear", + "round": false, + "nice": false, + "zero": true, + "domain": {"data": "sampled_prob", "field": "max_max_prob"}, + "range": [0, 1], + "reverse": false + }, + { + "name": "density", + "type": "linear", + "zero": true, + "domain": [0, 1], + "range": ["#fff", "#666"], + "reverse": false + } + ], + "marks": [ + { + "type": "image", //density plot, first entry as it serves as background + "from": {"data": "sampled_density"}, + "encode": { + "update": { + "x": {"value": 0}, + "y": {"value": 0}, + "width": {"signal": "width"}, + "height": {"signal": "height"}, + "aspect": {"value": false}, + "smooth": {"value": true} + } + }, + "transform": [ + { + "type": "heatmap", + "field": "datum.grid", + "resolve": "shared", + "color": {"expr": "scale('color', warn(datum.datum.max_cht))"} + } + ] + }, + { + "name": "marks", // scatterplot points on top of density plot + "type": "symbol", + "from": {"data": "source"}, + "encode": { + "update": { + "x": {"scale": "x", "field": "x"}, + "y": {"scale": "y", "field": "y"}, + "fill": {"scale": "color", "field": "cht"}, + "opacity": {"value": 0.7}, + "size": {"value": 15} + } + } + }, + { + // invisible heatmap over everything else for regional tooltips + "type": "rect", + "style": ["rect"], + "from": {"data": "sampled_prob"}, + "encode": { + "update": { + "x": {"scale": "x", "field": "bin_x", "offset": 0.5}, + "x2": {"scale": "x", "field": "bin_x_end", "offset": 0.5}, + "y": {"scale": "y", "field": "bin_y", "offset": 0.5}, + "y2": {"scale": "y", "field": "bin_y_end", "offset": 0.5}, + "tooltip": { + "signal": "{\"cht\": datum[\"max_cht\"], \"prob\": format(datum[\"max_max_prob\"], \".0%\")}" + }, + "opacity": {"value": 0} + } + } + } + ], + "data": [ + { + "name": "source", // used by the scatterplot points + "values": this.data + }, + { + "name": "sampled_prob", // bin the data and aggregate by max so that the "density" will be computed on uniformly distributed data + "source": "source", + "transform": [ + {"type": "extent", "field": "x", "signal": "bin_x_extent"}, + { + "type": "bin", + "field": "x", + "as": ["bin_x", "bin_x_end"], + "signal": "bin_x_bins", + "extent": {"signal": "bin_x_extent"}, + "maxbins": 60, + "nice": false + }, + {"type": "extent", "field": "y", "signal": "bin_y_extent"}, + { + "type": "bin", + "field": "y", + "as": ["bin_y", "bin_y_end"], + "signal": "bin_y_bins", + "extent": {"signal": "bin_y_extent"}, + "maxbins": 60, + "nice": false + }, + { + "type": "aggregate", + "groupby": ["bin_x", "bin_x_end", "bin_y", "bin_y_end"], + "ops": ["argmax"], + "fields": ["max_prob"], + "as": ["max"], + "drop": false + }, + { + "type": "formula", + "expr": "datum.max.cht", + "as": "max_cht" + }, + { + "type": "formula", + "expr": "datum.max.max_prob", + "as": "max_max_prob" + }, + { + "type": "formula", + "expr": "(datum.bin_x + datum.bin_x_end)/2", + "as": "x_sampled" + }, + { + "type": "formula", + "expr": "(datum.bin_y + datum.bin_y_end)/2", + "as": "y_sampled" + } + ] + }, + { + "name": "sampled_density", // calc density on binned data + "source": "sampled_prob", + "transform": [ + { + "type": "kde2d", + "groupby": ["max_cht"], + "size": [{"signal": "width"}, {"signal": "height"}], + "x": {"expr": "scale('x', datum.x_sampled)"}, + "y": {"expr": "scale('y', datum.y_sampled)"}, + "weight": {"expr": "scale('prob', datum.max_max_prob)"}, + "bandwidth": [10,10], + "cellSize": 4 + }, + { + "type": "heatmap", + "field": "grid", + "color": {"expr": "scale('density', datum.$value / datum.$max)"}, + "opacity": 0.9 + } + ] + }, + {"name": "zoom_store"} + ],"signals": [ + { + "name": "width", + "init": "isFinite(containerSize()[0]) ? containerSize()[0] : 200", + "on": [ + { + "update": "isFinite(containerSize()[0]) ? containerSize()[0] : 200", + "events": "window:resize" + } + ] + }, + { + "name": "height", + "init": "isFinite(containerSize()[1]) ? containerSize()[1] : 200", + "on": [ + { + "update": "isFinite(containerSize()[1]) ? containerSize()[1] : 200", + "events": "window:resize" + } + ] + }, + { + "name": "unit", + "value": {}, + "on": [ + {"events": "mousemove", "update": "isTuple(group()) ? group() : unit"} + ] + }, + {"name": "zoom", "update": "vlSelectionResolve(\"zoom_store\", \"union\")"}, + { + "name": "zoom_x", + "on": [ + {"events": [{"source": "view", "type": "dblclick"}], "update": "null"}, + { + "events": {"signal": "zoom_translate_delta"}, + "update": "panLinear(zoom_translate_anchor.extent_x, -zoom_translate_delta.x / width)" + }, + { + "events": {"signal": "zoom_zoom_delta"}, + "update": "zoomLinear(domain(\"x\"), zoom_zoom_anchor.x, zoom_zoom_delta)" + } + ] + }, + { + "name": "zoom_y", + "on": [ + {"events": [{"source": "view", "type": "dblclick"}], "update": "null"}, + { + "events": {"signal": "zoom_translate_delta"}, + "update": "panLinear(zoom_translate_anchor.extent_y, zoom_translate_delta.y / height)" + }, + { + "events": {"signal": "zoom_zoom_delta"}, + "update": "zoomLinear(domain(\"y\"), zoom_zoom_anchor.y, zoom_zoom_delta)" + } + ] + }, + { + "name": "zoom_tuple", + "on": [ + { + "events": [{"signal": "zoom_x || zoom_y"}], + "update": "zoom_x && zoom_y ? {unit: \"layer_1\", fields: zoom_tuple_fields, values: [zoom_x,zoom_y]} : null" + } + ] + }, + { + "name": "zoom_tuple_fields", + "value": [ + {"field": "x", "channel": "x", "type": "R"}, + {"field": "y", "channel": "y", "type": "R"} + ] + }, + { + "name": "zoom_translate_anchor", + "value": {}, + "on": [ + { + "events": [{"source": "scope", "type": "mousedown"}], + "update": "{x: x(unit), y: y(unit), extent_x: domain(\"x\"), extent_y: domain(\"y\")}" + } + ] + }, + { + "name": "zoom_translate_delta", + "value": {}, + "on": [ + { + "events": [ + { + "source": "window", + "type": "mousemove", + "consume": true, + "between": [ + {"source": "scope", "type": "mousedown"}, + {"source": "window", "type": "mouseup"} + ] + } + ], + "update": "{x: zoom_translate_anchor.x - x(unit), y: zoom_translate_anchor.y - y(unit)}" + } + ] + }, + { + "name": "zoom_zoom_anchor", + "on": [ + { + "events": [{"source": "scope", "type": "wheel", "consume": true}], + "update": "{x: invert(\"x\", x(unit)), y: invert(\"y\", y(unit))}" + } + ] + }, + { + "name": "zoom_zoom_delta", + "on": [ + { + "events": [{"source": "scope", "type": "wheel", "consume": true}], + "force": true, + "update": "pow(1.001, event.deltaY * pow(16, event.deltaMode))" + } + ] + }, + { + "name": "zoom_modify", + "on": [ + { + "events": {"signal": "zoom_tuple"}, + "update": "modify(\"zoom_store\", zoom_tuple, true)" + } + ] + } + ], + } + } +} \ No newline at end of file diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index ac3a9e6..bbeddd0 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -56,4 +56,13 @@ justify-content: center; align-items: center; } + + .resizeable { + flex-grow: 1; + flex-shrink: 1; + + &.filled { + flex-basis: 400px; + } + } } \ No newline at end of file From f26a4ea6adb887bb596644d0758f83cdda061666 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Wed, 3 Aug 2022 17:46:33 +0200 Subject: [PATCH 41/60] add probability ranking --- dist/Taskview/tasks/Characterize.d.ts | 11 +- dist/Taskview/tasks/Characterize.js | 133 ++++++++-------- dist/Taskview/tasks/Characterize.js.map | 2 +- .../Characterize/ProbabilityScatterplot.js | 2 +- .../ProbabilityScatterplot.js.map | 2 +- dist/scss/components/task/_characterize.scss | 13 +- src/Taskview/tasks/Characterize.ts | 143 ++++++++++-------- .../Characterize/ProbabilityScatterplot.ts | 2 +- src/scss/components/task/_characterize.scss | 13 +- 9 files changed, 179 insertions(+), 142 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 3b2e9fc..64208e8 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -17,8 +17,10 @@ export declare class Characterize extends ATask { private ids; private ws; private progressBar; - private lineup; - private dataProv; + private attributeRanking; + private attributeRankingData; + private itemRanking; + private itemRankingData; private cohorts; private definingAttributes; private chart; @@ -30,15 +32,14 @@ export declare class Characterize extends ATask { setDefiningAttributeTooltip(hintText: HTMLElement): void; private compare; updateConfusionMatrix(responseData: any): Promise; - createLineUp(data: any, showCategoryColumn?: boolean): Promise; - updateLineUp(importances: any): void; + createAttributeRanking(data: any, showCategoryColumn?: boolean): Promise; + createItemRanking(data: any): Promise; addProgressBar(): void; setProgress(iteration: number, done?: boolean): void; setProgressIndefinite(): void; setProgressDone(): void; fadeOutProgressBar(delay?: number): Promise; getData(attributes: IAttribute[], cohorts: Cohort[]): Promise; - postData(endpoint: string, data?: {}): Promise; } export declare class MyDistributionRenderer implements ICellRendererFactory { private cohorts; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 8f55434..54bd606 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -13,6 +13,7 @@ import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; import { ProbabilityScatterplot } from './Characterize/ProbabilityScatterplot'; +import { log } from '../../util'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -52,45 +53,54 @@ export class Characterize extends ATask { this.$container.innerHTML = `
    -

    Cohort Differences

    +

    Cohort Comparison

      Exclude the cohorts' defining attributes +
    -
    - +
    +

    Attribute Importance

    +

    Cohort Differentiation

    +
    -
    -
    +
    +
    -
    + +
    + +

    Cohort Characterization

    -
    TODO: Items ranked by predicition probability
    -
    +

    Indistinguishable Items

    +

    Cohort Association

    + +
    +
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { - var _a, _b; - (_a = this.lineup) === null || _a === void 0 ? void 0 : _a.destroy(); + var _a, _b, _c; + (_a = this.attributeRanking) === null || _a === void 0 ? void 0 : _a.destroy(); + (_b = this.itemRanking) === null || _b === void 0 ? void 0 : _b.destroy(); this.$container.querySelector('.attribute-ranking').innerHTML = ''; - (_b = this.chart) === null || _b === void 0 ? void 0 : _b.forEach((view) => view.finalize()); + (_c = this.chart) === null || _c === void 0 ? void 0 : _c.forEach((view) => view.finalize()); this.chart = []; this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; @@ -217,11 +227,10 @@ export class Characterize extends ATask { return true; }) .map((attr) => 'gene' in attr ? attr.gene : attr.id); - const maxDepth = parseInt(this.$container.querySelector('input#max-depth').value); - const minGroupSize = parseInt(this.$container.querySelector('input#min-group-size').value); + const maxDepth = 100; // parseInt((this.$container.querySelector('input#max-depth') as HTMLInputElement).value); + const minGroupSize = 1; //parseInt((this.$container.querySelector('input#min-group-size') as HTMLInputElement).value); const url = new URL(`/kokiri/${endpoint}/`, location.href); url.protocol = url.protocol.replace('http', 'ws'); - console.log('url', url); this.ws = new WebSocket(url); this.ws.onopen = async () => { const data = JSON.stringify({ @@ -231,51 +240,50 @@ export class Characterize extends ATask { min_samples_leaf: minGroupSize, ids: this.ids, }); - console.log('Socket is open'); try { this.ws.send(data); } - catch { - console.error('error sending data'); + catch (e) { + log.error('error sending data', e); } - console.log('sent comparison data'); }; let first = true; this.ws.onmessage = async (message) => { + var _a, _b; const responseData = JSON.parse(message.data); - console.log('response', responseData); if (responseData.trees) { try { - console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { + first = false; this.$container.querySelectorAll('.resizeable').forEach((elem) => elem.classList.add('filled')); const showCategoryColumn = endpoint === 'cmp_meta'; - await this.createLineUp(responseData.importances, showCategoryColumn); // await so its ready for the next response - first = false; + await this.createAttributeRanking(responseData.importances, showCategoryColumn); // await so its ready for the next response + await this.createItemRanking(responseData.probabilities); // await so its ready for the next response } else { - this.updateLineUp(responseData.importances); + (_a = this.attributeRankingData) === null || _a === void 0 ? void 0 : _a.setData(responseData.importances); + (_b = this.itemRankingData) === null || _b === void 0 ? void 0 : _b.setData(responseData.probabilities); } - this.$container.querySelector('.accuracy-container').innerHTML = `

    Differentiation: ${Characterize.formatPercent(responseData.oobError)}

    `; + this.$container.querySelector('.accuracy-container').innerHTML = ` +

    Accuracy: ${Characterize.formatPercent(responseData.accuracy)}

    + `; this.updateConfusionMatrix(responseData); } catch (e) { - console.error('could not read JSON data', e); + log.error('could not read JSON data', e); } } else if (responseData.embedding) { - console.log('create plot'); const vegaContainer = this.$container .querySelector('.chart-container'); const scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); const result = await vegaEmbed(vegaContainer, scatterplot.getSpec(), { actions: false, renderer: 'svg' }); this.chart.push(result.view); - console.log('scatter', result.spec); } }; this.ws.onclose = () => { - console.log('the socket is done'); + log.debug('the socket is done'); this.setProgressDone(); }; } @@ -302,13 +310,13 @@ export class Characterize extends ATask { } } this.$container.querySelector('.cohort-confusion').innerHTML = ''; - let vegaContainer = this.$container.querySelector('.cohort-confusion').insertAdjacentElement('beforeend', document.createElement('div')); + let vegaContainer = this.$container.querySelector('.cohort-confusion'); let result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "data": { "values": confPlotData }, padding: 20, height: { step: 30 }, - width: 400, + width: "container", "encoding": { "x": { "field": "share", "type": "quantitative", @@ -341,16 +349,15 @@ export class Characterize extends ATask { range: { category: this.cohorts.map((cht) => cht.colorTaskView) } } }, { actions: false, renderer: 'svg' }); - // this.chart.push(result.view); - console.log('conf', result.spec); + this.chart.push(result.view); } - async createLineUp(data, showCategoryColumn = true) { + async createAttributeRanking(data, showCategoryColumn = true) { const builder = LineUpJS.builder(data); const categoryCol = LineUpJS.buildStringColumn('category').label('Category').width(200); if (!showCategoryColumn) { categoryCol.hidden(); } - this.lineup = builder + this.attributeRanking = builder .column(LineUpJS.buildNumberColumn('importance', [0, 1]) .label('Importance') .width(150) @@ -374,17 +381,40 @@ export class Characterize extends ATask { .sidePanel(false) .rowHeight(50) .buildTaggle(this.$container.querySelector('.attribute-ranking')); - this.dataProv = this.lineup.data; - const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + this.attributeRankingData = this.attributeRanking.data; + const children = this.attributeRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... children[children.length - 1].setFilter({ filterMissing: true, min: 0.001, max: Infinity }); } - updateLineUp(importances) { - var _a; - (_a = this.dataProv) === null || _a === void 0 ? void 0 : _a.setData(importances); + async createItemRanking(data) { + const builder = LineUpJS.builder(data); + console.log('item data', data); + this.itemRanking = builder + .column(LineUpJS.buildNumberColumn('prob_max', [0, 1]) + .label('Max') + .width(150) + .colorMapping(colors.barColor) + .numberFormat('.3f')) + // .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150)) + .column(LineUpJS.buildStringColumn('cht').label('cht').width(100)) + .deriveColors() + .ranking(LineUpJS.buildRanking() + .supportTypes() + .allColumns() + .sortBy('Max', 'desc')) + .sidePanel(false) + // .rowHeight(50) + .buildTaggle(this.$container.querySelector('.item-ranking')); + this.itemRankingData = this.itemRanking.data; + // const children = this.itemRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + // (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ + // filterMissing: true, + // min: 0.001, + // max: Infinity + // }); } addProgressBar() { const wrapper = this.$container.querySelector('.progress-wrapper'); @@ -456,26 +486,6 @@ export class Characterize extends ATask { const data = await Promise.all(dataPromises); return data; } - // Example POST method implementation: - async postData(endpoint, data = {}) { - const url = '/kokiri/' + endpoint + '/'; - // Default options are marked with * - const response = await fetch(url, { - method: 'POST', - mode: 'cors', - cache: 'no-cache', - credentials: 'same-origin', - headers: { - 'Content-Type': 'application/json' - // 'Content-Type': 'application/x-www-form-urlencoded', - }, - redirect: 'follow', - referrerPolicy: 'no-referrer', - body: JSON.stringify(data), // body data type must match "Content-Type" header - //TODO abortController - }); - return response; - } } Characterize.TREES = 300; Characterize.formatPercent = format('.1~%'); @@ -522,7 +532,6 @@ export class MyDistributionRenderer { d3.select(n).select('.xaxis path').attr('stroke', colors.barColor); const chart = d3.select(n).select('#chart g'); if (d.v.type === 'cat') { - console.log(`OK: ${d.v.attribute}`); // X axis var x = d3.scaleBand() .range([0, MyDistributionRenderer.WIDTH]) diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 3f5141e..a1048e2 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js index 68e2b22..e3bb711 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js @@ -118,7 +118,7 @@ export class ProbabilityScatterplot { "y": { "scale": "y", "field": "bin_y", "offset": 0.5 }, "y2": { "scale": "y", "field": "bin_y_end", "offset": 0.5 }, "tooltip": { - "signal": "{\"cht\": datum[\"max_cht\"], \"prob\": format(datum[\"max_max_prob\"], \".0%\")}" + "signal": "{\"Prediction\": datum[\"max_cht\"], \"Likelihood\": format(datum[\"max_max_prob\"], \".0%\")}" }, "opacity": { "value": 0 } } diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map index 6cce237..e792b84 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index bbeddd0..7c4b2e2 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -38,17 +38,18 @@ } h1 { - font-size: 1.1em; + font-size: 1.2em; } h2 { - font-size: 1em; + font-size: 1.1em; } .classifier-result, .probabilities { display: grid; grid-template-columns: 2fr 1fr; - grid-template-rows: 1fr; + grid-template-rows: auto 1fr; + column-gap: 1em; } .center { @@ -62,7 +63,11 @@ flex-shrink: 1; &.filled { - flex-basis: 400px; + flex-basis: 30em; } } + + .separator-left { + border-left: 1px solid $color-border-light; + } } \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 33c0f27..09f80d3 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -16,6 +16,7 @@ import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn'; import {ProbabilityScatterplot} from './Characterize/ProbabilityScatterplot'; +import {CohortColorSchema, IFilterDesc, log} from '../../util'; export class Characterize extends ATask { static readonly TREES = 300; @@ -30,8 +31,12 @@ export class Characterize extends ATask { private ws: WebSocket; private progressBar: any; - private lineup: LineUpJS.Taggle; - private dataProv: LineUpJS.LocalDataProvider; + + private attributeRanking: LineUpJS.Taggle; + private attributeRankingData: LineUpJS.LocalDataProvider; + private itemRanking: LineUpJS.Taggle; + private itemRankingData: LineUpJS.LocalDataProvider; + private cohorts: Cohort[]; private definingAttributes: IAttribute[]; private chart: VegaView[]; @@ -85,43 +90,52 @@ export class Characterize extends ATask { this.$container.innerHTML = `
    -

    Cohort Differences

    +

    Cohort Comparison

      Exclude the cohorts' defining attributes +
    -
    - +
    +

    Attribute Importance

    +

    Cohort Differentiation

    +
    -
    -
    +
    +
    -
    + +
    + +

    Cohort Characterization

    -
    TODO: Items ranked by predicition probability
    -
    +

    Indistinguishable Items

    +

    Cohort Association

    + +
    +
    `; this.$container.querySelectorAll('button').forEach((btn) => btn.addEventListener('click', () => { - this.lineup?.destroy(); + this.attributeRanking?.destroy(); + this.itemRanking?.destroy(); this.$container.querySelector('.attribute-ranking').innerHTML = ''; this.chart?.forEach((view) => view.finalize()); this.chart = []; @@ -266,12 +280,11 @@ export class Characterize extends ATask { }) .map((attr) => 'gene' in attr ? (attr as GeneScoreAttribute).gene : attr.id); - const maxDepth = parseInt((this.$container.querySelector('input#max-depth') as HTMLInputElement).value); - const minGroupSize = parseInt((this.$container.querySelector('input#min-group-size') as HTMLInputElement).value); + const maxDepth = 100; // parseInt((this.$container.querySelector('input#max-depth') as HTMLInputElement).value); + const minGroupSize = 1; //parseInt((this.$container.querySelector('input#min-group-size') as HTMLInputElement).value); const url = new URL(`/kokiri/${endpoint}/`, location.href); url.protocol = url.protocol.replace('http', 'ws'); - console.log('url', url) this.ws = new WebSocket(url) this.ws.onopen = async () => { const data = JSON.stringify({ // send as string, because sending JSON apparantly only works this way 🤷‍♀️ (see https://developer.mozilla.org/en-US/docs/Web/API/WebSockets_API/Writing_WebSocket_client_applications) @@ -281,54 +294,52 @@ export class Characterize extends ATask { min_samples_leaf: minGroupSize, ids: this.ids, }) - console.log('Socket is open') try { this.ws.send(data) - } catch { - console.error('error sending data') + } catch (e) { + log.error('error sending data', e) } - console.log('sent comparison data') }; let first = true; this.ws.onmessage = async (message) => { const responseData = JSON.parse(message.data); - console.log('response', responseData); if(responseData.trees) { try { - console.log(responseData.trees); this.setProgress(responseData.trees); if (first) { + first = false; this.$container.querySelectorAll('.resizeable').forEach((elem) => elem.classList.add('filled')); const showCategoryColumn = endpoint === 'cmp_meta'; - await this.createLineUp(responseData.importances, showCategoryColumn); // await so its ready for the next response - first = false; + await this.createAttributeRanking(responseData.importances, showCategoryColumn); // await so its ready for the next response + await this.createItemRanking(responseData.probabilities); // await so its ready for the next response } else { - this.updateLineUp(responseData.importances); + this.attributeRankingData?.setData(responseData.importances); + this.itemRankingData?.setData(responseData.probabilities); } - this.$container.querySelector('.accuracy-container').innerHTML = `

    Differentiation: ${Characterize.formatPercent(responseData.oobError)}

    `; + this.$container.querySelector('.accuracy-container').innerHTML = ` +

    Accuracy: ${Characterize.formatPercent(responseData.accuracy)}

    + `; this.updateConfusionMatrix(responseData); } catch (e) { - console.error('could not read JSON data', e); + log.error('could not read JSON data', e); } } else if (responseData.embedding) { - console.log('create plot') const vegaContainer = this.$container .querySelector('.chart-container') as HTMLDivElement; const scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); const result = await vegaEmbed(vegaContainer, scatterplot.getSpec(), {actions: false, renderer: 'svg'}); this.chart.push(result.view); - console.log('scatter', result.spec); } } this.ws.onclose = () => { - console.log('the socket is done'); + log.debug('the socket is done'); this.setProgressDone(); } } @@ -356,13 +367,13 @@ export class Characterize extends ATask { } } this.$container.querySelector('.cohort-confusion').innerHTML = ''; - let vegaContainer = this.$container.querySelector('.cohort-confusion').insertAdjacentElement('beforeend', document.createElement('div')) as HTMLDivElement; + let vegaContainer = this.$container.querySelector('.cohort-confusion') as HTMLDivElement; let result = await vegaEmbed(vegaContainer, { "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "data": {"values": confPlotData}, padding: 20, height: {step: 30}, - width: 400, + width: "container", "encoding": { "x": { "field": "share", "type": "quantitative", @@ -395,18 +406,17 @@ export class Characterize extends ATask { range: {category: this.cohorts.map((cht) => cht.colorTaskView)} } }, {actions: false, renderer: 'svg'}); - // this.chart.push(result.view); - console.log('conf', result.spec); + this.chart.push(result.view); } - async createLineUp(data, showCategoryColumn=true) { + async createAttributeRanking(data, showCategoryColumn=true) { const builder = LineUpJS.builder(data); const categoryCol = LineUpJS.buildStringColumn('category').label('Category').width(200) if (!showCategoryColumn) { categoryCol.hidden(); } - this.lineup = builder + this.attributeRanking = builder .column( LineUpJS.buildNumberColumn('importance', [0, 1]) .label('Importance') @@ -438,9 +448,9 @@ export class Characterize extends ATask { .rowHeight(50) .buildTaggle(this.$container.querySelector('.attribute-ranking')); - this.dataProv = this.lineup.data as LineUpJS.LocalDataProvider; + this.attributeRankingData = this.attributeRanking.data as LineUpJS.LocalDataProvider; - const children = this.lineup.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + const children = this.attributeRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ filterMissing: true, min: 0.001, @@ -448,8 +458,38 @@ export class Characterize extends ATask { }); } - updateLineUp(importances: any) { - this.dataProv?.setData(importances); + async createItemRanking(data) { + const builder = LineUpJS.builder(data); + console.log('item data', data) + + this.itemRanking = builder + .column( + LineUpJS.buildNumberColumn('prob_max', [0, 1]) + .label('Max') + .width(150) + .colorMapping(colors.barColor) + .numberFormat('.3f') + ) + // .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150)) + .column(LineUpJS.buildStringColumn('cht').label('cht').width(100)) + .deriveColors() + .ranking(LineUpJS.buildRanking() + .supportTypes() + .allColumns() + .sortBy('Max', 'desc') + ) + .sidePanel(false) + // .rowHeight(50) + .buildTaggle(this.$container.querySelector('.item-ranking')); + + this.itemRankingData = this.itemRanking.data as LineUpJS.LocalDataProvider; + + // const children = this.itemRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... + // (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ + // filterMissing: true, + // min: 0.001, + // max: Infinity + // }); } addProgressBar() { @@ -526,28 +566,6 @@ export class Characterize extends ATask { const data = await Promise.all(dataPromises); return data; } - - // Example POST method implementation: - async postData(endpoint: string, data = {}) { - const url = '/kokiri/' + endpoint + '/'; - // Default options are marked with * - const response = await fetch(url, { - method: 'POST', // *GET, POST, PUT, DELETE, etc. - mode: 'cors', // no-cors, *cors, same-origin - cache: 'no-cache', // *default, no-cache, reload, force-cache, only-if-cached - credentials: 'same-origin', // include, *same-origin, omit - headers: { - 'Content-Type': 'application/json' - // 'Content-Type': 'application/x-www-form-urlencoded', - }, - redirect: 'follow', // manual, *follow, error - referrerPolicy: 'no-referrer', // no-referrer, *no-referrer-when-downgrade, origin, origin-when-cross-origin, same-origin, strict-origin, strict-origin-when-cross-origin, unsafe-url - body: JSON.stringify(data), // body data type must match "Content-Type" header - //TODO abortController - }); - - return response; - } } export class MyDistributionRenderer implements ICellRendererFactory { @@ -597,7 +615,6 @@ export class MyDistributionRenderer implements ICellRendererFactory { const chart = d3.select(n).select('#chart g') if (d.v.type === 'cat') { - console.log(`OK: ${d.v.attribute}`); // X axis var x = d3.scaleBand() .range([ 0, MyDistributionRenderer.WIDTH ]) diff --git a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts index ad0f769..de6c65d 100644 --- a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts +++ b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts @@ -120,7 +120,7 @@ export class ProbabilityScatterplot{ "y": {"scale": "y", "field": "bin_y", "offset": 0.5}, "y2": {"scale": "y", "field": "bin_y_end", "offset": 0.5}, "tooltip": { - "signal": "{\"cht\": datum[\"max_cht\"], \"prob\": format(datum[\"max_max_prob\"], \".0%\")}" + "signal": "{\"Prediction\": datum[\"max_cht\"], \"Likelihood\": format(datum[\"max_max_prob\"], \".0%\")}" }, "opacity": {"value": 0} } diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index bbeddd0..7c4b2e2 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -38,17 +38,18 @@ } h1 { - font-size: 1.1em; + font-size: 1.2em; } h2 { - font-size: 1em; + font-size: 1.1em; } .classifier-result, .probabilities { display: grid; grid-template-columns: 2fr 1fr; - grid-template-rows: 1fr; + grid-template-rows: auto 1fr; + column-gap: 1em; } .center { @@ -62,7 +63,11 @@ flex-shrink: 1; &.filled { - flex-basis: 400px; + flex-basis: 30em; } } + + .separator-left { + border-left: 1px solid $color-border-light; + } } \ No newline at end of file From 566b88e7f9f171478642ec940ac99f6173353cf9 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Thu, 4 Aug 2022 11:14:17 +0200 Subject: [PATCH 42/60] item ranking --- dist/Taskview/tasks/Characterize.d.ts | 1 + dist/Taskview/tasks/Characterize.js | 46 ++++++++--------- dist/Taskview/tasks/Characterize.js.map | 2 +- dist/scss/components/task/_characterize.scss | 6 ++- src/Taskview/tasks/Characterize.ts | 54 ++++++++++---------- src/scss/components/task/_characterize.scss | 6 ++- 6 files changed, 59 insertions(+), 56 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 64208e8..24f43b9 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -14,6 +14,7 @@ export declare class Characterize extends ATask { id: string; hasOutput: boolean; private eventID; + private _entityName; private ids; private ws; private progressBar; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 54bd606..59a374c 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -1,19 +1,19 @@ import * as aq from 'arquero'; import { format } from 'd3-format'; +import * as d3 from 'd3v7'; import * as LineUpJS from 'lineupjs'; import { ERenderMode, renderMissingDOM } from 'lineupjs'; -import * as d3 from 'd3v7'; import tippy from 'tippy.js'; import vegaEmbed from 'vega-embed'; import { getCohortLabel } from '../../Cohort'; import { colors } from '../../colors'; import { ServerColumnAttribute } from '../../data/Attribute'; -import { getAnimatedLoadingText } from '../../util'; +import { getAnimatedLoadingText, log } from '../../util'; +import { getIdTypeFromCohort } from '../../utilIdTypes'; import { DATA_LABEL } from '../visualizations'; import { ATask } from './ATask'; import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; import { ProbabilityScatterplot } from './Characterize/ProbabilityScatterplot'; -import { log } from '../../util'; export class Characterize extends ATask { constructor() { super(...arguments); @@ -21,6 +21,7 @@ export class Characterize extends ATask { this.id = `characterize`; this.hasOutput = false; this.eventID = 0; + this._entityName = null; } supports(attributes, cohorts) { return cohorts.length >= 2; @@ -29,6 +30,8 @@ export class Characterize extends ATask { return false; } async show(columnHeader, container, attributes, cohorts) { + const idType = getIdTypeFromCohort(cohorts[0]); + this._entityName = idType.entityName; super.show(columnHeader, container, attributes, cohorts); const eventId = ++this.eventID; // get new eventID, we will compare it with the field again to see if it is still up to date this.cohorts = cohorts; @@ -268,6 +271,7 @@ export class Characterize extends ATask { this.$container.querySelector('.accuracy-container').innerHTML = `

    Accuracy: ${Characterize.formatPercent(responseData.accuracy)}

    `; + log.info(`OOB Score ${Characterize.formatPercent(responseData.oobError)} for ${responseData.trees} trees`); this.updateConfusionMatrix(responseData); } catch (e) { @@ -362,7 +366,7 @@ export class Characterize extends ATask { .label('Importance') .width(150) .colorMapping(colors.barColor) - .numberFormat('.3f')) + .numberFormat('.1%')) .column(showCategoryColumn ? LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150) : LineUpJS.buildStringColumn('attribute').label('Attribute').width(200)) @@ -385,36 +389,28 @@ export class Characterize extends ATask { const children = this.attributeRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... children[children.length - 1].setFilter({ filterMissing: true, - min: 0.001, + min: 0.005, max: Infinity }); } async createItemRanking(data) { - const builder = LineUpJS.builder(data); - console.log('item data', data); - this.itemRanking = builder - .column(LineUpJS.buildNumberColumn('prob_max', [0, 1]) - .label('Max') - .width(150) + this.itemRanking = LineUpJS.builder(data) + .column(LineUpJS.buildStringColumn(this._entityName).label('Id').width(200)) + .column(LineUpJS.buildCategoricalColumn('cht', this.cohorts.map((cht, i) => ({ name: '' + i, label: cht.label, color: cht.colorTaskView }))) + .label('Cohort') + .renderer('catheatmap', 'categorical').asSet()) + .column(LineUpJS.buildNumberColumn('probs', [0, 1]) + .label('Prob') + .width(100) .colorMapping(colors.barColor) - .numberFormat('.3f')) - // .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150)) - .column(LineUpJS.buildStringColumn('cht').label('cht').width(100)) + .numberFormat('.1%') + .asArray(this.cohorts.map((cht, i) => cht.label))) + .column(LineUpJS.buildNumberColumn('prob_max', [0, 1]).label('Max Probality').width(100).colorMapping(colors.barColor).numberFormat('.1%')) .deriveColors() - .ranking(LineUpJS.buildRanking() - .supportTypes() - .allColumns() - .sortBy('Max', 'desc')) + .ranking(LineUpJS.buildRanking().supportTypes().allColumns().sortBy('prob_max', 'asc')) .sidePanel(false) - // .rowHeight(50) .buildTaggle(this.$container.querySelector('.item-ranking')); this.itemRankingData = this.itemRanking.data; - // const children = this.itemRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... - // (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ - // filterMissing: true, - // min: 0.001, - // max: Infinity - // }); } addProgressBar() { const wrapper = this.$container.querySelector('.progress-wrapper'); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index a1048e2..6ef1c68 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 7c4b2e2..03ce03a 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -50,6 +50,10 @@ grid-template-columns: 2fr 1fr; grid-template-rows: auto 1fr; column-gap: 1em; + + &.probabilities { + grid-template-columns: 1fr 1fr; + } } .center { @@ -63,7 +67,7 @@ flex-shrink: 1; &.filled { - flex-basis: 30em; + flex-basis: 20em; } } diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 09f80d3..19c66d2 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -1,8 +1,8 @@ import * as aq from 'arquero'; import {format} from 'd3-format'; +import * as d3 from 'd3v7'; import * as LineUpJS from 'lineupjs'; import {ERenderMode, ICellRenderer, ICellRendererFactory, IDataRow, renderMissingDOM} from 'lineupjs'; -import * as d3 from 'd3v7'; import tippy from 'tippy.js'; import {View as VegaView} from 'vega'; import vegaEmbed from 'vega-embed'; @@ -11,12 +11,12 @@ import {ICohort} from '../../CohortInterfaces'; import {colors} from '../../colors'; import {GeneScoreAttribute, IAttribute, ServerColumnAttribute} from '../../data/Attribute'; import {Task} from '../../Tasks'; -import {getAnimatedLoadingText} from '../../util'; +import {getAnimatedLoadingText, log} from '../../util'; +import {getIdTypeFromCohort} from '../../utilIdTypes'; import {DATA_LABEL} from '../visualizations'; import {ATask} from './ATask'; import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn'; import {ProbabilityScatterplot} from './Characterize/ProbabilityScatterplot'; -import {CohortColorSchema, IFilterDesc, log} from '../../util'; export class Characterize extends ATask { static readonly TREES = 300; @@ -26,6 +26,7 @@ export class Characterize extends ATask { public id = `characterize`; public hasOutput = false; private eventID = 0; + private _entityName: string = null; private ids: any[]; private ws: WebSocket; @@ -56,6 +57,8 @@ export class Characterize extends ATask { attributes: IAttribute[], cohorts: ICohort[] ) { + const idType = getIdTypeFromCohort(cohorts[0] as Cohort); + this._entityName = idType.entityName; super.show(columnHeader, container, attributes, cohorts); const eventId = ++this.eventID; // get new eventID, we will compare it with the field again to see if it is still up to date @@ -323,6 +326,7 @@ export class Characterize extends ATask { this.$container.querySelector('.accuracy-container').innerHTML = `

    Accuracy: ${Characterize.formatPercent(responseData.accuracy)}

    `; + log.info(`OOB Score ${Characterize.formatPercent(responseData.oobError)} for ${responseData.trees} trees`) this.updateConfusionMatrix(responseData); } catch (e) { @@ -422,7 +426,7 @@ export class Characterize extends ATask { .label('Importance') .width(150) .colorMapping(colors.barColor) - .numberFormat('.3f') + .numberFormat('.1%') ) .column( showCategoryColumn ? @@ -453,43 +457,37 @@ export class Characterize extends ATask { const children = this.attributeRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ filterMissing: true, - min: 0.001, + min: 0.005, max: Infinity }); } async createItemRanking(data) { - const builder = LineUpJS.builder(data); - console.log('item data', data) - this.itemRanking = builder + this.itemRanking = LineUpJS.builder(data) + .column(LineUpJS.buildStringColumn(this._entityName).label('Id').width(200)) .column( - LineUpJS.buildNumberColumn('prob_max', [0, 1]) - .label('Max') - .width(150) - .colorMapping(colors.barColor) - .numberFormat('.3f') + LineUpJS .buildCategoricalColumn( + 'cht', + this.cohorts.map((cht, i) => ({name: ''+i, label: cht.label, color: (cht as Cohort).colorTaskView})) ) - // .column(LineUpJS.buildCategoricalColumn('attribute').label('Attribute').width(150)) - .column(LineUpJS.buildStringColumn('cht').label('cht').width(100)) - .deriveColors() - .ranking(LineUpJS.buildRanking() - .supportTypes() - .allColumns() - .sortBy('Max', 'desc') + .label('Cohort') + .renderer('catheatmap', 'categorical').asSet()) + .column( + LineUpJS.buildNumberColumn('probs', [0, 1]) + .label('Prob') + .width(100) + .colorMapping(colors.barColor) + .numberFormat('.1%') + .asArray(this.cohorts.map((cht, i) => cht.label)) ) + .column( LineUpJS.buildNumberColumn('prob_max', [0, 1]).label('Max Probality').width(100).colorMapping(colors.barColor).numberFormat('.1%')) + .deriveColors() + .ranking(LineUpJS.buildRanking().supportTypes().allColumns().sortBy('prob_max', 'asc') ) .sidePanel(false) - // .rowHeight(50) .buildTaggle(this.$container.querySelector('.item-ranking')); this.itemRankingData = this.itemRanking.data as LineUpJS.LocalDataProvider; - - // const children = this.itemRanking.data.getFirstRanking().children; // alternative: builder.buildData().getFirstRanking(),... - // (children[children.length - 1] as LineUpJS.NumberColumn).setFilter({ - // filterMissing: true, - // min: 0.001, - // max: Infinity - // }); } addProgressBar() { diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 7c4b2e2..03ce03a 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -50,6 +50,10 @@ grid-template-columns: 2fr 1fr; grid-template-rows: auto 1fr; column-gap: 1em; + + &.probabilities { + grid-template-columns: 1fr 1fr; + } } .center { @@ -63,7 +67,7 @@ flex-shrink: 1; &.filled { - flex-basis: 30em; + flex-basis: 20em; } } From de44e1a8a1266bb274b4f709afc4835f67c17fb7 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Fri, 5 Aug 2022 08:13:50 +0200 Subject: [PATCH 43/60] increase view height --- dist/scss/components/task/_characterize.scss | 2 +- src/scss/components/task/_characterize.scss | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 03ce03a..8b26ad9 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -67,7 +67,7 @@ flex-shrink: 1; &.filled { - flex-basis: 20em; + flex-basis: 40em; } } diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 03ce03a..8b26ad9 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -67,7 +67,7 @@ flex-shrink: 1; &.filled { - flex-basis: 20em; + flex-basis: 40em; } } From 40b2f2da07efa6fe15ebc203a5f6e6ec207332b6 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Fri, 5 Aug 2022 08:14:00 +0200 Subject: [PATCH 44/60] fix confusion bar chart --- dist/Taskview/tasks/Characterize.js | 5 +++-- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 5 +++-- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 59a374c..2336488 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -332,8 +332,8 @@ export class Characterize extends ATask { "layer": [{ "mark": { "type": "bar", "tooltip": true, }, "encoding": { - "color": { "field": "predict", legend: null }, - "y": { "field": "target", "title": null }, + "color": { "field": "predict", legend: null, sort: null }, + "y": { "field": "target", "title": null, sort: null }, "order": { "field": "share", "type": "quantitative", "sort": "descending" }, "opacity": { "condition": { "test": { "field": "correct", "equal": true }, "value": 1 }, @@ -353,6 +353,7 @@ export class Characterize extends ATask { range: { category: this.cohorts.map((cht) => cht.colorTaskView) } } }, { actions: false, renderer: 'svg' }); + console.log('confusion', result.spec); this.chart.push(result.view); } async createAttributeRanking(data, showCategoryColumn = true) { diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 6ef1c68..b98b055 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 19c66d2..9bd8273 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -389,8 +389,8 @@ export class Characterize extends ATask { "layer": [{ "mark": {"type": "bar", "tooltip": true, }, "encoding": { - "color": {"field": "predict", legend: null}, - "y": {"field": "target", "title": null}, + "color": {"field": "predict", legend: null, sort: null}, + "y": {"field": "target", "title": null, sort: null}, "order": {"field": "share", "type": "quantitative", "sort": "descending"}, "opacity": { "condition": {"test": {"field": "correct", "equal":true}, "value": 1}, @@ -410,6 +410,7 @@ export class Characterize extends ATask { range: {category: this.cohorts.map((cht) => cht.colorTaskView)} } }, {actions: false, renderer: 'svg'}); + console.log('confusion', result.spec); this.chart.push(result.view); } From b86a19540e891e30f017332415614e3582128900 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 9 Aug 2022 12:56:31 +0200 Subject: [PATCH 45/60] sync lineup selection to plot --- dist/Taskview/tasks/Characterize.d.ts | 2 ++ dist/Taskview/tasks/Characterize.js | 27 ++++++++++++-- dist/Taskview/tasks/Characterize.js.map | 2 +- .../Characterize/ProbabilityScatterplot.d.ts | 8 +++-- .../Characterize/ProbabilityScatterplot.js | 25 +++++++++++-- .../ProbabilityScatterplot.js.map | 2 +- dist/scss/components/task/_characterize.scss | 4 +-- src/Taskview/tasks/Characterize.ts | 31 ++++++++++++++-- .../Characterize/ProbabilityScatterplot.ts | 35 ++++++++++++++++--- src/scss/components/task/_characterize.scss | 4 +-- 10 files changed, 122 insertions(+), 18 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 24f43b9..8cffe4a 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -25,6 +25,7 @@ export declare class Characterize extends ATask { private cohorts; private definingAttributes; private chart; + private scatterplot; supports(attributes: IAttribute[], cohorts: ICohort[]): boolean; showSearchBar(): boolean; show(columnHeader: HTMLDivElement, container: HTMLDivElement, attributes: IAttribute[], cohorts: ICohort[]): Promise; @@ -35,6 +36,7 @@ export declare class Characterize extends ATask { updateConfusionMatrix(responseData: any): Promise; createAttributeRanking(data: any, showCategoryColumn?: boolean): Promise; createItemRanking(data: any): Promise; + lineUpItemSelection(dataIndices: number[]): void; addProgressBar(): void; setProgress(iteration: number, done?: boolean): void; setProgressIndefinite(): void; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 2336488..f14ecd5 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -105,6 +105,7 @@ export class Characterize extends ATask { this.$container.querySelector('.attribute-ranking').innerHTML = ''; (_c = this.chart) === null || _c === void 0 ? void 0 : _c.forEach((view) => view.finalize()); this.chart = []; + this.scatterplot = null; this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; this.$container.querySelector('.cohort-confusion').innerHTML = ''; @@ -281,9 +282,11 @@ export class Characterize extends ATask { else if (responseData.embedding) { const vegaContainer = this.$container .querySelector('.chart-container'); - const scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); - const result = await vegaEmbed(vegaContainer, scatterplot.getSpec(), { actions: false, renderer: 'svg' }); + this.scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); + const result = await vegaEmbed(vegaContainer, this.scatterplot.getSpec(), { actions: false, renderer: 'svg' }); + this.scatterplot.setView(result.view); this.chart.push(result.view); + console.log('embedding', result.spec); } }; this.ws.onclose = () => { @@ -412,6 +415,26 @@ export class Characterize extends ATask { .sidePanel(false) .buildTaggle(this.$container.querySelector('.item-ranking')); this.itemRankingData = this.itemRanking.data; + this.itemRanking.on('selectionChanged', (dataIndices) => this.lineUpItemSelection(dataIndices)); + } + lineUpItemSelection(dataIndices) { + var _a; + console.log('lineup selection indices', dataIndices); + console.log('lineup selection data', dataIndices.map((i) => this.itemRankingData.data[i])); + if (this.scatterplot) { + const selectedItems = dataIndices.map((i) => this.itemRankingData.data[i][this._entityName]); + console.log('lineup selection tissuzes', selectedItems); + const plotData = this.scatterplot.getData(); + for (const [i, item] of plotData.entries()) { + if (selectedItems.includes(item[this._entityName])) { + item.selected = true; + } + else { + item.selected = false; + } + } + (_a = this.scatterplot) === null || _a === void 0 ? void 0 : _a.setData(plotData); + } } addProgressBar() { const wrapper = this.$container.querySelector('.progress-wrapper'); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index b98b055..f104e54 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts index 1319e8b..96fb63c 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts @@ -1,7 +1,11 @@ -import { Spec as VegaSpec } from 'vega'; +import { Spec as VegaSpec, View } from 'vega'; export declare class ProbabilityScatterplot { - private data; private cohorts; + view: View; + data: any[]; + setView(view: View): void; + setData(data: any[]): void; + getData(): any[]; constructor(data: any, cohorts: any); getSpec(): VegaSpec; } diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js index e3bb711..8d2a3eb 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js @@ -1,7 +1,19 @@ +import { colors } from '../../../colors'; export class ProbabilityScatterplot { constructor(data, cohorts) { - this.data = data; this.cohorts = cohorts; + this.data = data.slice(); + } + setView(view) { + this.view = view; + } + setData(data) { + this.data = data.slice(); + this.view.data('source', this.data); + this.view.runAsync().then((view) => console.log('view updated', view)); + } + getData() { + return this.view.data('source').slice(); } getSpec() { return { @@ -50,6 +62,12 @@ export class ProbabilityScatterplot { }, "range": this.cohorts.map(c => c.colorTaskView) }, + { + "name": "strokeOpacity", + "type": "point", + "domain": [false, true], + "range": [0, 1] + }, { "name": "prob", "type": "linear", @@ -102,7 +120,10 @@ export class ProbabilityScatterplot { "y": { "scale": "y", "field": "y" }, "fill": { "scale": "color", "field": "cht" }, "opacity": { "value": 0.7 }, - "size": { "value": 15 } + "size": { "value": 15 }, + "stroke": { "value": colors.barColor }, + "strokeWidth": { "value": 5 }, + "strokeOpacity": { "scale": "strokeOpacity", "field": "selected" } } } }, diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map index e792b84..9efbf7e 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 8b26ad9..e6a53f0 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -47,7 +47,7 @@ .classifier-result, .probabilities { display: grid; - grid-template-columns: 2fr 1fr; + grid-template-columns: 1fr 1fr; grid-template-rows: auto 1fr; column-gap: 1em; @@ -67,7 +67,7 @@ flex-shrink: 1; &.filled { - flex-basis: 40em; + flex-basis: 25em; } } diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 9bd8273..7e1f92a 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -41,6 +41,7 @@ export class Characterize extends ATask { private cohorts: Cohort[]; private definingAttributes: IAttribute[]; private chart: VegaView[]; + private scatterplot: ProbabilityScatterplot; supports(attributes: IAttribute[], cohorts: ICohort[]) { @@ -142,6 +143,7 @@ export class Characterize extends ATask { this.$container.querySelector('.attribute-ranking').innerHTML = ''; this.chart?.forEach((view) => view.finalize()); this.chart = []; + this.scatterplot = null; this.$container.querySelector('.chart-container').innerHTML = ''; this.$container.querySelector('.accuracy-container').innerHTML = ''; this.$container.querySelector('.cohort-confusion').innerHTML = ''; @@ -336,9 +338,12 @@ export class Characterize extends ATask { const vegaContainer = this.$container .querySelector('.chart-container') as HTMLDivElement; - const scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); - const result = await vegaEmbed(vegaContainer, scatterplot.getSpec(), {actions: false, renderer: 'svg'}); + const embeddingData = responseData.embedding as any[]; + embeddingData.forEach((i) => i.selected=false); + this.scatterplot = new ProbabilityScatterplot(embeddingData, this.cohorts); + this.scatterplot.setView(result.view); this.chart.push(result.view); + console.log('embedding', result.spec); } } @@ -489,6 +494,28 @@ export class Characterize extends ATask { .buildTaggle(this.$container.querySelector('.item-ranking')); this.itemRankingData = this.itemRanking.data as LineUpJS.LocalDataProvider; + this.itemRanking.on('selectionChanged', (dataIndices) => this.lineUpItemSelection(dataIndices)) + } + + lineUpItemSelection(dataIndices: number[]) { + console.log('lineup selection indices', dataIndices); + console.log('lineup selection data', dataIndices.map((i) => this.itemRankingData.data[i])); + + if(this.scatterplot) { + const selectedItems = dataIndices.map((i) => this.itemRankingData.data[i][this._entityName]); + console.log('lineup selection tissuzes', selectedItems); + + const plotData = this.scatterplot.getData() + for (const [i, item] of plotData.entries()) { + if (selectedItems.includes(item[this._entityName])) { + item.selected = true; + } else { + item.selected = false; + } + } + + this.scatterplot?.setData(plotData); + } } addProgressBar() { diff --git a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts index de6c65d..6064b9b 100644 --- a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts +++ b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts @@ -1,8 +1,26 @@ -import {Spec as VegaSpec} from 'vega'; +import {Spec as VegaSpec, View} from 'vega'; +import {colors} from '../../../colors'; export class ProbabilityScatterplot{ - constructor(private data, private cohorts) { - + view: View; + data: any[]; + + setView(view: View) { + this.view = view; + } + + setData(data: any[]) { + this.data = data.slice(); + this.view.data('source', this.data); + this.view.runAsync().then((view) => console.log('view updated', view)); + } + + getData(): any[] { + return this.view.data('source').slice(); + } + + constructor(data, private cohorts) { + this.data = data.slice(); } public getSpec(): VegaSpec { @@ -52,6 +70,12 @@ export class ProbabilityScatterplot{ }, "range": this.cohorts.map(c => c.colorTaskView) }, + { + "name": "strokeOpacity", + "type": "point", + "domain": [false, true], + "range": [ 0, 1 ] + }, { "name": "prob", "type": "linear", @@ -104,7 +128,10 @@ export class ProbabilityScatterplot{ "y": {"scale": "y", "field": "y"}, "fill": {"scale": "color", "field": "cht"}, "opacity": {"value": 0.7}, - "size": {"value": 15} + "size": {"value": 15}, + "stroke": { "value": colors.barColor }, + "strokeWidth": { "value": 5 }, + "strokeOpacity": { "scale": "strokeOpacity", "field": "selected" } } } }, diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 8b26ad9..e6a53f0 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -47,7 +47,7 @@ .classifier-result, .probabilities { display: grid; - grid-template-columns: 2fr 1fr; + grid-template-columns: 1fr 1fr; grid-template-rows: auto 1fr; column-gap: 1em; @@ -67,7 +67,7 @@ flex-shrink: 1; &.filled { - flex-basis: 40em; + flex-basis: 25em; } } From 4e122b7743210ba489f8b023a5ffd879282359a1 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 9 Aug 2022 12:56:41 +0200 Subject: [PATCH 46/60] switch canvas for scatterplot --- dist/Taskview/tasks/Characterize.js | 6 ++++-- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 1 + 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index f14ecd5..f3739f5 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -282,8 +282,10 @@ export class Characterize extends ATask { else if (responseData.embedding) { const vegaContainer = this.$container .querySelector('.chart-container'); - this.scatterplot = new ProbabilityScatterplot(responseData.embedding, this.cohorts); - const result = await vegaEmbed(vegaContainer, this.scatterplot.getSpec(), { actions: false, renderer: 'svg' }); + const embeddingData = responseData.embedding; + embeddingData.forEach((i) => i.selected = false); + this.scatterplot = new ProbabilityScatterplot(embeddingData, this.cohorts); + const result = await vegaEmbed(vegaContainer, this.scatterplot.getSpec(), { actions: false, renderer: 'canvas' }); this.scatterplot.setView(result.view); this.chart.push(result.view); console.log('embedding', result.spec); diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index f104e54..20cadea 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 7e1f92a..601d374 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -341,6 +341,7 @@ export class Characterize extends ATask { const embeddingData = responseData.embedding as any[]; embeddingData.forEach((i) => i.selected=false); this.scatterplot = new ProbabilityScatterplot(embeddingData, this.cohorts); + const result = await vegaEmbed(vegaContainer, this.scatterplot.getSpec(), {actions: false, renderer: 'canvas'}); this.scatterplot.setView(result.view); this.chart.push(result.view); console.log('embedding', result.spec); From 9567a3f553fecfb114280eb55157a981c530b0ae Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 9 Aug 2022 13:02:20 +0200 Subject: [PATCH 47/60] adjust separator color --- dist/scss/components/task/_characterize.scss | 6 +++++- src/scss/components/task/_characterize.scss | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index e6a53f0..090db88 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -72,6 +72,10 @@ } .separator-left { - border-left: 1px solid $color-border-light; + border-left: 1px solid $color-background-darker; + } + + .progress-wrapper { + border-left: 1px solid $color-background-darker; } } \ No newline at end of file diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index e6a53f0..090db88 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -72,6 +72,10 @@ } .separator-left { - border-left: 1px solid $color-border-light; + border-left: 1px solid $color-background-darker; + } + + .progress-wrapper { + border-left: 1px solid $color-background-darker; } } \ No newline at end of file From b4422281263843461669f960879f5822f60bb45d Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 9 Aug 2022 13:42:42 +0200 Subject: [PATCH 48/60] selection from plot --- dist/Taskview/tasks/Characterize.d.ts | 2 +- dist/Taskview/tasks/Characterize.js | 4 +- dist/Taskview/tasks/Characterize.js.map | 2 +- .../Characterize/ProbabilityScatterplot.d.ts | 5 +- .../Characterize/ProbabilityScatterplot.js | 335 ++++++++++++++++- .../ProbabilityScatterplot.js.map | 2 +- dist/scss/components/task/_characterize.scss | 2 +- src/Taskview/tasks/Characterize.ts | 4 +- .../Characterize/ProbabilityScatterplot.ts | 355 +++++++++++++++++- src/scss/components/task/_characterize.scss | 2 +- 10 files changed, 690 insertions(+), 23 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 8cffe4a..8031034 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -6,7 +6,7 @@ import { IAttribute } from '../../data/Attribute'; import { ATask } from './ATask'; import { LineUpDistributionColumn } from './Characterize/LineUpDistributionColumn'; export declare class Characterize extends ATask { - static readonly TREES = 300; + static readonly TREES = 150; static readonly formatPercent: (n: number | { valueOf(): number; }) => string; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index f3739f5..8977d91 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -284,7 +284,7 @@ export class Characterize extends ATask { .querySelector('.chart-container'); const embeddingData = responseData.embedding; embeddingData.forEach((i) => i.selected = false); - this.scatterplot = new ProbabilityScatterplot(embeddingData, this.cohorts); + this.scatterplot = new ProbabilityScatterplot(embeddingData, this.cohorts, this.itemRanking); const result = await vegaEmbed(vegaContainer, this.scatterplot.getSpec(), { actions: false, renderer: 'canvas' }); this.scatterplot.setView(result.view); this.chart.push(result.view); @@ -509,7 +509,7 @@ export class Characterize extends ATask { return data; } } -Characterize.TREES = 300; +Characterize.TREES = 150; Characterize.formatPercent = format('.1~%'); export class MyDistributionRenderer { constructor(cohorts) { diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 20cadea..1bbd8b6 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts index 96fb63c..4c1b63e 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts @@ -1,11 +1,14 @@ import { Spec as VegaSpec, View } from 'vega'; +import * as LineUpJS from 'lineupjs'; export declare class ProbabilityScatterplot { private cohorts; + private lineup; view: View; data: any[]; setView(view: View): void; + handleVegaIntervalEvent(name: any, value: any): void; setData(data: any[]): void; getData(): any[]; - constructor(data: any, cohorts: any); + constructor(data: any, cohorts: any, lineup: LineUpJS.Taggle); getSpec(): VegaSpec; } diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js index 8d2a3eb..d43e07e 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js @@ -1,11 +1,30 @@ +import { inRange } from 'lodash'; +import { BaseUtils } from 'tdp_core'; import { colors } from '../../../colors'; export class ProbabilityScatterplot { - constructor(data, cohorts) { + constructor(data, cohorts, lineup) { this.cohorts = cohorts; + this.lineup = lineup; this.data = data.slice(); } setView(view) { this.view = view; + this.view.addSignalListener('brush', BaseUtils.debounce(this.handleVegaIntervalEvent.bind(this), 250)); + } + handleVegaIntervalEvent(name, value) { + console.log('debounced?', name, value); + const xRange = value.x; + const yRange = value.y; + const plotSelection = this.getData().filter((d) => inRange(d.x, xRange[0], xRange[1]) && inRange(d.y, yRange[0], yRange[1])).map((d) => d.tissuename); + const lineUpSelection = this.lineup.data.data + .map((item, i) => { + if (plotSelection.includes(item.tissuename)) { + return i; + } + return undefined; // to be filtered out + }) + .filter((item) => item !== undefined); + this.lineup.setSelection(lineUpSelection); } setData(data) { this.data = data.slice(); @@ -109,6 +128,43 @@ export class ProbabilityScatterplot { "color": { "expr": "scale('color', warn(datum.datum.max_cht))" } } ] + }, { + "name": "brush_brush_bg", + "type": "rect", + "clip": true, + "encode": { + "enter": { "fill": { "value": "#333" }, "fillOpacity": { "value": 0.125 } }, + "update": { + "x": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[0]" + }, + { "value": 0 } + ], + "y": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[0]" + }, + { "value": 0 } + ], + "x2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[1]" + }, + { "value": 0 } + ], + "y2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[1]" + }, + { "value": 0 } + ] + } + } }, { "name": "marks", @@ -127,6 +183,51 @@ export class ProbabilityScatterplot { } } }, + { + "name": "brush_brush", + "type": "rect", + "clip": true, + "encode": { + "enter": { "fill": { "value": "transparent" } }, + "update": { + "x": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[0]" + }, + { "value": 0 } + ], + "y": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[0]" + }, + { "value": 0 } + ], + "x2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[1]" + }, + { "value": 0 } + ], + "y2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[1]" + }, + { "value": 0 } + ], + "stroke": [ + { + "test": "brush_x[0] !== brush_x[1] && brush_y[0] !== brush_y[1]", + "value": "white" + }, + { "value": null } + ] + } + } + }, { // invisible heatmap over everything else for regional tooltips "type": "rect", @@ -227,7 +328,8 @@ export class ProbabilityScatterplot { } ] }, - { "name": "zoom_store" } + { "name": "zoom_store" }, + { "name": "brush_store" } ], "signals": [ { "name": "width", @@ -257,6 +359,10 @@ export class ProbabilityScatterplot { ] }, { "name": "zoom", "update": "vlSelectionResolve(\"zoom_store\", \"union\")" }, + { + "name": "brush", + "update": "vlSelectionResolve(\"brush_store\", \"union\")" + }, { "name": "zoom_x", "on": [ @@ -320,6 +426,7 @@ export class ProbabilityScatterplot { { "source": "window", "type": "mousemove", + "filter": ["!event.ctrlKey"], "consume": true, "between": [ { "source": "scope", "type": "mousedown" }, @@ -358,6 +465,230 @@ export class ProbabilityScatterplot { "update": "modify(\"zoom_store\", zoom_tuple, true)" } ] + }, + { + "name": "brush_x", + "value": [], + "on": [ + { + "events": { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + "update": "[x(unit), x(unit)]" + }, + { + "events": { + "source": "scope", + "type": "mousemove", + "between": [ + { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + { "source": "scope", "type": "mouseup" } + ] + }, + "update": "[brush_x[0], clamp(x(unit), 0, width)]" + }, + { + "events": { "signal": "brush_scale_trigger" }, + "update": "[scale(\"x\", brush_xAttr[0]), scale(\"x\", brush_xAttr[1])]" + }, + { + "events": [{ "source": "view", "type": "dblclick" }], + "update": "[0, 0]" + }, + { + "events": { "signal": "brush_translate_delta" }, + "update": "clampRange(panLinear(brush_translate_anchor.extent_x, brush_translate_delta.x / span(brush_translate_anchor.extent_x)), 0, width)" + }, + { + "events": { "signal": "brush_zoom_delta" }, + "update": "clampRange(zoomLinear(brush_x, brush_zoom_anchor.x, brush_zoom_delta), 0, width)" + } + ] + }, + { + "name": "brush_xAttr", + "on": [ + { + "events": { "signal": "brush_x" }, + "update": "brush_x[0] === brush_x[1] ? null : invert(\"x\", brush_x)" + } + ] + }, + { + "name": "brush_y", + "value": [], + "on": [ + { + "events": { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + "update": "[y(unit), y(unit)]" + }, + { + "events": { + "source": "scope", + "type": "mousemove", + "between": [ + { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + { "source": "scope", "type": "mouseup" } + ] + }, + "update": "[brush_y[0], clamp(y(unit), 0, height)]" + }, + { + "events": { "signal": "brush_scale_trigger" }, + "update": "[scale(\"y\", brush_yAttr[0]), scale(\"y\", brush_yAttr[1])]" + }, + { + "events": [{ "source": "view", "type": "dblclick" }], + "update": "[0, 0]" + }, + { + "events": { "signal": "brush_translate_delta" }, + "update": "clampRange(panLinear(brush_translate_anchor.extent_y, brush_translate_delta.y / span(brush_translate_anchor.extent_y)), 0, height)" + }, + { + "events": { "signal": "brush_zoom_delta" }, + "update": "clampRange(zoomLinear(brush_y, brush_zoom_anchor.y, brush_zoom_delta), 0, height)" + } + ] + }, + { + "name": "brush_yAttr", + "on": [ + { + "events": { "signal": "brush_y" }, + "update": "brush_y[0] === brush_y[1] ? null : invert(\"y\", brush_y)" + } + ] + }, + { + "name": "brush_scale_trigger", + "value": {}, + "on": [ + { + "events": [{ "scale": "x" }, { "scale": "y" }], + "update": "(!isArray(brush_xAttr) || (+invert(\"x\", brush_x)[0] === +brush_xAttr[0] && +invert(\"x\", brush_x)[1] === +brush_xAttr[1])) && (!isArray(brush_yAttr) || (+invert(\"y\", brush_y)[0] === +brush_yAttr[0] && +invert(\"y\", brush_y)[1] === +brush_yAttr[1])) ? brush_scale_trigger : {}" + } + ] + }, + { + "name": "brush_tuple", + "on": [ + { + "events": [{ "signal": "brush_xAttr || brush_yAttr" }], + "update": "brush_xAttr && brush_yAttr ? {unit: \"\", fields: brush_tuple_fields, values: [brush_xAttr,brush_yAttr]} : null" + } + ] + }, + { + "name": "brush_tuple_fields", + "value": [ + { "field": "x", "channel": "x", "type": "R" }, + { "field": "y", "channel": "y", "type": "R" } + ] + }, + { + "name": "brush_translate_anchor", + "value": {}, + "on": [ + { + "events": [ + { "source": "scope", "type": "mousedown", "markname": "brush_brush" } + ], + "update": "{x: x(unit), y: y(unit), extent_x: slice(brush_x), extent_y: slice(brush_y)}" + } + ] + }, + { + "name": "brush_translate_delta", + "value": {}, + "on": [ + { + "events": [ + { + "source": "window", + "type": "mousemove", + "consume": true, + "between": [ + { + "source": "scope", + "type": "mousedown", + "markname": "brush_brush" + }, + { "source": "window", "type": "mouseup" } + ] + } + ], + "update": "{x: brush_translate_anchor.x - x(unit), y: brush_translate_anchor.y - y(unit)}" + } + ] + }, + { + "name": "brush_zoom_anchor", + "on": [ + { + "events": [ + { + "source": "scope", + "type": "wheel", + "consume": true, + "markname": "brush_brush" + } + ], + "update": "{x: x(unit), y: y(unit)}" + } + ] + }, + { + "name": "brush_zoom_delta", + "on": [ + { + "events": [ + { + "source": "scope", + "type": "wheel", + "consume": true, + "markname": "brush_brush" + } + ], + "force": true, + "update": "pow(1.001, event.deltaY * pow(16, event.deltaMode))" + } + ] + }, + { + "name": "brush_modify", + "on": [ + { + "events": { "signal": "brush_tuple" }, + "update": "modify(\"brush_store\", brush_tuple, true)" + } + ] } ], }; diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map index 9efbf7e..07562cc 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scss/components/task/_characterize.scss b/dist/scss/components/task/_characterize.scss index 090db88..991eaa9 100644 --- a/dist/scss/components/task/_characterize.scss +++ b/dist/scss/components/task/_characterize.scss @@ -76,6 +76,6 @@ } .progress-wrapper { - border-left: 1px solid $color-background-darker; + border-bottom: 1px solid $color-background-darker; } } \ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index 601d374..aaf2abb 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -19,7 +19,7 @@ import {LineUpDistributionColumn} from './Characterize/LineUpDistributionColumn' import {ProbabilityScatterplot} from './Characterize/ProbabilityScatterplot'; export class Characterize extends ATask { - static readonly TREES = 300; + static readonly TREES = 150; static readonly formatPercent = format('.1~%'); public label = `Characterize`; @@ -340,7 +340,7 @@ export class Characterize extends ATask { const embeddingData = responseData.embedding as any[]; embeddingData.forEach((i) => i.selected=false); - this.scatterplot = new ProbabilityScatterplot(embeddingData, this.cohorts); + this.scatterplot = new ProbabilityScatterplot(embeddingData, this.cohorts, this.itemRanking); const result = await vegaEmbed(vegaContainer, this.scatterplot.getSpec(), {actions: false, renderer: 'canvas'}); this.scatterplot.setView(result.view); this.chart.push(result.view); diff --git a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts index 6064b9b..e00d229 100644 --- a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts +++ b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts @@ -1,12 +1,33 @@ +import {inRange} from 'lodash'; +import {BaseUtils} from 'tdp_core'; import {Spec as VegaSpec, View} from 'vega'; import {colors} from '../../../colors'; +import * as LineUpJS from 'lineupjs'; +import {LocalDataProvider} from 'lineupjs'; -export class ProbabilityScatterplot{ +export class ProbabilityScatterplot { view: View; data: any[]; setView(view: View) { this.view = view; + this.view.addSignalListener('brush', BaseUtils.debounce(this.handleVegaIntervalEvent.bind(this), 250)); + } + + handleVegaIntervalEvent(name, value) { + console.log('debounced?', name, value) + const xRange = value.x; + const yRange = value.y; + const plotSelection = this.getData().filter((d) => inRange(d.x, xRange[0], xRange[1]) && inRange(d.y, yRange[0], yRange[1])).map((d) => d.tissuename); + const lineUpSelection = (this.lineup.data as LocalDataProvider).data + .map((item, i) => { + if (plotSelection.includes(item.tissuename)) { + return i; + } + return undefined; // to be filtered out + }) + .filter((item) => item !== undefined) + this.lineup.setSelection(lineUpSelection); } setData(data: any[]) { @@ -19,7 +40,7 @@ export class ProbabilityScatterplot{ return this.view.data('source').slice(); } - constructor(data, private cohorts) { + constructor(data, private cohorts, private lineup: LineUpJS.Taggle) { this.data = data.slice(); } @@ -33,7 +54,7 @@ export class ProbabilityScatterplot{ "round": true, "nice": true, "zero": true, - "domain": { + "domain": { "fields": [ { "signal": "[bin_x_bins.start, bin_x_bins.stop]" @@ -74,7 +95,7 @@ export class ProbabilityScatterplot{ "name": "strokeOpacity", "type": "point", "domain": [false, true], - "range": [ 0, 1 ] + "range": [0, 1] }, { "name": "prob", @@ -117,6 +138,43 @@ export class ProbabilityScatterplot{ "color": {"expr": "scale('color', warn(datum.datum.max_cht))"} } ] + }, { + "name": "brush_brush_bg", + "type": "rect", + "clip": true, + "encode": { + "enter": {"fill": {"value": "#333"}, "fillOpacity": {"value": 0.125}}, + "update": { + "x": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[0]" + }, + {"value": 0} + ], + "y": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[0]" + }, + {"value": 0} + ], + "x2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[1]" + }, + {"value": 0} + ], + "y2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[1]" + }, + {"value": 0} + ] + } + } }, { "name": "marks", // scatterplot points on top of density plot @@ -128,10 +186,55 @@ export class ProbabilityScatterplot{ "y": {"scale": "y", "field": "y"}, "fill": {"scale": "color", "field": "cht"}, "opacity": {"value": 0.7}, - "size": {"value": 15}, - "stroke": { "value": colors.barColor }, - "strokeWidth": { "value": 5 }, - "strokeOpacity": { "scale": "strokeOpacity", "field": "selected" } + "size": {"value": 15}, + "stroke": {"value": colors.barColor}, + "strokeWidth": {"value": 5}, + "strokeOpacity": {"scale": "strokeOpacity", "field": "selected"} + } + } + }, + { + "name": "brush_brush", + "type": "rect", + "clip": true, + "encode": { + "enter": {"fill": {"value": "transparent"}}, + "update": { + "x": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[0]" + }, + {"value": 0} + ], + "y": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[0]" + }, + {"value": 0} + ], + "x2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_x[1]" + }, + {"value": 0} + ], + "y2": [ + { + "test": "data(\"brush_store\").length && data(\"brush_store\")[0].unit === \"\"", + "signal": "brush_y[1]" + }, + {"value": 0} + ], + "stroke": [ + { + "test": "brush_x[0] !== brush_x[1] && brush_y[0] !== brush_y[1]", + "value": "white" + }, + {"value": null} + ] } } }, @@ -224,7 +327,7 @@ export class ProbabilityScatterplot{ "x": {"expr": "scale('x', datum.x_sampled)"}, "y": {"expr": "scale('y', datum.y_sampled)"}, "weight": {"expr": "scale('prob', datum.max_max_prob)"}, - "bandwidth": [10,10], + "bandwidth": [10, 10], "cellSize": 4 }, { @@ -235,8 +338,9 @@ export class ProbabilityScatterplot{ } ] }, - {"name": "zoom_store"} - ],"signals": [ + {"name": "zoom_store"}, + {"name": "brush_store"} + ], "signals": [ { "name": "width", "init": "isFinite(containerSize()[0]) ? containerSize()[0] : 200", @@ -265,6 +369,10 @@ export class ProbabilityScatterplot{ ] }, {"name": "zoom", "update": "vlSelectionResolve(\"zoom_store\", \"union\")"}, + { + "name": "brush", + "update": "vlSelectionResolve(\"brush_store\", \"union\")" + }, { "name": "zoom_x", "on": [ @@ -328,6 +436,7 @@ export class ProbabilityScatterplot{ { "source": "window", "type": "mousemove", + "filter": ["!event.ctrlKey"], "consume": true, "between": [ {"source": "scope", "type": "mousedown"}, @@ -366,6 +475,230 @@ export class ProbabilityScatterplot{ "update": "modify(\"zoom_store\", zoom_tuple, true)" } ] + }, + { + "name": "brush_x", + "value": [], + "on": [ + { + "events": { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + "update": "[x(unit), x(unit)]" + }, + { + "events": { + "source": "scope", + "type": "mousemove", + "between": [ + { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + {"source": "scope", "type": "mouseup"} + ] + }, + "update": "[brush_x[0], clamp(x(unit), 0, width)]" + }, + { + "events": {"signal": "brush_scale_trigger"}, + "update": "[scale(\"x\", brush_xAttr[0]), scale(\"x\", brush_xAttr[1])]" + }, + { + "events": [{"source": "view", "type": "dblclick"}], + "update": "[0, 0]" + }, + { + "events": {"signal": "brush_translate_delta"}, + "update": "clampRange(panLinear(brush_translate_anchor.extent_x, brush_translate_delta.x / span(brush_translate_anchor.extent_x)), 0, width)" + }, + { + "events": {"signal": "brush_zoom_delta"}, + "update": "clampRange(zoomLinear(brush_x, brush_zoom_anchor.x, brush_zoom_delta), 0, width)" + } + ] + }, + { + "name": "brush_xAttr", + "on": [ + { + "events": {"signal": "brush_x"}, + "update": "brush_x[0] === brush_x[1] ? null : invert(\"x\", brush_x)" + } + ] + }, + { + "name": "brush_y", + "value": [], + "on": [ + { + "events": { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + "update": "[y(unit), y(unit)]" + }, + { + "events": { + "source": "scope", + "type": "mousemove", + "between": [ + { + "source": "scope", + "type": "mousedown", + "filter": [ + "event.ctrlKey", + "!event.item || event.item.mark.name !== \"brush_brush\"" + ] + }, + {"source": "scope", "type": "mouseup"} + ] + }, + "update": "[brush_y[0], clamp(y(unit), 0, height)]" + }, + { + "events": {"signal": "brush_scale_trigger"}, + "update": "[scale(\"y\", brush_yAttr[0]), scale(\"y\", brush_yAttr[1])]" + }, + { + "events": [{"source": "view", "type": "dblclick"}], + "update": "[0, 0]" + }, + { + "events": {"signal": "brush_translate_delta"}, + "update": "clampRange(panLinear(brush_translate_anchor.extent_y, brush_translate_delta.y / span(brush_translate_anchor.extent_y)), 0, height)" + }, + { + "events": {"signal": "brush_zoom_delta"}, + "update": "clampRange(zoomLinear(brush_y, brush_zoom_anchor.y, brush_zoom_delta), 0, height)" + } + ] + }, + { + "name": "brush_yAttr", + "on": [ + { + "events": {"signal": "brush_y"}, + "update": "brush_y[0] === brush_y[1] ? null : invert(\"y\", brush_y)" + } + ] + }, + { + "name": "brush_scale_trigger", + "value": {}, + "on": [ + { + "events": [{"scale": "x"}, {"scale": "y"}], + "update": "(!isArray(brush_xAttr) || (+invert(\"x\", brush_x)[0] === +brush_xAttr[0] && +invert(\"x\", brush_x)[1] === +brush_xAttr[1])) && (!isArray(brush_yAttr) || (+invert(\"y\", brush_y)[0] === +brush_yAttr[0] && +invert(\"y\", brush_y)[1] === +brush_yAttr[1])) ? brush_scale_trigger : {}" + } + ] + }, + { + "name": "brush_tuple", + "on": [ + { + "events": [{"signal": "brush_xAttr || brush_yAttr"}], + "update": "brush_xAttr && brush_yAttr ? {unit: \"\", fields: brush_tuple_fields, values: [brush_xAttr,brush_yAttr]} : null" + } + ] + }, + { + "name": "brush_tuple_fields", + "value": [ + {"field": "x", "channel": "x", "type": "R"}, + {"field": "y", "channel": "y", "type": "R"} + ] + }, + { + "name": "brush_translate_anchor", + "value": {}, + "on": [ + { + "events": [ + {"source": "scope", "type": "mousedown", "markname": "brush_brush"} + ], + "update": "{x: x(unit), y: y(unit), extent_x: slice(brush_x), extent_y: slice(brush_y)}" + } + ] + }, + { + "name": "brush_translate_delta", + "value": {}, + "on": [ + { + "events": [ + { + "source": "window", + "type": "mousemove", + "consume": true, + "between": [ + { + "source": "scope", + "type": "mousedown", + "markname": "brush_brush" + }, + {"source": "window", "type": "mouseup"} + ] + } + ], + "update": "{x: brush_translate_anchor.x - x(unit), y: brush_translate_anchor.y - y(unit)}" + } + ] + }, + { + "name": "brush_zoom_anchor", + "on": [ + { + "events": [ + { + "source": "scope", + "type": "wheel", + "consume": true, + "markname": "brush_brush" + } + ], + "update": "{x: x(unit), y: y(unit)}" + } + ] + }, + { + "name": "brush_zoom_delta", + "on": [ + { + "events": [ + { + "source": "scope", + "type": "wheel", + "consume": true, + "markname": "brush_brush" + } + ], + "force": true, + "update": "pow(1.001, event.deltaY * pow(16, event.deltaMode))" + } + ] + }, + { + "name": "brush_modify", + "on": [ + { + "events": {"signal": "brush_tuple"}, + "update": "modify(\"brush_store\", brush_tuple, true)" + } + ] } ], } diff --git a/src/scss/components/task/_characterize.scss b/src/scss/components/task/_characterize.scss index 090db88..991eaa9 100644 --- a/src/scss/components/task/_characterize.scss +++ b/src/scss/components/task/_characterize.scss @@ -76,6 +76,6 @@ } .progress-wrapper { - border-left: 1px solid $color-background-darker; + border-bottom: 1px solid $color-background-darker; } } \ No newline at end of file From 310085a15ce9822b09fb98126ddf2eba8aa2772e Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 9 Aug 2022 16:25:25 +0200 Subject: [PATCH 49/60] sort by lineup selection --- dist/Taskview/tasks/Characterize.js | 11 ++++++----- dist/Taskview/tasks/Characterize.js.map | 2 +- .../tasks/Characterize/ProbabilityScatterplot.d.ts | 2 +- .../tasks/Characterize/ProbabilityScatterplot.js | 4 ++++ .../tasks/Characterize/ProbabilityScatterplot.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 11 ++++++----- .../tasks/Characterize/ProbabilityScatterplot.ts | 9 +++++++-- 7 files changed, 26 insertions(+), 15 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index 8977d91..a6315eb 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -91,7 +91,7 @@ export class Characterize extends ATask {

    Cohort Characterization

    -

    Indistinguishable Items

    +

    Item Predictions

    Cohort Association

    @@ -401,17 +401,18 @@ export class Characterize extends ATask { } async createItemRanking(data) { this.itemRanking = LineUpJS.builder(data) - .column(LineUpJS.buildStringColumn(this._entityName).label('Id').width(200)) + .column(LineUpJS.buildStringColumn(this._entityName).label('Item Id').width(200)) .column(LineUpJS.buildCategoricalColumn('cht', this.cohorts.map((cht, i) => ({ name: '' + i, label: cht.label, color: cht.colorTaskView }))) .label('Cohort') + .width(Math.min(Math.max(this.cohorts.length * 30, 100), 200)) .renderer('catheatmap', 'categorical').asSet()) .column(LineUpJS.buildNumberColumn('probs', [0, 1]) - .label('Prob') - .width(100) + .label('Cohort Probability') + .width(150) .colorMapping(colors.barColor) .numberFormat('.1%') .asArray(this.cohorts.map((cht, i) => cht.label))) - .column(LineUpJS.buildNumberColumn('prob_max', [0, 1]).label('Max Probality').width(100).colorMapping(colors.barColor).numberFormat('.1%')) + .column(LineUpJS.buildNumberColumn('prob_max', [0, 1]).label('Max Probability').width(120).colorMapping(colors.barColor).numberFormat('.1%')) .deriveColors() .ranking(LineUpJS.buildRanking().supportTypes().allColumns().sortBy('prob_max', 'asc')) .sidePanel(false) diff --git a/dist/Taskview/tasks/Characterize.js.map b/dist/Taskview/tasks/Characterize.js.map index 1bbd8b6..6a58745 100644 --- a/dist/Taskview/tasks/Characterize.js.map +++ b/dist/Taskview/tasks/Characterize.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts index 4c1b63e..514afe8 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.d.ts @@ -1,5 +1,5 @@ -import { Spec as VegaSpec, View } from 'vega'; import * as LineUpJS from 'lineupjs'; +import { Spec as VegaSpec, View } from 'vega'; export declare class ProbabilityScatterplot { private cohorts; private lineup; diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js index d43e07e..539b2c6 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js @@ -25,6 +25,10 @@ export class ProbabilityScatterplot { }) .filter((item) => item !== undefined); this.lineup.setSelection(lineUpSelection); + const selCol = this.lineup.data + .find((d) => d.desc.type === "selection"); + selCol.toggleMySorting(); + selCol.sortByMe(false); } setData(data) { this.data = data.slice(); diff --git a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map index 07562cc..4bfbe77 100644 --- a/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map +++ b/dist/Taskview/tasks/Characterize/ProbabilityScatterplot.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/src/Taskview/tasks/Characterize.ts b/src/Taskview/tasks/Characterize.ts index aaf2abb..43527c3 100644 --- a/src/Taskview/tasks/Characterize.ts +++ b/src/Taskview/tasks/Characterize.ts @@ -129,7 +129,7 @@ export class Characterize extends ATask {

    Cohort Characterization

    -

    Indistinguishable Items

    +

    Item Predictions

    Cohort Association

    @@ -472,23 +472,24 @@ export class Characterize extends ATask { async createItemRanking(data) { this.itemRanking = LineUpJS.builder(data) - .column(LineUpJS.buildStringColumn(this._entityName).label('Id').width(200)) + .column(LineUpJS.buildStringColumn(this._entityName).label('Item Id').width(200)) .column( LineUpJS .buildCategoricalColumn( 'cht', this.cohorts.map((cht, i) => ({name: ''+i, label: cht.label, color: (cht as Cohort).colorTaskView})) ) .label('Cohort') + .width(Math.min(Math.max(this.cohorts.length * 30, 100), 200)) .renderer('catheatmap', 'categorical').asSet()) .column( LineUpJS.buildNumberColumn('probs', [0, 1]) - .label('Prob') - .width(100) + .label('Cohort Probability') + .width(150) .colorMapping(colors.barColor) .numberFormat('.1%') .asArray(this.cohorts.map((cht, i) => cht.label)) ) - .column( LineUpJS.buildNumberColumn('prob_max', [0, 1]).label('Max Probality').width(100).colorMapping(colors.barColor).numberFormat('.1%')) + .column( LineUpJS.buildNumberColumn('prob_max', [0, 1]).label('Max Probability').width(120).colorMapping(colors.barColor).numberFormat('.1%')) .deriveColors() .ranking(LineUpJS.buildRanking().supportTypes().allColumns().sortBy('prob_max', 'asc') ) .sidePanel(false) diff --git a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts index e00d229..f6e6166 100644 --- a/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts +++ b/src/Taskview/tasks/Characterize/ProbabilityScatterplot.ts @@ -1,9 +1,9 @@ +import * as LineUpJS from 'lineupjs'; +import {LocalDataProvider} from 'lineupjs'; import {inRange} from 'lodash'; import {BaseUtils} from 'tdp_core'; import {Spec as VegaSpec, View} from 'vega'; import {colors} from '../../../colors'; -import * as LineUpJS from 'lineupjs'; -import {LocalDataProvider} from 'lineupjs'; export class ProbabilityScatterplot { view: View; @@ -27,7 +27,12 @@ export class ProbabilityScatterplot { return undefined; // to be filtered out }) .filter((item) => item !== undefined) + this.lineup.setSelection(lineUpSelection); + const selCol = this.lineup.data + .find((d) => (d.desc as any).type === "selection"); + selCol.toggleMySorting(); + selCol.sortByMe(false); } setData(data: any[]) { From 2f4ea60ffd89c05de66f475b3df89dc5655b4322 Mon Sep 17 00:00:00 2001 From: Klaus Eckelt Date: Tue, 9 Aug 2022 16:54:58 +0200 Subject: [PATCH 50/60] add buttons to exclude/limit attribute --- dist/Taskview/tasks/Characterize.d.ts | 1 + dist/Taskview/tasks/Characterize.js | 22 +++++++++++++++++---- dist/Taskview/tasks/Characterize.js.map | 2 +- src/Taskview/tasks/Characterize.ts | 26 ++++++++++++++++++++----- 4 files changed, 41 insertions(+), 10 deletions(-) diff --git a/dist/Taskview/tasks/Characterize.d.ts b/dist/Taskview/tasks/Characterize.d.ts index 8031034..bb195c8 100644 --- a/dist/Taskview/tasks/Characterize.d.ts +++ b/dist/Taskview/tasks/Characterize.d.ts @@ -35,6 +35,7 @@ export declare class Characterize extends ATask { private compare; updateConfusionMatrix(responseData: any): Promise; createAttributeRanking(data: any, showCategoryColumn?: boolean): Promise; + lineUpAttributeSelection(dataIndices: number[]): void; createItemRanking(data: any): Promise; lineUpItemSelection(dataIndices: number[]): void; addProgressBar(): void; diff --git a/dist/Taskview/tasks/Characterize.js b/dist/Taskview/tasks/Characterize.js index a6315eb..908c27f 100644 --- a/dist/Taskview/tasks/Characterize.js +++ b/dist/Taskview/tasks/Characterize.js @@ -57,10 +57,13 @@ export class Characterize extends ATask {

    Cohort Comparison

    - - + +   +   Exclude the cohorts' defining attributes +    +
    + -
    +