Updated Custom Data Enhancements for Plots Tab

cBioPortal · Sep 13, 2024 · 0836d7a · 0836d7a
1 parent 6450eae
commit 0836d7a
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Showing 7 changed files with 17 additions and 18 deletions.
diff --git a/src/pages/resultsView/ResultsViewPage.tsx b/src/pages/resultsView/ResultsViewPage.tsx
@@ -266,9 +266,7 @@ export default class ResultsViewPage extends React.Component<
                                 sampleKeyToSample={store.sampleKeyToSample}
                                 genes={store.genes}
                                 clinicalAttributes={store.clinicalAttributes}
-                                customAttributes={
-                                    store.clinicalAttributes_customCharts
-                                }
+                                customAttributes={store.customAttributes}
                                 genesets={store.genesets}
                                 genericAssayEntitiesGroupByMolecularProfileId={
                                     store.genericAssayEntitiesGroupByMolecularProfileId

diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -1093,6 +1093,7 @@ export class ResultsViewPageStore extends AnalysisStore
             this.studyIds,
             this.clinicalAttributes_profiledIn,
             this.clinicalAttributes_comparisonGroupMembership,
+            this.customAttributes,
             this.samples,
             this.patients,
         ],
@@ -1141,6 +1142,7 @@ export class ResultsViewPageStore extends AnalysisStore
                 ...specialAttributes,
                 ...this.clinicalAttributes_profiledIn.result!,
                 ...this.clinicalAttributes_comparisonGroupMembership.result!,
+                ...this.customAttributes.result!,
             ];
         },
     });
@@ -1185,7 +1187,7 @@ export class ResultsViewPageStore extends AnalysisStore
             this.studyToDataQueryFilter,
             this.clinicalAttributes_profiledIn,
             this.clinicalAttributes_comparisonGroupMembership,
-            this.clinicalAttributes_customCharts,
+            this.customAttributes,
         ],
         invoke: async () => {
             let clinicalAttributeCountFilter: ClinicalAttributeCountFilter;
@@ -1268,7 +1270,7 @@ export class ResultsViewPageStore extends AnalysisStore
                 );
             }
             // add counts for custom chart clinical attributes
-            for (const attr of this.clinicalAttributes_customCharts.result!) {
+            for (const attr of this.customAttributes.result!) {
                 ret[attr.clinicalAttributeId] = attr.data!.filter(
                     d => d.value !== 'NA'
                 ).length;
@@ -2721,7 +2723,7 @@ export class ResultsViewPageStore extends AnalysisStore
         default: [],
     });
 
-    readonly clinicalAttributes_customCharts = remoteData({
+    readonly customAttributes = remoteData({
         await: () => [this.sampleMap],
         invoke: async () => {
             let ret: ExtendedClinicalAttribute[] = [];
@@ -5691,7 +5693,7 @@ export class ResultsViewPageStore extends AnalysisStore
         this.coverageInformation,
         this.filteredSampleKeyToSample,
         this.filteredPatientKeyToPatient,
-        this.clinicalAttributes_customCharts
+        this.customAttributes
     );
 
     public mutationCache = new MobxPromiseCache<

diff --git a/src/pages/resultsView/oncoprint/TracksMenu.tsx b/src/pages/resultsView/oncoprint/TracksMenu.tsx
@@ -151,7 +151,7 @@ export default class TracksMenu extends React.Component<IAddTrackProps, {}> {
         await: () => [
             this.props.store.clinicalAttributes,
             this.clinicalAttributeIdToAvailableFrequency,
-            this.props.store.clinicalAttributes_customCharts,
+            this.props.store.customAttributes,
         ],
         invoke: () => {
             const uniqueAttributes = _.uniqBy(
@@ -167,7 +167,7 @@ export default class TracksMenu extends React.Component<IAddTrackProps, {}> {
             };
 
             const customChartClinicalAttributeIds = _.keyBy(
-                this.props.store.clinicalAttributes_customCharts.result!,
+                this.props.store.customAttributes.result!,
                 a => a.clinicalAttributeId
             );
 

diff --git a/src/pages/studyView/StudyViewPage.tsx b/src/pages/studyView/StudyViewPage.tsx
@@ -773,8 +773,7 @@ export default class StudyViewPage extends React.Component<
                                                 this.store.clinicalAttributes
                                             }
                                             customAttributes={
-                                                this.store
-                                                    .clinicalAttributes_customCharts
+                                                this.store.customAttributes
                                             }
                                             genesets={this.store.genesets}
                                             genericAssayEntitiesGroupByMolecularProfileId={

diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts
@@ -11439,7 +11439,7 @@ export class StudyViewPageStore
             ),
     });
 
-    readonly clinicalAttributes_customCharts = remoteData({
+    readonly customAttributes = remoteData({
         await: () => [this.sampleMap],
         invoke: async () => {
             let ret: ExtendedClinicalAttribute[] = [];
@@ -11485,7 +11485,7 @@ export class StudyViewPageStore
         this.coverageInformation,
         this.filteredSampleKeyToSample,
         this.filteredPatientKeyToPatient,
-        this.clinicalAttributes_customCharts
+        this.customAttributes
     );
 
     private _numericGeneMolecularDataCache = new MobxPromiseCache<

diff --git a/src/shared/components/plots/PlotsTab.tsx b/src/shared/components/plots/PlotsTab.tsx
@@ -1176,7 +1176,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     (self.horzSelection.dataType === CLIN_ATTR_DATA_TYPE ||
                         self.horzSelection.dataType === CUSTOM_ATTR_DATA_TYPE)
                 ) {
-                    // if vertical gene set option is "same as horizontal", and horizontal is clinical, then use the actual
+                    // if vertical gene set option is "same as horizontal", and horizontal is clinical or custom, then use the actual
                     //      gene set option value instead of "Same gene" option value, because that would be slightly weird UX
                     return self.horzSelection.selectedGenesetOption;
                 } else {
@@ -1251,7 +1251,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     (self.horzSelection.dataType === CLIN_ATTR_DATA_TYPE ||
                         self.horzSelection.dataType === CUSTOM_ATTR_DATA_TYPE)
                 ) {
-                    // if vertical gene set option is "same as horizontal", and horizontal is clinical, then use the actual
+                    // if vertical gene set option is "same as horizontal", and horizontal is clinical or custom, then use the actual
                     //      gene set option value instead of "Same gene" option value, because that would be slightly weird UX
                     return self.horzSelection.selectedGenericAssayOption;
                 } else {
@@ -2585,7 +2585,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 dataTypeIds.push(CLIN_ATTR_DATA_TYPE);
             }
 
-            if (this.customAttributeOptions.result!.length) {
+            if (!_.isEmpty(this.customAttributeOptions.result)) {
                 dataTypeIds.push(CUSTOM_ATTR_DATA_TYPE);
             }
 
@@ -2699,7 +2699,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 ] = this.clinicalAttributeOptions.result!;
             }
 
-            if (this.customAttributeOptions.result!.length) {
+            if (!_.isEmpty(this.customAttributeOptions.result)) {
                 // add custom attributes
                 map[
                     CUSTOM_ATTR_DATA_TYPE

diff --git a/src/shared/components/plots/PlotsTabUtils.tsx b/src/shared/components/plots/PlotsTabUtils.tsx
@@ -1663,7 +1663,7 @@ export function getAxisDescription(
     switch (selection.dataType) {
         case CUSTOM_ATTR_DATA_TYPE:
             const customAttr =
-                clinicalAttributeIdToClinicalAttribute[selection.dataSourceId!];
+                customAttributeIdToClinicalAttribute[selection.dataSourceId!];
             if (customAttr) {
                 ret = customAttr.description;
             }