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hadexversum · Apr 17, 2024 · afe70a5 · afe70a5
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diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -13,16 +13,22 @@ name: pkgdown
 
 jobs:
   pkgdown:
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.fork == false
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+      NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+      isPush: ${{ github.event_name == 'push' || github.event_name == 'workflow_dispatch' }}
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-tinytex@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -35,14 +41,40 @@ jobs:
           extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Build and deploy pkgdown site
+        if: contains(env.isPush, 'true')
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+
+      - name: Create website
+        if: contains(env.isPush, 'false')
+        run: |
+          pkgdown::build_site()
         shell: Rscript {0}
 
-      - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected]
+      - name: Create index file
+        if: contains(env.isPush, 'false')
+        run: |
+          echo '<!DOCTYPE html><html><head><meta http-equiv="refresh" content="0;URL=/dev/index.html" />  <script language="javascript"> window.location.replace('/dev/index.html')</script></head></html>' > ./docs/index.html
+
+      - name: Deploy to Netlify
+        if: contains(env.isPush, 'false')
+        id: netlify-deploy
+        uses: nwtgck/[email protected]
         with:
-          clean: false
-          branch: gh-pages
-          folder: docs
+          publish-dir: './docs'
+          production-branch: master
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message:
+            'Deploy from GHA: ${{ github.event.pull_request.title || github.event.head_commit.message }} (${{ github.sha }})'
+          # these all default to 'true'
+          enable-pull-request-comment: false
+          enable-commit-comment: false
+          # enable-commit-status: true
+          # overwrites-pull-request-comment: true
+        timeout-minutes: 1
diff --git a/R/plot_3d_structure_hires.R b/R/plot_3d_structure_hires.R
@@ -1,5 +1,26 @@
+#' Presents classification results on 3D structure
+#'
 #' @import r3dmol
 #'
+#' @param hires_params ...
+#' @param pdb_file_path ...
+#'
+#' @description Plots the color classification on supplied 3d structure.
+#'
+#' @return a r3dmol object.
+#'
+#' @seealso calculate_hires
+#'
+#' @examples
+#' dat <- HaDeX::read_hdx(...)
+#' pdb_file_path <- ...
+#' fit_k_params <- get_example_fit_k_params()
+#' control <- get_example_control()
+#' kin_dat <- prepare_kin_dat(dat)
+#' fit_values <- create_fit_dataset(kin_dat, control, fit_k_params)
+#' hires_params <- calculate_hires(fit_values)
+#' plot_3d_structure_hires(hires_params, pdb_file_path)
+#'
 #' @export
 
 plot_3d_structure_hires <- function(hires_params,

diff --git a/R/plot_cov_class.R b/R/plot_cov_class.R
@@ -1,4 +1,28 @@
+#' Plots coverage with classification results
+#'
 #' @importFrom ggplot2 geom_rect aes element_blank
+#'
+#' @param fit_values
+#' @param fractional ...
+#' @param interactive ...
+#'
+#' @description This function is used for visualization of the classification method
+#' for peptides. It uses the traditional form of coverage, with length present and easily
+#' estimated redundancy. It also allows to see if the tendencies for exchange are coherent
+#' in regions.
+#'
+#' @return a girafe object.
+#'
+#' @seealso create_fit_dataset
+#'
+#' @examples
+#' HaDeX::read_hdx(...)
+#' kin_dat <- prepare_kin_dat(dat, state = state_1)
+#' fit_k_params <- get_example_fit_k_params()
+#' control <- get_example_control()
+#' fit_values <- create_fit_dataset(kin_dat, control, fit_k_params)
+#' plot_cov_class(fit_values)
+#'
 #' @export
 plot_cov_class <- function(fit_values,
                            fractional = T,

diff --git a/R/plot_double_uc.R b/R/plot_double_uc.R
@@ -1,6 +1,31 @@
-## wrapper for GUI
-## for previous plot function for regular uc and fitted uc
-
+#' Plots two uc plots side by side
+#'
+#' @param fit_dat uptake data for selected peptide.
+#' @param fit_values fit values for selected peptide.
+#' @param replicate
+#' @param fractional
+#'
+#' @description This function plots two plots side by side for a peptide. The left
+#' plot is uc plot with fitted model with its components. The right plot is singular
+#' uc without logarithmic axis for the comparison of shape.
+#' Basically, this function calls for other functions and plots the results side by side.
+#' This function is aimed for the summary `Plots` panel in HRaDeXGUI and does not have
+#' an interactive mode.
+#'
+#' @return a ggplot object.
+#'
+#' @seelaso plot_fitted_uc plot_singular_uc
+#'
+#' @examples
+#' dat <- HaDeX::read_hdx(...)
+#' kin_dat <- prepare_kin_dat(dat, state = state_1)
+#' fit_dat <- kin_dat[kin_dat[["id"]]==1, ]
+#' fit_k_params <- get_example_fit_k_params()
+#' control <- get_example_control()
+#' fit_values_all <- create_fit_dataset(kin_dat, control, fit_k_params)
+#' fit_values <- fit_values_all[fit_values_all[["id"]]==1, ]
+#' plot_double_uc(fit_dat, fit_values)
+#'
 #' @export
 
 plot_double_uc <- function(fit_dat,

diff --git a/R/plot_estimated_k.R b/R/plot_estimated_k.R
@@ -1,4 +1,25 @@
+#' Plots estimated k
 #'
+#' @param hires_params data.frame with hires results, calculate using
+#' calculate_hires.
+#' @param interactive ...
+#'
+#' @description Plots the estimated k for residues. Estimated k for each are calculated
+#' from classification results, treating the n (population) as the probability of getting
+#' corresponding rate of exchange. The aggregation of results is described in the vignette.
+#'
+#' @return a girafe object.
+#'
+#' @seealso calculate_hires
+#'
+#' @examples
+#' dat <- HaDeX::read_hdx(...)
+#' kin_dat <- prepare_kin_dat(dat)
+#' fit_k_params <- get_example_fit_k_params()
+#' control <- get_example_control()
+#' fit_values <- create_fit_dataset(kin_dat, control, fit_k_params)
+#' hires_params <- calculate_hires(fit_values)
+#' plot_estimated_k(hires_params)
 #'
 #' @export
 

diff --git a/R/plot_fitted_uc.R b/R/plot_fitted_uc.R
@@ -1,8 +1,34 @@
+#' Plots uptake curve with fit components
+#'
 #' @importFrom gridExtra grid.arrange
 #' @importFrom ggplot2 stat_function geom_line annotate theme_bw geom_errorbar geom_linerange
 #' @importFrom dplyr summarize group_by
 #' @importFrom ggiraph geom_point_interactive geom_line_interactive
 #'
+#' @param fit_dat uptake data for selected peptide.
+#' @param fit_values fit values for selected peptide.
+#' @param replicate indicator if the replicate data is plotted, or aggregated.
+#' @param fractional ...
+#' @param interactive ...
+#'
+#' @description FUnction plots the uptake values for one, selected peptide. Alongside the
+#' fitted model is plotted in black, with its components (fast - red, medium - green,
+#' slow - blue). In case when peptide is classified as a edge case, the linear model is used.
+#'
+#' @return a ggplot object. Need converstion to girafe for interactivity.
+#'
+#' @seealso plot_lm
+#'
+#' @examples
+#' HaDeX::read_hdx(...)
+#' kin_dat <- prepare_kin_dat(dat, state = state_1)
+#' fit_dat <- kin_dat[kin_dat[["id"]]==1, ]
+#' fit_k_params <- get_example_fit_k_params()
+#' control <- get_example_control()
+#' fit_values_all <- create_fit_dataset(kin_dat, control, fit_k_params)
+#' fit_values <- fit_values_all[fit_values_all[["id"]]==1, ]
+#' plot_fitted_uc(fit_dat, fit_values)
+#'
 #' @export
 plot_fitted_uc <- function(fit_dat,
                            fit_values,

diff --git a/R/plot_hires.R b/R/plot_hires.R
@@ -4,8 +4,25 @@
 #' @importFrom ggiraph geom_rect_interactive girafe girafe_options opts_tooltip
 #' @importFrom glue glue
 #'
+#' @param hires_params data.frame with hires results, calculate using
+#' calculate_hires.
+#' @param interactive ...
+#'
+#' @description Plot the result of color classification analysis in
+#' high resolution in a linear form.
+#'
+#' @return a girafe object.
+#'
+#' @seealso calculate_hires
+#'
 #' @examples
 #' dat <- HaDeX::read_hdx()
+#' kin_dat <- prepare_kin_dat(dat, state = state_1)
+#' fit_k_params <- get_example_fit_k_params()
+#' control <- get_example_control()
+#' fit_values <- create_fit_dataset(kin_dat, control, fit_k_params)
+#' hires_params <- calculate_hires(fit_values)
+#' plot_hires(hires_params)
 #'
 #' @export
 

diff --git a/R/plot_interactive.R b/R/plot_interactive.R
@@ -1,5 +1,9 @@
+#' Wrapper for interactivity
+#'
 #' @importFrom ggiraph girafe opts_hover opts_sizing opts_hover_inv
 #'
+#' @description Currently not in use.
+#'
 #' @export plot_interactive
 
 plot_interactive <- function(plot_function, ...){

diff --git a/R/plot_lm.R b/R/plot_lm.R
@@ -15,7 +15,11 @@
 #' @seealso
 #'
 #' @examples
-#' dat <-
+#' dat <- HaDeX::read_hdx()
+#' kin_dat <- prepare_kin_dat(dat, state = state_1)
+#' fit_dat <- kin_dat[kin_dat[["id"]]==1, ]
+#' plot_lm(fit_dat, class_name = unique(fit_dat[["class_name"]]))
+#'
 #' @export plot_lm
 
 plot_lm <- function(fit_dat,