All features 202403

.Rbuildignore

@@ -7,3 +7,5 @@
 ^\.github$
 ^LICENSE\.md$
 _\.new\.png$
+^doc$
+^Meta$

.Rprofile

@@ -1 +1,10 @@
 source("renv/activate.R")
+
+options("repos" = c(
+  "BioCsoft" = "https://bioconductor.org/packages/3.16/bioc",
+  "BioCann" = "https://bioconductor.org/packages/3.16/data/annotation",
+  "BioCexp" = "https://bioconductor.org/packages/3.16/data/experiment",
+  "BioCworkflows" = "https://bioconductor.org/packages/3.16/workflows",
+  "BioCbooks" = "https://bioconductor.org/packages/3.16/books",
+  "CRAN" = "https://cloud.r-project.org"
+))

.github/workflows/check-standard.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -28,3 +28,5 @@ jobs:
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.gitignore

@@ -53,3 +53,6 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+inst/doc
+/doc/
+/Meta/

.renvignore

@@ -0,0 +1,2 @@
+scripts/create_browser_data.R
+inst/app/www/data/

DESCRIPTION

@@ -9,16 +9,19 @@ License: MIT + file LICENSE
 Depends: 
     R (>= 4.0.0)
 Imports:
+    bsicons,
     bslib,
     data.table,
     dplyr,
     fs,
     ggiraph (>= 0.8.4),
     ggplot2,
+    ggtree,
     glue,
     htmltools,
     janitor,
     magrittr,
+    markdown,
     purrr,
     reactable,
     readr,
@@ -29,11 +32,15 @@ Imports:
     stringr,
     tibble
 Suggests:
-    ggtree,
+    knitr,
+    rmarkdown,
     shinytest2,
     testthat,
     usethis
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
+Remotes: 
+    YuLab-SMU/ggtree@daf3371
+VignetteBuilder: knitr

R/app_server.R

@@ -19,10 +19,11 @@ app_server = function(input, output, session) {
 
   shiny::observe({
     mutation_set = available_mutations(data_dir = data_dir)
-    shiny::updateSelectInput(
+    shiny::updateSelectizeInput(
       session = session,
       inputId = "mutationChoice",
-      choices = mutation_set
+      choices = mutation_set,
+      server = TRUE
     )
   })
 
@@ -36,77 +37,54 @@ app_server = function(input, output, session) {
   # create ggiraph output from saved ggplot2 outputs
   output$treeview = ggiraph::renderGirafe({
     shiny::req(input$widgetChoice)
-    # define tooltip
-    tooltip_css = paste0(
-      "background-color:black;",
-      "color:grey;",
-      "padding:14px;",
-      "border-radius:8px;",
-      "font-family:\"Courier New\",monospace;"
-    )
-    # set options
-    if (input$widgetChoice == "tree-mutations.rds") {
-      girafe_options = list(
-        ggiraph::opts_selection(css = "fill:red;"),
-        ggiraph::opts_selection_inv(css = "fill:grey;"),
-        ggiraph::opts_sizing(rescale = FALSE),
-        ggiraph::opts_zoom(max = 5),
-        ggiraph::opts_tooltip(
-          css = tooltip_css,
-          use_fill = FALSE
-        )
-      )
+
+    # set the relative height/width of the ggiraph-based graphs
+    is_dendrogram = grepl("^tree-", x = input$widgetChoice)
+    width = shinybrowser::get_width() / 72
+    height = if (is_dendrogram) {
+      (1800 - 40) / 72
     } else {
-      girafe_options = list(
-        ggiraph::opts_selection(type = "single"),
-        ggiraph::opts_sizing(rescale = FALSE),
-        ggiraph::opts_zoom(max = 5),
-        ggiraph::opts_tooltip(
-          css = tooltip_css,
-          use_fill = FALSE
-        )
-      )
+      (600 - 40) / 72
     }
-    # set size
-    w = shinybrowser::get_width() / 72
-    h = (1800 - 40) / 72
-    # make tree
-    suppressWarnings(
-      ggiraph::girafe(
-        ggobj = imported_ggtree(),
-        width_svg = w,
-        height_svg = h,
-        options = girafe_options
-      )
+
+    create_girafe(
+      ggobj = imported_ggtree(),
+      widget_choice = input$widgetChoice,
+      width_svg = width,
+      height_svg = height,
+      suppress_warnings = TRUE
     )
   }) %>%
     shiny::bindCache(input$widgetChoice)
 
-
-# Mutation colouring ------------------------------------------------------
+  # Mutation colouring ------------------------------------------------------
 
   # disable dropdown unless mutation treeview
   shiny::observe({
     choice = ifelse(input$widgetChoice != "", input$widgetChoice, "")
     # toggle mutation dropdown
-    shinyjs::toggleElement(id = "mutationChoice",
-                         condition = choice == "tree-mutations.rds")
+    shinyjs::toggleElement(
+      id = "mutationChoice",
+      condition = choice == "tree-mutations.rds"
+    )
     # toggle sequence dropdown
-    shinyjs::toggleElement(id = "sequenceChoice",
-                         condition = choice == "tree-sequences.rds")
+    shinyjs::toggleElement(
+      id = "sequenceChoice",
+      condition = choice == "tree-sequences.rds"
+    )
     # select input for sequences
     if (choice == "tree-sequences.rds") {
-      avail_seqs = data.table::as.data.table(available_sequences(data_dir))
-      names(avail_seqs) = "Sequences"
-      shiny::updateSelectInput(inputId = "sequenceChoice",
-                                  choices = avail_seqs
-                                  )
+      avail_seqs = available_sequences(data_dir)
+      shiny::updateSelectizeInput(
+        inputId = "sequenceChoice",
+        choices = avail_seqs,
+        server = TRUE
+      )
     }
   })
 
   # get selected nodes from mutation choice
   shiny::observeEvent(input$mutationChoice, {
-
     nodeChoice = selected_mut_nodes(input$mutationChoice, data_dir)
 
     # the 'node' column contains integers that define the IDs for graph-nodes in the htmlwidget
@@ -124,11 +102,10 @@ app_server = function(input, output, session) {
     )
   })
 
-# Sequence colouring ------------------------------------------------------
+  # Sequence colouring ------------------------------------------------------
 
   # get selected nodes from sequence choice
   shiny::observeEvent(input$sequenceChoice, {
-
     nodeChoice = selected_seq_nodes(input$sequenceChoice, data_dir)
 
     # the 'node' column contains integers that define the IDs for graph-nodes in the htmlwidget
@@ -146,15 +123,17 @@ app_server = function(input, output, session) {
     )
   })
 
-# Get click ---------------------------------------------------------------
+  # Get click ---------------------------------------------------------------
 
   # get selected cluster id based on widget choice
   selected_cluster_id = shiny::reactive({
     shiny::req(input$widgetChoice)
     shiny::req(input$treeview_selected)
-    get_selected_cluster_id(widgetChoice = input$widgetChoice,
-                            treeviewSelected = utils::tail(input$treeview_selected, 1),
-                            data_dir = data_dir)
+    get_selected_cluster_id(
+      widgetChoice = input$widgetChoice,
+      treeviewSelected = utils::tail(input$treeview_selected, 1),
+      data_dir = data_dir
+    )
   }) %>%
     shiny::bindCache(input$widgetChoice, input$treeview_selected)
 
@@ -169,9 +148,10 @@ app_server = function(input, output, session) {
     shiny::req(input$widgetChoice)
     fname = stringr::str_replace(input$widgetChoice, ".rds", ".md")
     shiny::includeMarkdown(system.file("app", "www", "content", "treeview",
-                                       fname,
-                                       package = "tfpbrowser",
-                                       mustWork = TRUE))
+      fname,
+      package = "tfpbrowser",
+      mustWork = TRUE
+    ))
   })
 
   # Tables Tab --------------------------------------------------------------
@@ -194,5 +174,4 @@ app_server = function(input, output, session) {
     cluster_choice = selected_cluster_id,
     data_dir = data_dir
   )
-
 } # end server function