Merge pull request #11 from jumpingrivers/data-dir

Data directory

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^tfpbrowser\.Rproj$
 ^\.Rproj\.user$
 .lintr

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.gitignore

@@ -1,6 +1,55 @@
-.Rproj.user
+# {shinytest2}: Ignore new debug snapshots for `$expect_values()`
+*_.new.png
+
+# Prevent the in-repo small example dataset being over-written with production data
+inst/app/www/data/
+
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
+.RDataTmp
+
+# User-specific files
 .Ruserdata
-# {shinytest2}: Ignore new debug snapshots for `$expect_values()`
-*_.new.png
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/

DESCRIPTION

@@ -36,4 +36,4 @@ Suggests:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3

NAMESPACE

@@ -1,12 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(create_all_node_lookups)
-export(empty_treeview)
 export(get_cluster_ID)
-export(get_sequences_lookup)
 export(run_app)
-export(update_data)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
 importFrom(rlang,.env)

R/add_ext_resources.R

@@ -1,11 +1,18 @@
 #' Add external resources to the shiny app
 #'
-#' Function is internally used to add external
-#' resources inside the Shiny application.
-add_ext_resources = function() {
+#' Function is internally used to add external resources inside the Shiny application.
+#'
+#' @param   data_dir   The (server-side) file-path for the directory containing the data for
+#'   presentation. This should contain a `scanner_output` subdirectory, which will be mounted as
+#'   /data/scanner_output/ in the browser.
+
+add_ext_resources = function(data_dir) {
   shiny::addResourcePath(
     "www", system.file("app/www", package = "tfpbrowser", mustWork = TRUE)
   )
+  shiny::addResourcePath(
+    "data/scanner_output", file.path(data_dir, "scanner_output")
+  )
   shiny::tags$head(
     shinyjs::useShinyjs(),
     shiny::tags$link(rel = "stylesheet", type = "text/css", href = "www/tfpbrowser-style.css")

R/app_server.R

@@ -2,11 +2,34 @@
 #' @param input,output,session Internal parameters for `{shiny}`.
 #' @noRd
 app_server = function(input, output, session) {
+  data_dir = get_data_dir()
+
+  # Update the available treeviews & mutations
+  shiny::observe({
+    new_choices = c(
+      c("None" = ""),
+      available_treeview(data_dir = data_dir)
+    )
+    shiny::updateSelectInput(
+      session = session,
+      inputId = "widgetChoice",
+      choices = new_choices
+    )
+  })
+
+  shiny::observe({
+    mutation_set = available_mutations(data_dir = data_dir)
+    shiny::updateSelectInput(
+      session = session,
+      inputId = "mutationChoice",
+      choices = mutation_set
+    )
+  })
 
   # Load treeview -----------------------------------------------------------
   imported_ggtree = shiny::reactive({
     shiny::req(input$widgetChoice)
-    filename = get_filename(input$widgetChoice)
+    filename = get_filename(input$widgetChoice, data_dir)
     readRDS(filename)
   })
 
@@ -64,19 +87,18 @@ app_server = function(input, output, session) {
 
   # disable dropdown unless mutation treeview
   shiny::observe({
-    shiny::req(input$widgetChoice)
+    choice = ifelse(input$widgetChoice != "", input$widgetChoice, "")
     # toggle mutation dropdown
-    shinyjs::toggleState(id = "mutationChoice",
-                         condition = input$widgetChoice == "tree-mutations.rds")
+    shinyjs::toggleElement(id = "mutationChoice",
+                         condition = choice == "tree-mutations.rds")
     # toggle sequence dropdown
-    shinyjs::toggleState(id = "sequenceChoice",
-                         condition = input$widgetChoice == "tree-sequences.rds")
+    shinyjs::toggleElement(id = "sequenceChoice",
+                         condition = choice == "tree-sequences.rds")
     # select input for sequences
-    if (input$widgetChoice == "tree-sequences.rds") {
-      avail_seqs = data.table::as.data.table(available_sequences())
+    if (choice == "tree-sequences.rds") {
+      avail_seqs = data.table::as.data.table(available_sequences(data_dir))
       names(avail_seqs) = "Sequences"
-      shiny::updateSelectizeInput(inputId = "sequenceChoice",
-                                  label = "Select sequence",
+      shiny::updateSelectInput(inputId = "sequenceChoice",
                                   choices = avail_seqs
                                   )
     }
@@ -85,7 +107,7 @@ app_server = function(input, output, session) {
   # get selected nodes from mutation choice
   shiny::observeEvent(input$mutationChoice, {
 
-    nodeChoice = selected_mut_nodes(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
     node_map = imported_ggtree()$data[c("cluster_id", "node")]
@@ -107,7 +129,7 @@ app_server = function(input, output, session) {
   # get selected nodes from sequence choice
   shiny::observeEvent(input$sequenceChoice, {
 
-    nodeChoice = selected_seq_nodes(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
     node_map = imported_ggtree()$data[c("cluster_id", "node")]
@@ -131,7 +153,8 @@ app_server = function(input, output, session) {
     shiny::req(input$widgetChoice)
     shiny::req(input$treeview_selected)
     get_selected_cluster_id(widgetChoice = input$widgetChoice,
-                            treeviewSelected = utils::tail(input$treeview_selected, 1))
+                            treeviewSelected = utils::tail(input$treeview_selected, 1),
+                            data_dir = data_dir)
   }) %>%
     shiny::bindCache(input$widgetChoice, input$treeview_selected)
 
@@ -154,19 +177,22 @@ app_server = function(input, output, session) {
   # Tables Tab --------------------------------------------------------------
   tablesServer(
     "table1",
-    cluster_choice = selected_cluster_id
+    cluster_choice = selected_cluster_id,
+    data_dir = data_dir
   )
 
   # Plots Tab ----------------------------------------------------------
   plotsServer(
     "plot1",
-    cluster_choice = selected_cluster_id
+    cluster_choice = selected_cluster_id,
+    data_dir = data_dir
   )
 
   # RDS Tab ----------------------------------------------------------
   rdsServer(
     "rds1",
-    cluster_choice = selected_cluster_id
+    cluster_choice = selected_cluster_id,
+    data_dir = data_dir
   )
 
 } # end server function

R/app_ui.R

@@ -3,6 +3,8 @@
 #' @param request Internal parameter for `{shiny}`.
 #' @noRd
 app_ui = function(request) {
+  data_dir <- get_data_dir()
+
   shiny::tagList(
 
     shinyjs::useShinyjs(),
@@ -12,7 +14,7 @@ app_ui = function(request) {
       # title
       title = place_title_logo(),
 
-      header = add_ext_resources(),
+      header = add_ext_resources(data_dir),
       # theme
       theme = bslib::bs_theme(version = 4,
                               bootswatch = "minty",
@@ -57,34 +59,48 @@ app_ui = function(request) {
 
         # Bottom row - show tree (static html output from tfpscanner)
         shiny::fluidRow(
-
           shiny::column(12,
-
-                        # choose type of treeview
-                        shiny::radioButtons(inputId = "widgetChoice",
-                                            label = "Select treeview",
-                                            choices = c(c("None" = ""), available_treeview()),
-                                            inline = TRUE),
-
-                        # choose type of mutation
-                        shiny::selectizeInput(inputId = "mutationChoice",
-                                              label = "Select mutation",
-                                              choices = available_mutations()),
-
-                        # choose type of sequence
-                        shiny::selectizeInput(inputId = "sequenceChoice",
-                                              label = "Select sequence",
-                                              choices = NULL),
-
-                        # markdown files to add description
-                        shiny::uiOutput("tree_md_files"),
-
-                        # show treeview widget
-                        shiny::wellPanel(
-                          ggiraph::girafeOutput("treeview"),
-                          style = "background: white; height: 1800px;",
-                        ),
-                        shiny::br()
+            id="view-container",
+                        shiny::div(id="view-selection",
+                          htmltools::tags$details(
+                            id="sidebar-toggle",
+                            open="open",
+                            `aria-role`="button",
+                            `aria-label`="Toggle sidebar visibility",
+                            htmltools::tags$summary(
+                              shiny::span(">>"),
+                              shiny::span("<<")
+                            )
+                          ),
+                          # choose type of treeview
+                          shiny::selectInput(inputId = "widgetChoice",
+                                                label = "View",
+                                                choices = c("None" = ""),
+                                                selectize = FALSE),
+
+                          # choose type of mutation
+                          shiny::selectInput(inputId = "mutationChoice",
+                                                label = "Mutation",
+                                                choices = character(0),
+                                                selectize = FALSE),
+
+                          # choose type of sequence
+                          shiny::selectInput(inputId = "sequenceChoice",
+                                                label = "Sequence",
+                                                choices = NULL,
+                                                selectize = FALSE),
+            ),
+            shiny::div(id="view-graphic",
+                          # markdown files to add description
+                          shiny::uiOutput("tree_md_files"),
+
+                          # show treeview widget
+                          shiny::wellPanel(
+                            ggiraph::girafeOutput("treeview"),
+                            style = "background: white; height: 1800px;",
+                          ),
+                          shiny::br()
+            )
           )
         ) # end fluid row
       ), # end "data" page

R/config.R

@@ -0,0 +1,15 @@
+#' Obtain the optionally-specified data directory for the app
+#'
+#' The user can specify a data-directory by specifying the environment variable `APP_DATA_DIR`.
+#' When given, this directory must have subdirectories: `mutations`, `scanner_output`, `sequences`,
+#' `treeview`.
+#' When not specified, data will be taken from the package-embedded directory `/app/www/data`.
+#'
+#' @return   Scalar string. The data-directory for use in the app.
+
+get_data_dir <- function() {
+  Sys.getenv(
+    "APP_DATA_DIR",
+    system.file("app", "www", "data", package = "tfpbrowser")
+  )
+}

R/module_plots.R

@@ -16,8 +16,9 @@ plotsUI = function(id) {
 #' Plots tab Server
 #' @param id ID for shiny module namespacing
 #' @param cluster_choice which cluster to display the data for
+#' @param   data_dir   The data directory for the app.
 #' @noRd
-plotsServer = function(id, cluster_choice) {
+plotsServer = function(id, cluster_choice, data_dir) {
   shiny::moduleServer(id, function(input, output, session) {
     ns = session$ns # nolint
 
@@ -28,7 +29,7 @@ plotsServer = function(id, cluster_choice) {
 
     # all available plots
     all_files = shiny::reactive({
-      return(get_all_files(cluster_choice()))
+      return(get_all_files(cluster_choice(), data_dir = data_dir))
     }) %>%
       shiny::bindCache(cluster_choice())
 
@@ -47,19 +48,25 @@ plotsServer = function(id, cluster_choice) {
                                choices = all_images)
     })
 
-    # get plot file
+    # the path to the plot, from the server's perspective
     plot_file = shiny::reactive({
       shiny::req(cluster_choice())
-      plot_file = system.file("app", "www", "data", "scanner_output",
-                              cluster_choice(), input$plot_type,
-                              package = "tfpbrowser")
+      plot_file = file.path(data_dir, "scanner_output", cluster_choice(), input$plot_type)
       return(plot_file)
     }) %>%
       shiny::bindCache(cluster_choice(), input$plot_type)
 
+    # the path to the plot, from the browser's perspective
+    plot_url = shiny::reactive({
+      shiny::req(plot_file())
+
+      plot_subpath <- fs::path_rel(plot_file(), data_dir)
+      glue::glue("data/{plot_subpath}")
+    })
+
     # check if plots available
     plot_avail = shiny::reactive({
-      src = fs::path_rel(plot_file(), system.file("app", package = "tfpbrowser"))
+      src = plot_url()
       if (length(src) != 0) {
         return(grepl(".png", tolower(src)))
       } else {
@@ -70,9 +77,7 @@ plotsServer = function(id, cluster_choice) {
     # display plot if available
     output$display_plot = shiny::renderUI({
       if (plot_avail()) {
-        shiny::img(src = fs::path_rel(plot_file(),
-                                      system.file("app", package = "tfpbrowser")),
-                   width = "400px")
+        shiny::img(src = plot_url(), width = "400px")
       } else {
         shiny::p("No plots available.", style = "color: red; text-align: left")
       }