Merge pull request #14 from jumpingrivers/ggiraph-demo

Ggiraph demo

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tfpbrowser
 Title: Builds Shiny application for 'tfpscanner' outputs
-Version: 0.0.5
+Version: 0.0.6
 Authors@R: 
     person("Jumping", "Rivers", , "[email protected]", role = c("aut", "cre"))
 Description: An R package to contain the code for the Shiny app to explore the 
@@ -12,6 +12,8 @@ Imports:
     bslib,
     dplyr,
     fs,
+    ggplot2,
+    ggiraph,
     glue,
     htmltools,
     janitor,
@@ -30,5 +32,5 @@ Suggests:
     usethis
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 LazyData: true

NEWS.md

@@ -1,3 +1,10 @@
+# tfpbrowser 0.0.6 _2022-11-08_
+
+- Switch to using rds inputs instead of html inputs
+- Use {ggiraph} widget as input to folder selection
+- Add functions to parse tooltip and extract cluster id
+- Remove unnecessary html files
+
 # tfpbrowser 0.0.5 _2022-11-02_
 
 - Move panels from RHS to collapsible above

R/app_server.R

@@ -16,37 +16,61 @@ app_server = function(input, output, session) {
                                      mustWork = TRUE)),
                        server = TRUE)
 
-  # load static html for treeview
-  output$treeview = shiny::renderUI({
+
+
+  # Load treeview -----------------------------------------------------------
+
+  # create plotly output from saved ggplot2 outputs
+  output$treeview = ggiraph::renderGirafe({
     filename = get_filename(input$widgetChoice)
-    shiny::div(
-      style = "width:100%; align:center",
-      id = "treeview",
-      htmltools::tags$iframe(src = filename,
-                             width = "100%",
-                             height = 600)
+    g = readRDS(filename)
+    tooltip_css = paste0(
+      "background-color:black;",
+      "color:grey;",
+      "padding:14px;",
+      "border-radius:8px;",
+      "font-family:\"Courier New\",monospace;"
     )
+    suppressWarnings(ggiraph::girafe(ggobj = g,
+                    options = list(
+                      ggiraph::opts_selection(
+                        type = "single"),
+                      ggiraph::opts_sizing(
+                        width = 0.8),
+                      ggiraph::opts_tooltip(
+                        css = tooltip_css,
+                        use_fill = FALSE)
+                      )
+                    ))
   })
 
-  # Choose Cluster ID -------------------------------------------------------
-  number_from_cluster_mod = cluster_idServer("choice1")
+  # get selected cluster id based on widget choice
+  selected_cluster_id = shiny::reactive({
+    get_selected_cluster_id(widgetChoice = input$widgetChoice,
+                            treeviewSelected = input$treeview_selected)
+  })
+
+  # output result of click
+  output$select_text = shiny::renderText({
+    paste("You have selected cluster ID:", selected_cluster_id())
+  })
 
   # Tables Tab --------------------------------------------------------------
   tablesServer(
     "table1",
-    cluster_choice = number_from_cluster_mod
+    cluster_choice = selected_cluster_id
   )
 
   # Plots Tab ----------------------------------------------------------
   plotsServer(
     "plot1",
-    cluster_choice = number_from_cluster_mod
+    cluster_choice = selected_cluster_id
   )
 
   # RDS Tab ----------------------------------------------------------
   rdsServer(
     "rds1",
-    cluster_choice = number_from_cluster_mod
+    cluster_choice = selected_cluster_id
   )
 
 } # end server function

R/app_ui.R

@@ -31,8 +31,11 @@ app_ui = function(request) {
                           # preview of expandable section
                           htmltools::tags$summary("Download Files (click to expand)"),
 
-                          # choose cluster id
-                          cluster_idUI("choice1"),
+                          shiny::br(),
+
+                          # text to print choice
+                          shiny::textOutput("select_text"),
+                          shiny::br(),
 
                           # output options
                           shiny::tabsetPanel(id = "plot_tabs",
@@ -67,10 +70,9 @@ app_ui = function(request) {
 
             # show treeview widget
             shiny::wellPanel(
-              shiny::htmlOutput("treeview"),
+              ggiraph::girafeOutput("treeview"),
               style = "background: white",
             ),
-
             shiny::br()
           )
         ) # end fluid row

R/utils.R

@@ -2,11 +2,14 @@
 #' @param type Character string detailing type of widget to show
 get_filename = function(type) {
   filename = switch(type,
-                    "Logistic growth rate" = "tree-logistic_growth_rate-2021-11-27.html", # nolint
-                    "Simple logistic growth rate" = "tree-simple_logistic_growth_rate-2021-11-27.html", # nolint
-                    "Simple trait log odds" = "tree-sim_trait_logodds-2021-11-27.html" # nolint
+                    "Logistic growth rate" = "tree-logistic_growth_rate.rds", # nolint
+                    "Simple logistic growth rate" = "tree-simple_logistic_growth_rate.rds", # nolint
+                    "Simple trait log odds" = "tree-sim_trait_logodds.rds" # nolint
   )
-  filename = file.path("www", "data", "treeview", filename)
+  filename = system.file("app", "www", "data", "treeview",
+                         filename,
+                         package = "tfpbrowser",
+                         mustWork = TRUE)
   return(filename)
 }
 
@@ -134,3 +137,31 @@ downloader_tab_panel = function(title,
     )
   )
 }
+
+#' function to get node id from data_id column of ggplot
+#' @param tooltip_input Character vector of tooltip content
+get_cluster_ID = function(tooltip_input) {
+  # start searching the string after the "Cluster.ID" text
+  # until the next new line
+  match_matrix = stringr::str_match(tooltip_input, r"(Cluster.ID\s+#(\d+))")
+  cluster_ids = as.numeric(match_matrix[, 2])
+  return(cluster_ids)
+}
+
+#' function to get node id from data_id column of ggplot
+#' @param widgetChoice From click of radio button to select widget to display
+#' @param treeviewSelected Output from clicking on treeview plot
+get_selected_cluster_id = function(widgetChoice,
+                                   treeviewSelected) {
+  filename = get_filename(widgetChoice)
+  g = readRDS(filename)
+  built = suppressWarnings(ggplot2::ggplot_build(g))
+  n_layers = length(built$data)
+  ids = built$data[n_layers][[1]]["data_id"]
+  tooltips = built$data[n_layers][[1]]$tooltip
+
+  tooltip_ids = get_cluster_ID(tooltips)
+  ids$cluster_ids = tooltip_ids
+  selected_cluster = as.numeric(ids[which(ids$data_id == treeviewSelected), 2])
+  return(selected_cluster)
+}