Move filtering to tabs that use it

R/details.R

@@ -2,6 +2,7 @@
 #' @noRd
 details_ui <- function(id) {
   verticalLayout(
+    filters_ui(NS(id, "filters")),
     div(
       style = "margin-top: 16px",
       splitLayout(
@@ -20,12 +21,13 @@ details_ui <- function(id) {
 #' Server for the detailed results panel.
 #'
 #' @param options Global options for the application.
-#' @param filtered_results A reactive containing the prefiltered results to be
+#' @param results A reactive containing the results to be displayed.
-#'   displayed.
 #'
 #' @noRd
-details_server <- function(id, options, filtered_results) {
+details_server <- function(id, options, results) {
   moduleServer(id, function(input, output, session) {
+    filtered_results <- filters_server("filters", results)
+
     output$copy <- renderUI({
       results <- filtered_results()
 

R/filters.R

@@ -1,16 +1,19 @@
 # Construct UI for the filter editor.
 filters_ui <- function(id) {
+  div(
+    class = "well",
+    style = "margin-top: 24px; margin-bottom: 16px; padding-top: 24px;",
     verticalLayout(
-    h3("Filter criteria"),
+      radioButtons(
-    selectInput(
         NS(id, "method"),
-      "Filter method",
+        label = NULL,
         choices = list(
-        "Percentiles" = "percentile",
+          "Filter percentiles" = "percentile",
-        "Scores" = "score",
+          "Filter scores" = "score",
-        "Ranks" = "rank",
+          "Filter ranks" = "rank",
-        "None" = "none"
+          "No filtering" = "none"
-      )
+        ),
+        inline = TRUE
       ),
       tabsetPanel(
         id = NS(id, "sliders"),
@@ -19,7 +22,7 @@ filters_ui <- function(id) {
           value = "percentile",
           sliderInput(
             NS(id, "percentile"),
-          label = "Included percentiles",
+            label = NULL,
             post = "%",
             min = 0,
             max = 100,
@@ -31,19 +34,18 @@ filters_ui <- function(id) {
           value = "score",
           sliderInput(
             NS(id, "score"),
-          label = "Included scores",
+            label = NULL,
-          post = "%",
             min = 0,
-          max = 100,
+            max = 1,
-          step = 1,
+            step = 0.01,
-          value = c(90, 100)
+            value = c(0.9, 1.0)
           )
         ),
         tabPanelBody(
           value = "rank",
           sliderInput(
             NS(id, "rank"),
-          label = "Included ranks",
+            label = NULL,
             min = 1,
             max = 2000,
             step = 10,
@@ -63,6 +65,7 @@ filters_ui <- function(id) {
         value = c(0, 150)
       )
     )
+  )
 }
 
 # Construct server for the filter editor.
@@ -90,15 +93,9 @@ filters_server <- function(id, results) {
             rank >= (1 - (input$percentile[2] / 100)) * n_ranks
         ]
       } else if (input$method == "score") {
-        results[
+        results[score >= input$score[1] & score <= input$score[2]]
-          score >= input$score[1] / 100 &
-            score <= input$score[2] / 100
-        ]
       } else if (input$method == "rank") {
-        results[
+        results[rank >= input$rank[1] & rank <= input$rank[2]]
-          rank >= input$rank[1] &
-            rank <= input$rank[2]
-        ]
       } else {
         results
       }

R/gsea.R

@@ -2,6 +2,12 @@
 #' @noRd
 gsea_ui <- function(id) {
   verticalLayout(
+    filters_ui(NS(id, "filters")),
+    actionButton(
+      NS(id, "gsea_run"),
+      "Update analysis",
+      class = "btn-primary"
+    ),
     div(
       style = "margin-top: 16px",
       plotly::plotlyOutput(NS(id, "plot")),
@@ -21,6 +27,8 @@ gsea_ui <- function(id) {
 #' @noRd
 gsea_server <- function(id, ranking) {
   moduleServer(id, function(input, output, session) {
+    ranking_filtered <- filters_server("filters", ranking)
+
     gsea_analysis <- reactive({
       withProgress(
         message = "Querying g:Profiler",
@@ -28,13 +36,15 @@ gsea_server <- function(id, ranking) {
         { # nolint
           setProgress(0.2)
           gprofiler2::gost(
-            ranking()[, gene],
+            ranking_filtered()$gene,
-            custom_bg = NULL, # TODO
+            custom_bg = ranking()$gene,
             domain_scope = "custom_annotated"
           )
         }
       )
-    }) |> bindCache(ranking())
+    }) |>
+      bindCache(ranking_filtered()) |>
+      bindEvent(input$gsea_run, ignoreNULL = FALSE)
 
     output$plot <- plotly::renderPlotly({
       gprofiler2::gostplot(

R/results.R

@@ -19,8 +19,7 @@ results_ui <- function(id, options) {
     sidebarPanel(
       width = 3,
       comparison_editor_ui(NS(id, "comparison_editor"), options),
-      methods_ui(NS(id, "methods"), options),
+      methods_ui(NS(id, "methods"), options)
-      filters_ui(NS(id, "filters"))
     ),
     mainPanel(
       width = 9,
@@ -150,14 +149,11 @@ results_ui <- function(id, options) {
         ),
         tabPanel(
           title = "g:Profiler",
-          div(
-            style = "margin-top: 16px",
           gsea_ui(NS(id, "gsea"))
         )
       )
     )
   )
-  )
 }
 
 #' Application logic for the results page.
@@ -198,11 +194,8 @@ results_server <- function(id, options, analysis) {
       )
     })
 
-    # Apply the filters.
-    results_filtered <- filters_server("filters", results)
-
     # Server for the detailed results panel.
-    details_server("results", options, results_filtered)
+    details_server("results", options, results)
 
     output$rank_plot <- plotly::renderPlotly({
       preset <- preset()
@@ -403,7 +396,7 @@ results_server <- function(id, options, analysis) {
       )
     })
 
-    gsea_server("gsea", results_filtered)
+    gsea_server("gsea", results)
   })
 }