Add rankings comparison section

R/server.R

@@ -105,24 +105,76 @@ server <- function(custom_dataset = NULL) {
       highlighted_genes = custom_genes()
     ))
 
-    selected_genes <- reactive({
+    selected_top_genes <- reactive({
       selected_points <- plotly::event_data("plotly_selected")
       ranked_data()[rank %in% selected_points$x]
     })
 
-    genes_table_server("selected_genes", reactive({
+    genes_table_server("selected_top_genes", reactive({
-      if (nrow(selected_genes()) > 0) {
+      if (nrow(selected_top_genes()) > 0) {
-        selected_genes()
+        selected_top_genes()
       } else {
         ranked_data()
       }
     }))
 
+    output$rankings_plot <- plotly::renderPlotly({
+      handle_axis <- function(ranking_id) {
+        if (ranking_id == "gtex_all") {
+          list(
+            ranking = rank_genes(ubigen::gtex_all),
+            label = "GTEx (across tissues and conditions)"
+          )
+        } else if (ranking_id == "gtex_tissues") {
+          list(
+            ranking = rank_genes(ubigen::gtex_tissues),
+            label = "GTEx (across tissues)"
+          )
+        } else if (ranking_id == "hpa_tissues") {
+          list(
+            ranking = rank_genes(ubigen::hpa_tissues),
+            label = "Human Protein Atlas (across tissues)"
+          )
+        } else if (ranking_id == "cmap") {
+          list(
+            ranking = rank_genes(ubigen::cmap),
+            label = "CMap"
+          )
+        } else {
+          list(
+            ranking = ranked_data(),
+            label = "Custom"
+          )
+        }
+      }
+
+      x <- handle_axis(input$ranking_x)
+      y <- handle_axis(input$ranking_y)
+
+      rankings_comparison_plot(
+        x$ranking,
+        y$ranking,
+        label_x = x$label,
+        label_y = y$label,
+        highlighted_genes = custom_genes(),
+        use_percentiles = input$rankings_comparison_mode == "percentiles"
+      )
+    })
+
+    selected_comparison_genes <- reactive({
+      selected_points <- plotly::event_data("plotly_selected")
+      ranked_data()[gene %chin% selected_points$customdata]
+    })
+
+    genes_table_server("selected_comparison_genes", reactive({
+      selected_comparison_genes()
+    }))
+
     gsea_genes <- reactive({
       sort(if (input$gsea_set == "top") {
         ranked_data()[rank >= input$gsea_ranks, gene]
       } else if (input$gsea_set == "selected") {
-        selected_genes()[, gene]
+        selected_top_genes()[, gene]
       } else {
         custom_genes()
       })

R/ui.R

@@ -126,7 +126,8 @@ ui <- function(custom_dataset = NULL) {
                 value = "top_genes",
                 div(paste0(
                   "Hover over the markers to see details on each gene. Click ",
-                  "or drag within the figure to select genes of interest."
+                  "or drag within the figure to select genes of interest. ",
+                  "Double-click removes the selection."
                 )),
                 plotly::plotlyOutput("scores_plot"),
                 div(class = "p-1"),
@@ -137,7 +138,67 @@ ui <- function(custom_dataset = NULL) {
                   "on."
                 )),
                 div(class = "p-1"),
-                genes_table_ui("selected_genes")
+                genes_table_ui("selected_top_genes")
+              ),
+              tabPanel(
+                "Compare rankings",
+                value = "rankings",
+                div(
+                  class = "flow-layout",
+                  selectInput(
+                    "ranking_y",
+                    label = NULL,
+                    list(
+                      "Custom" = "custom",
+                      "GTEx (across tissues and conditions)" = "gtex_all",
+                      "GTEx (across tissues)" = "gtex_tissues",
+                      "Human Protein Atlas (across tissues)" = "hpa_tissues",
+                      "CMap" = "cmap"
+                    ),
+                    selected = "cmap"
+                  ),
+                  span(
+                    style = paste0(
+                      "display: inline-block;",
+                      "margin-right: 12px;",
+                      "padding: 0.375rem 0.75rem;"
+                    ),
+                    "~"
+                  ),
+                  selectInput(
+                    "ranking_x",
+                    label = NULL,
+                    list(
+                      "Custom" = "custom",
+                      "GTEx (across tissues and conditions)" = "gtex_all",
+                      "GTEx (across tissues)" = "gtex_tissues",
+                      "Human Protein Atlas (across tissues)" = "hpa_tissues",
+                      "CMap" = "cmap"
+                    )
+                  ),
+                  selectInput(
+                    "rankings_comparison_mode",
+                    label = NULL,
+                    list(
+                      "Compare scores" = "scores",
+                      "Compare percentiles" = "percentiles"
+                    )
+                  )
+                ),
+                div(class = "p-1"),
+                div(paste0(
+                  "Hover over the markers to see the HGNC symbols for the ",
+                  "genes. Click or draw within the figure to select genes of ",
+                  "interest. Double-click removes the selection."
+                )),
+                div(class = "p-1"),
+                plotly::plotlyOutput(
+                  "rankings_plot",
+                  width = "800px",
+                  height = "800px"
+                ),
+                div(class = "p-1"),
+                genes_table_ui("selected_comparison_genes")
               ),
               tabPanel(
                 "GSEA",