From 90c9d18f261b3ffe4d4a4c14ec23ec677cb79174 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 2 Jun 2022 10:17:49 +0200
Subject: [PATCH] Add gprofiler integration

---
 DESCRIPTION |  1 +
 R/server.R  | 69 ++++++++++++++++++++++++++++++++++++++++++++++++++---
 R/style.R   |  9 ++++++-
 R/ui.R      | 36 ++++++++++++++++++++++++++++
 4 files changed, 111 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 12c3576..b7d0656 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,5 +25,6 @@ Imports:
     DT,
     plotly,
     glue,
+    gprofiler2,
     shiny,
     shinyvs
diff --git a/R/server.R b/R/server.R
index d5a8669..e637895 100644
--- a/R/server.R
+++ b/R/server.R
@@ -76,17 +76,80 @@ server <- function(input, output, session) {
     highlighted_genes = custom_genes()
   ))
 
-  output$selected_genes <- DT::renderDataTable({
+  selected_genes <- reactive({
     selected_points <- plotly::event_data("plotly_selected")
+    ranked_data()[rank %in% selected_points$x]
+  })
 
-    data <- if (is.null(selected_points)) {
+  output$selected_genes <- DT::renderDataTable({
+    data <- if (length(selected_genes()) > 0) {
       ranked_data()
     } else {
-      ranked_data()[rank %in% selected_points$x]
+      selected_genes()
     }
 
     genes_table(data)
   })
+
+  gsea_genes <- reactive({
+    sort(if (input$gsea_set == "top") {
+      ranked_data()[rank >= input$gsea_ranks, gene]
+    } else if (input$gsea_set == "selected") {
+      selected_genes()[, gene]
+    } else {
+      custom_genes()
+    })
+  })
+
+  gsea_result <- reactive({
+    withProgress(
+      message = "Querying g:Profiler",
+      value = 0.0,
+      { # nolint
+        setProgress(0.2)
+        gprofiler2::gost(gsea_genes())
+      }
+    )
+  }) |>
+    bindCache(gsea_genes()) |>
+    bindEvent(input$gsea_run, ignoreNULL = FALSE)
+
+  output$gsea_plot <- plotly::renderPlotly({
+    gprofiler2::gostplot(gsea_result(), interactive = TRUE)
+  })
+
+  output$gsea_details <- DT::renderDT({
+    data <- data.table(gsea_result()$result)
+    setorder(data, p_value)
+
+    data[, total_ratio := term_size / effective_domain_size]
+    data[, query_ratio := intersection_size / query_size]
+
+    data <- data[, .(
+      source,
+      term_name,
+      total_ratio,
+      query_ratio,
+      p_value
+    )]
+
+    DT::datatable(
+      data,
+      rownames = FALSE,
+      colnames = c(
+        "Source",
+        "Term",
+        "Total ratio",
+        "Query ratio",
+        "p-value"
+      ),
+      options = list(
+        pageLength = 25
+      )
+    ) |>
+      DT::formatRound("p_value", digits = 4) |>
+      DT::formatPercentage(c("total_ratio", "query_ratio"), digits = 1)
+  })
 }
 
 #' Create a displayable data table from the gene results data.
diff --git a/R/style.R b/R/style.R
index 2bf4c58..5eabdeb 100644
--- a/R/style.R
+++ b/R/style.R
@@ -2,6 +2,13 @@
 #' @noRd
 custom_css <- function() {
   tags$head(
-    tags$style(".nav-hidden { height: 0 }")
+    tags$style(HTML(
+      ".nav-hidden { height: 0 }",
+      ".flow-layout > div {",
+      "display: inline-block;",
+      "vertical-align: top;",
+      "margin-right: 12px;",
+      "}"
+    ))
   )
 }
diff --git a/R/ui.R b/R/ui.R
index f87a655..0294337 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -81,6 +81,42 @@ ui <- function() {
               )),
               div(class = "p-1"),
               DT::dataTableOutput("selected_genes")
+            ),
+            tabPanel(
+              "GSEA",
+              value = "gsea",
+              div(
+                class = "flow-layout",
+                selectInput(
+                  "gsea_set",
+                  label = NULL,
+                  list(
+                    "Top genes" = "top",
+                    "Selected genes" = "selected",
+                    "Your genes" = "custom"
+                  )
+                ),
+                conditionalPanel(
+                  "input.gsea_set == 'top'",
+                  sliderInput(
+                    "gsea_ranks",
+                    label = NULL,
+                    min = 10,
+                    max = 1000,
+                    value = 100,
+                    step = 10,
+                    ticks = FALSE
+                  )
+                ),
+                actionButton(
+                  "gsea_run",
+                  "Update analysis",
+                  class = "btn-primary"
+                )
+              ),
+              plotly::plotlyOutput("gsea_plot"),
+              div(class = "p-2"),
+              DT::dataTableOutput("gsea_details")
             )
           )
         )