From 36546570e0604b986ac91b2bb06dfcbc506b831c Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Wed, 8 Dec 2021 14:38:38 +0100
Subject: [PATCH] Update gprofiler integration

---
 R/filters.R |  2 +-
 R/server.R  | 59 +++++++++++++++++++++++++++++++++++++++++------------
 R/ui.R      | 17 ++++++---------
 3 files changed, 53 insertions(+), 25 deletions(-)

diff --git a/R/filters.R b/R/filters.R
index 6859583..1091d82 100644
--- a/R/filters.R
+++ b/R/filters.R
@@ -22,7 +22,7 @@ filters_ui <- function(id) {
                     min = 0,
                     max = 100,
                     step = 1,
-                    value = 60
+                    value = 75
                 )
             ),
             tabPanelBody(
diff --git a/R/server.R b/R/server.R
index e5e21b1..c28b5f2 100644
--- a/R/server.R
+++ b/R/server.R
@@ -172,20 +172,53 @@ server <- function(input, output, session) {
         geposan::plot_boxplot(ranking(), gene_sets)
     })
 
-    output$gost <- plotly::renderPlotly({
-        if (input$enable_gost) {
-            result <- gprofiler2::gost(
-                results_filtered()[, gene],
-                ordered_query = TRUE
-            )
+    gost <- reactive({
+         withProgress(
+            message = "Querying g:Profiler",
+            value = 0.0,
+            { # nolint
+                setProgress(0.2)
+                gprofiler2::gost(results_filtered()[, gene])
+            }
+         )
+    })
 
-            gprofiler2::gostplot(
-                result,
-                capped = FALSE,
-                interactive = TRUE
+    output$gost_plot <- plotly::renderPlotly({
+        gprofiler2::gostplot(
+            gost(),
+            capped = FALSE,
+            interactive = TRUE
+        )
+    })
+
+    output$gost_details <- DT::renderDT({
+        data <- data.table(gost()$result)
+        setorder(data, p_value)
+
+        data[, total_ratio := term_size / effective_domain_size]
+        data[, query_ratio := intersection_size / query_size]
+
+        dt <- DT::datatable(
+            data[, .(source, term_name, total_ratio, query_ratio, p_value)],
+            rownames = FALSE,
+            colnames = c(
+                "Source",
+                "Term",
+                "Total ratio",
+                "Query ratio",
+                "p-Value"
+            ),
+            style = "bootstrap",
+            options = list(
+                pageLength = 25
             )
-        } else {
-            NULL
-        }
+        )
+
+        dt <- DT::formatRound(dt, "p_value", digits = 4)
+        dt <- DT::formatPercentage(
+            dt,
+            c("total_ratio", "query_ratio"),
+            digits = 1
+        )
     })
 }
diff --git a/R/ui.R b/R/ui.R
index 12ef353..029286b 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -85,18 +85,13 @@ ui <- div(
                         ),
                         tabPanel(
                             title = "g:Profiler",
-                            checkboxInput(
-                                "enable_gost",
-                                "Perform a gene set enrichment analysis on the \
-                                filtered result genes."
+                            div(
+                                style = "margin-top: 16px",
+                                plotly::plotlyOutput("gost_plot"),
                             ),
-                            conditionalPanel(
-                                "input.enable_gost == true",
-                                plotly::plotlyOutput(
-                                    "gost",
-                                    width = "100%",
-                                    height = "600px"
-                                )
+                            div(
+                                style = "margin-top: 16px",
+                                DT::DTOutput("gost_details")
                             )
                         )
                     )