From 9fb6ca428eb155b8c374871e6cb4d9990b2ad48a Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 18 Aug 2022 10:00:05 +0200
Subject: [PATCH] gsea: Move to separate module

---
 R/gsea.R    | 86 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 R/results.R | 68 ++----------------------------------------
 2 files changed, 88 insertions(+), 66 deletions(-)
 create mode 100644 R/gsea.R

diff --git a/R/gsea.R b/R/gsea.R
new file mode 100644
index 0000000..c090036
--- /dev/null
+++ b/R/gsea.R
@@ -0,0 +1,86 @@
+#' Create a GSEA page.
+#' @noRd
+gsea_ui <- function(id) {
+  verticalLayout(
+    div(
+      style = "margin-top: 16px",
+      plotly::plotlyOutput(NS(id, "plot")),
+    ),
+    div(
+      style = "margin-top: 16px",
+      DT::DTOutput(NS(id, "details"))
+    )
+  )
+}
+
+#' Create a server for the comparison editor.
+#'
+#' @param id ID for namespacing the inputs and outputs.
+#' @param ranking The ranking to be analyzed.
+#'
+#' @noRd
+gsea_server <- function(id, ranking) {
+  moduleServer(id, function(input, output, session) {
+    gsea_analysis <- reactive({
+      withProgress(
+        message = "Querying g:Profiler",
+        value = 0.0,
+        { # nolint
+          setProgress(0.2)
+          gprofiler2::gost(
+            ranking()[, gene],
+            custom_bg = NULL, # TODO
+            domain_scope = "custom_annotated"
+          )
+        }
+      )
+    }) |> bindCache(ranking())
+
+    output$plot <- plotly::renderPlotly({
+      gprofiler2::gostplot(
+        gsea_analysis(),
+        capped = FALSE,
+        interactive = TRUE
+      )
+    })
+
+    output$details <- DT::renderDT({
+      data <- data.table(gsea_analysis()$result)
+      setorder(data, p_value)
+
+      data[, total_ratio := term_size / effective_domain_size]
+      data[, query_ratio := intersection_size / query_size]
+      data[, increase := (query_ratio - total_ratio) / total_ratio]
+
+      data <- data[, .(
+        source,
+        term_name,
+        total_ratio,
+        query_ratio,
+        increase,
+        p_value
+      )]
+
+      DT::datatable(
+        data,
+        rownames = FALSE,
+        colnames = c(
+          "Source",
+          "Term",
+          "Total ratio",
+          "Query ratio",
+          "Increase",
+          "p-value"
+        ),
+        options = list(
+          pageLength = 25
+        )
+      ) |>
+        DT::formatRound("p_value", digits = 4) |>
+        DT::formatPercentage(
+          c("total_ratio", "query_ratio", "increase"),
+          digits = 2
+        )
+    })
+  })
+}
diff --git a/R/results.R b/R/results.R
index 899d5f9..eb712b6 100644
--- a/R/results.R
+++ b/R/results.R
@@ -152,11 +152,7 @@ results_ui <- function(id, options) {
           title = "g:Profiler",
           div(
             style = "margin-top: 16px",
-            plotly::plotlyOutput("gost_plot"),
-          ),
-          div(
-            style = "margin-top: 16px",
-            DT::DTOutput(NS(id, "gost_details"))
+            gsea_ui(NS(id, "gsea"))
           )
         )
       )
@@ -407,67 +403,7 @@ results_server <- function(id, options, analysis) {
       )
     })
 
-    gost <- reactive({
-      withProgress(
-        message = "Querying g:Profiler",
-        value = 0.0,
-        { # nolint
-          setProgress(0.2)
-          gprofiler2::gost(
-            results_filtered()[, gene],
-            custom_bg = preset()$gene_ids,
-            domain_scope = "custom_annotated"
-          )
-        }
-      )
-    }) |> bindCache(results_filtered(), preset())
-
-    output$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]
-      data[, increase := (query_ratio - total_ratio) / total_ratio]
-
-      data <- data[, .(
-        source,
-        term_name,
-        total_ratio,
-        query_ratio,
-        increase,
-        p_value
-      )]
-
-      dt <- DT::datatable(
-        data,
-        rownames = FALSE,
-        colnames = c(
-          "Source",
-          "Term",
-          "Total ratio",
-          "Query ratio",
-          "Increase",
-          "p-value"
-        ),
-        options = list(
-          pageLength = 25
-        )
-      ) |>
-        DT::formatRound("p_value", digits = 4) |>
-        DT::formatPercentage(
-          c("total_ratio", "query_ratio", "increase"),
-          digits = 2
-        )
-    })
+    gsea_server("gsea", results_filtered)
   })
 }