Improve gene results tables

R/genes_table.R

@@ -0,0 +1,108 @@
+#' Construct UI for the genes table.
+#' @noRd
+genes_table_ui <- function(id) {
+  verticalLayout(
+    div(
+      style = "margin-top: 16px",
+      splitLayout(
+        cellWidths = "auto",
+        uiOutput(NS(id, "copy")),
+        downloadButton(
+          NS(id, "download"),
+          "Download CSV",
+          class = "btn-outline-primary"
+        )
+      )
+    ),
+    div(
+      style = "margin-top: 16px; margin-bottom: 8px;",
+      DT::DTOutput(NS(id, "genes"))
+    )
+  )
+}
+
+#' Server for the genes table.
+#'
+#' @param data A reactive containing the results to be displayed.
+#'
+#' @noRd
+genes_table_server <- function(id, data) {
+  moduleServer(id, function(input, output, session) {
+    output$copy <- renderUI({
+      data <- data()
+
+      gene_ids <- data[, gene]
+      names <- data[hgnc_name != "", hgnc_name]
+
+      genes_text <- paste(gene_ids, collapse = "\n")
+      names_text <- paste(names, collapse = "\n")
+
+      splitLayout(
+        cellWidths = "auto",
+        rclipboard::rclipButton(
+          "copy_ids_button",
+          "Copy gene IDs",
+          genes_text,
+          icon = icon("clipboard"),
+          class = "btn-outline-primary"
+        ),
+        rclipboard::rclipButton(
+          "copy_names_button",
+          "Copy HGNC symbols",
+          names_text,
+          icon = icon("clipboard"),
+          class = "btn-outline-primary"
+        )
+      )
+    })
+
+    output$download <- downloadHandler(
+      filename = "ubigen.csv",
+      content = \(file) fwrite(data(), file = file),
+      contentType = "text/csv"
+    )
+
+    output$genes <- DT::renderDT({
+      DT::datatable(
+        data()[, .(
+          "Gene" = glue::glue_data(
+            data(),
+            "<a href=\"https://gtexportal.org/home/gene/{hgnc_name}\" ",
+            "target=\"_blank\">{hgnc_name}</a>"
+          ),
+          "Rank" = rank,
+          "Percentile" = percentile,
+          "Score" = score,
+          "Median" = median_expression,
+          "Mean" = mean_expression,
+          "Standard deviation" = sd_expression,
+          "Expressed" = above_zero,
+          "Above median" = above_median,
+          "Above 95%" = above_95
+        )],
+        options = list(
+          dom = "frtip",
+          pageLength = 100
+        ),
+        rownames = FALSE,
+        escape = FALSE,
+        selection = "none"
+      ) |>
+        DT::formatPercentage(
+          c(
+            "Percentile",
+            "Score",
+            "Expressed",
+            "Above median",
+            "Above 95%"
+          ),
+          digits = 2,
+        ) |>
+        DT::formatRound(c(
+          "Median",
+          "Mean",
+          "Standard deviation"
+        ))
+    })
+  })
+}