Allow setting a custom default dataset

R/app.R

@@ -2,8 +2,19 @@
 #'
 #' @param host The hostname to serve the application on.
 #' @param port The port to serve the application on.
+#' @param custom_dataset This allows to set a custom dataset (return value of
+#'   [analyze()]) as the default dataset of the UI.
 #'
 #' @export
-run_app <- function(host = "127.0.0.1", port = 3464) {
-  runApp(shinyApp(ui, server), host = host, port = port)
+run_app <- function(host = "127.0.0.1",
+                    port = 3464,
+                    custom_dataset = NULL) {
+  runApp(
+    shinyApp(
+      ui(custom_dataset = custom_dataset),
+      server(custom_dataset = custom_dataset)
+    ),
+    host = host,
+    port = port
+  )
 }

R/server.R

@@ -1,13 +1,16 @@
 #' Server implementing the main user interface.
 #' @noRd
-server <- function(input, output, session) {
+server <- function(custom_dataset = NULL) {
+  function(input, output, session) {
     dataset <- reactive({
       analysis <- if (input$dataset == "gtex_tissues") {
         ubigen::gtex_tissues
       } else if (input$dataset == "hpa_tissues") {
         ubigen::hpa_tissues
-    } else {
+      } else if (input$dataset == "gtex_all") {
         ubigen::gtex_all
+      } else {
+        custom_dataset
       }
 
       merge(analysis, ubigen::genes, by = "gene")
@@ -181,4 +184,5 @@ server <- function(input, output, session) {
     })
 
     output$gsea_plot_ranking <- plotly::renderPlotly(gsea_plot_ranking)
+  }
 }

R/ui.R

@@ -1,6 +1,6 @@
 #' Function for creating the main user interface.
 #' @noRd
-ui <- function() {
+ui <- function(custom_dataset = NULL) {
   div(
     custom_css(),
     rclipboard::rclipboardSetup(),
@@ -22,11 +22,19 @@ ui <- function() {
             selectInput(
               "dataset",
               label = strong("Expression dataset"),
-              list(
+              {
+                choices <- list(
                   "GTEx (across tissues and conditions)" = "gtex_all",
                   "GTEx (across tissues)" = "gtex_tissues",
                   "Human Protein Atlas (across tissues)" = "hpa_tissues"
                 )
+
+                if (!is.null(custom_dataset)) {
+                  c(list("Custom dataset" = "custom"), choices)
+                } else {
+                  choices
+                }
+              }
             ),
             selectInput(
               "cross_sample_metric",

man/run_app.Rd

@@ -4,12 +4,15 @@
 \alias{run_app}
 \title{Run the application server.}
 \usage{
-run_app(host = "127.0.0.1", port = 3464)
+run_app(host = "127.0.0.1", port = 3464, custom_dataset = NULL)
 }
 \arguments{
 \item{host}{The hostname to serve the application on.}
 
 \item{port}{The port to serve the application on.}
+
+\item{custom_dataset}{This allows to set a custom dataset (return value of
+\code{\link[=analyze]{analyze()}}) as the default dataset of the UI.}
 }
 \description{
 Run the application server.