Add options to configure default gene sets

R/app.R

@@ -1,15 +1,40 @@
 #' Run the application server.
 #'
+#' @param gene_sets A list of predefined gene sets. This should be a named list
+#'   containing vectors of gene IDs for each set. The names will be used to
+#'   present the gene set throughout the user interface. You have to provide *at
+#'   least one gene set* which will be selected as the initial reference gene
+#'   set.
+#' @param species_sets A list of predefined species sets. This should be a named
+#'   list containing vectors of species IDs for each set. The names will be used
+#'   to present the species set throughout the user interface.
+#' @param locked Whether the application should be locked and prohibit
+#'   performing custom analyses. If this is set to `TRUE`, only the predefined
+#'   gene and species sets are available for customizing the analysis. This may
+#'   be useful to limit resource usage on a publicly available instance.
 #' @param port The port to serve the application on.
 #'
 #' @export
-run_app <- function(port = 3464) {
-    # These function calls make the required java scripts available.
+run_app <- function(gene_sets,
+                    species_sets = NULL,
+                    locked = FALSE,
+                    port = 3464) {
+    stopifnot(!is.null(gene_sets) & !is.null(gene_sets[[1]]))
 
+    # These function calls make the required java scripts available.
     shinyjs::useShinyjs()
     rclipboard::rclipboardSetup()
 
-    # Actually run the app.
+    # Bundle of global options to redue broilerplate.
+    options <- list(
+        gene_sets = gene_sets,
+        species_sets = species_sets,
+        locked = locked
+    )
 
-    shiny::runApp(shiny::shinyApp(ui, server), port = port)
+    # Actually run the app.
+    shiny::runApp(
+        shiny::shinyApp(ui(options), server(options)),
+        port = port
+    )
 }