Separate reference and comparison gene sets

R/app.R

@@ -1,13 +1,14 @@
 #' Run the application server.
 #'
-#' @param gene_sets A list of predefined gene sets. This should be a named list
+#' @param reference_gene_sets A list of predefined gene sets to be used as
-#'   containing vectors of gene IDs for each set. The names will be used to
+#'   reference genes. This should be a named list containing vectors of gene IDs
-#'   present the gene set throughout the user interface. You have to provide *at
+#'   for each set. You have to provide *at least one gene set* which will be
-#'   least one gene set* which will be selected as the initial reference gene
+#'   selected as the initial reference gene set.
-#'   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 comparison_gene_sets A named list of predefined gene sets to be used
+#'   as comparison genes.
 #' @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
@@ -16,12 +17,13 @@
 #' @param port The port to serve the application on.
 #'
 #' @export
-run_app <- function(gene_sets,
+run_app <- function(reference_gene_sets,
                     species_sets = NULL,
+                    comparison_gene_sets = NULL,
                     locked = FALSE,
                     title = "Gene Position Analysis",
                     port = 3464) {
-  stopifnot(!is.null(gene_sets) & !is.null(gene_sets[[1]]))
+  stopifnot(!is.null(reference_gene_sets) & !is.null(reference_gene_sets[[1]]))
 
   # These function calls make the required java scripts available.
   shinyjs::useShinyjs()
@@ -29,8 +31,9 @@ run_app <- function(gene_sets,
 
   # Bundle of global options to redue broilerplate.
   options <- list(
-    gene_sets = gene_sets,
+    reference_gene_sets = reference_gene_sets,
     species_sets = species_sets,
+    comparison_gene_sets = comparison_gene_sets,
     locked = locked,
     title = title
   )

R/comparison_editor.R

@@ -11,7 +11,7 @@ comparison_editor_ui <- function(id, options) {
       choices = c(
         "Your genes",
         "Random genes",
-        names(options$gene_sets)
+        names(options$comparison_gene_sets)
       )
     ),
     conditionalPanel(
@@ -47,7 +47,7 @@ comparison_editor_server <- function(id, preset, options) {
       } else if (input$comparison_genes == "Your genes") {
         custom_gene_ids()
       } else {
-        options$gene_sets[[input$comparison_genes]]
+        options$comparison_gene_sets[[input$comparison_genes]]
       }
     })
   })

R/input_page.R

@@ -44,7 +44,10 @@ input_page_ui <- function(id, options) {
 #' @noRd
 input_page_server <- function(id, options) {
   moduleServer(id, function(input, output, session) {
-    current_preset <- reactiveVal(geposan::preset(options$gene_sets[[1]]))
+    current_preset <- reactiveVal(
+      geposan::preset(options$reference_gene_sets[[1]])
+    )
+
     potential_preset <- preset_editor_server("preset_editor", options)
 
     output$positions_plot <- plotly::renderPlotly({

R/preset_editor.R

@@ -8,7 +8,7 @@
 #' @noRd
 preset_editor_ui <- function(id, options) {
   species_choices <- c("All species", names(options$species_sets))
-  gene_choices <- names(options$gene_sets)
+  gene_choices <- names(options$reference_gene_sets)
 
   if (!options$locked) {
     species_choices <- c(species_choices, "Customize")
@@ -97,7 +97,7 @@ preset_editor_server <- function(id, options) {
       reference_gene_ids <- if (input$reference_genes == "Customize") {
         custom_gene_ids()
       } else {
-        options$gene_sets[[input$reference_genes]]
+        options$reference_gene_sets[[input$reference_genes]]
       }
 
       species_ids <- if (input$species == "All species") {

man/run_app.Rd

@@ -5,24 +5,27 @@
 \title{Run the application server.}
 \usage{
 run_app(
-  gene_sets,
+  reference_gene_sets,
   species_sets = NULL,
+  comparison_gene_sets = NULL,
   locked = FALSE,
   title = "Gene Position Analysis",
   port = 3464
 )
 }
 \arguments{
-\item{gene_sets}{A list of predefined gene sets. This should be a named list
+\item{reference_gene_sets}{A list of predefined gene sets to be used as
-containing vectors of gene IDs for each set. The names will be used to
+reference genes. This should be a named list containing vectors of gene IDs
-present the gene set throughout the user interface. You have to provide \emph{at
+for each set. You have to provide \emph{at least one gene set} which will be
-least one gene set} which will be selected as the initial reference gene
+selected as the initial reference gene set.}
-set.}
 
 \item{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.}
 
+\item{comparison_gene_sets}{A named list of predefined gene sets to be used
+as comparison genes.}
+
 \item{locked}{Whether the application should be locked and prohibit
 performing custom analyses. If this is set to \code{TRUE}, only the predefined
 gene and species sets are available for customizing the analysis. This may