Allow selecting the expression dataset

R/data.R

@@ -1,2 +1,9 @@
-#' A `data.table` containig data on genes and their expression behavior.
+#' A `data.table` containig mappings of Ensembl gene ID to HGNC symbol.
 "genes"
+
+#' The results from the analysis across all GTEx samples.
+"gtex_all"
+
+#' The results from the analysis across Human Protein Atlas' tissue aggregated
+#' data.
+"hpa_tissues"

R/ranking.R

@@ -10,7 +10,7 @@
 #'   percentiles for each gene.
 #'
 #' @export
-rank_genes <- function(data = ubigen::genes,
+rank_genes <- function(data = ubigen::gtex_all,
                        cross_sample_metric = "above_95",
                        cross_sample_weight = 0.5,
                        level_metric = "median_expression_normalized",

R/server.R

@@ -1,8 +1,19 @@
 #' Server implementing the main user interface.
 #' @noRd
 server <- function(input, output, session) {
+  dataset <- reactive({
+    analysis <- if (input$dataset == "hpa_tissues") {
+      ubigen::hpa_tissues
+    } else {
+      ubigen::gtex_all
+    }
+
+    merge(analysis, ubigen::genes, by = "gene")
+  })
+
   ranked_data <- reactive({
     rank_genes(
+      data = dataset(),
       cross_sample_metric = input$cross_sample_metric,
       cross_sample_weight = input$cross_sample_weight,
       level_metric = input$level_metric,

R/ui.R

@@ -19,6 +19,14 @@ ui <- function() {
             h3("Your genes"),
             gene_selector_ui("custom_genes"),
             h3("Method"),
+            selectInput(
+              "dataset",
+              label = strong("Expression dataset"),
+              list(
+                "GTEx (all samples)" = "gtex_all",
+                "Human Protein Atlas (tissues)" = "hpa_tissues"
+              )
+            ),
             selectInput(
               "cross_sample_metric",
               verticalLayout(