From 375c5b27bafb0807da2bde9dc38d1a0c543095b7 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Fri, 16 Dec 2022 15:11:29 +0100
Subject: [PATCH] Add sample data to gene selector

---
 R/gene_selector.R    | 35 +++++++++++++++++++++++++++++++++--
 inst/content/help.md |  4 +++-
 2 files changed, 36 insertions(+), 3 deletions(-)

diff --git a/R/gene_selector.R b/R/gene_selector.R
index 5c8d710..0bf108b 100644
--- a/R/gene_selector.R
+++ b/R/gene_selector.R
@@ -23,7 +23,8 @@ gene_selector_ui <- function(id) {
       choices = list(
         "Select from list" = "list",
         "Enter HGNC symbols" = "hgnc",
-        "Enter Ensembl gene IDs" = "ensembl"
+        "Enter Ensembl gene IDs" = "ensembl",
+        "Sample data: Glycolysis" = "sample"
       )
     ),
     tabsetPanel(
@@ -97,10 +98,40 @@ gene_selector_server <- function(id) {
         inputs <- unique(strsplit(input$hgnc_names_raw, "\\s+")[[1]])
         inputs <- inputs[inputs != ""]
         ubigen::genes[hgnc_name %chin% inputs, gene]
-      } else {
+      } else if (input$identifier_type == "ensembl") {
         inputs <- unique(strsplit(input$gene_ids_raw, "\\s+")[[1]])
         inputs <- inputs[inputs != ""]
         ubigen::genes[gene %chin% inputs, gene]
+      } else {
+        # Sample genes involved in glycolysis according to the KEGG pathways
+        # database [KEGG:hsa00010+M00001].
+        c(
+          "ENSG00000111640",
+          "ENSG00000111669",
+          "ENSG00000149925",
+          "ENSG00000074800",
+          "ENSG00000105220",
+          "ENSG00000067225",
+          "ENSG00000102144",
+          "ENSG00000141959",
+          "ENSG00000156515",
+          "ENSG00000171314",
+          "ENSG00000067057",
+          "ENSG00000111674",
+          "ENSG00000159322",
+          "ENSG00000152556",
+          "ENSG00000109107",
+          "ENSG00000159399",
+          "ENSG00000108515",
+          "ENSG00000160883",
+          "ENSG00000226784",
+          "ENSG00000188316",
+          "ENSG00000106633",
+          "ENSG00000136872",
+          "ENSG00000156510",
+          "ENSG00000143627",
+          "ENSG00000170950"
+        )
       }
 
       if (length(gene_ids) > 100) {
diff --git a/inst/content/help.md b/inst/content/help.md
index bfa7ac9..037497c 100644
--- a/inst/content/help.md
+++ b/inst/content/help.md
@@ -14,7 +14,9 @@ You can easily analyze your genes of interest for their ubiquity. In the
 initial state of the application, you can select genes by their HGNC symbols
 from a dropdown menu. To paste your genes as a whitespace separated list of
 either HGNC symbols or Ensembl gene IDs (in the form `ENSG00000164362`), change
-the top dropdown from "Select from list" to the desired input method.
+the top dropdown from "Select from list" to the desired input method. It is also
+possible to select sample data (genes involved in glycolysis according to the
+KEGG pathways database [`KEGG:hsa00010+M00001`]).
 
 ![Screenshot of the gene selector](gene_selector.png)