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Add sample data to gene selector

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This commit is contained in:
Elias Projahn 2022-12-16 15:11:29 +01:00
parent 673bad39f7
commit 375c5b27ba
2 changed files with 36 additions and 3 deletions
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35
R/gene_selector.R
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@ -23,7 +23,8 @@ gene_selector_ui <- function(id) {
choices = list( choices = list(
"Select from list" = "list", "Select from list" = "list",
"Enter HGNC symbols" = "hgnc", "Enter HGNC symbols" = "hgnc",
"Enter Ensembl gene IDs" = "ensembl" "Enter Ensembl gene IDs" = "ensembl",
"Sample data: Glycolysis" = "sample"
) )
), ),
tabsetPanel( tabsetPanel(
@ -97,10 +98,40 @@ gene_selector_server <- function(id) {
inputs <- unique(strsplit(input$hgnc_names_raw, "\\s+")[[1]]) inputs <- unique(strsplit(input$hgnc_names_raw, "\\s+")[[1]])
inputs <- inputs[inputs != ""] inputs <- inputs[inputs != ""]
ubigen::genes[hgnc_name %chin% inputs, gene] ubigen::genes[hgnc_name %chin% inputs, gene]
} else { } else if (input$identifier_type == "ensembl") {
inputs <- unique(strsplit(input$gene_ids_raw, "\\s+")[[1]]) inputs <- unique(strsplit(input$gene_ids_raw, "\\s+")[[1]])
inputs <- inputs[inputs != ""] inputs <- inputs[inputs != ""]
ubigen::genes[gene %chin% inputs, gene] 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) { if (length(gene_ids) > 100) {

4
inst/content/help.md
View file

@ -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 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 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 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) ![Screenshot of the gene selector](gene_selector.png)