johrpan/geposanui
1
0
Fork 0
mirror of https://github.com/johrpan/geposanui.git synced 2025-10-26 11:17:24 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions

Add options to configure default gene sets

Browse source
This commit is contained in:
Elias Projahn 2022-05-19 16:24:23 +02:00
parent 22f5e86625
commit 74d7865389
9 changed files with 391 additions and 370 deletions
Download patch file Download diff file Expand all files Collapse all files

52
R/comparison_editor.R
View file

@ -1,22 +1,23 @@
# Create a comparison editor.
comparison_editor_ui <- function(id) {
#' Create a comparison editor.
#'
#' @param options Global application options
#' @noRd
comparison_editor_ui <- function(id, options) {
verticalLayout(
h3("Comparison"),
selectInput(
NS(id, "comparison_genes"),
"Comparison genes",
choices = list(
"None" = "none",
"Random genes" = "random",
"Verified or suggested TPE-OLD genes" = "tpeold",
"Only verified TPE-OLD genes" = "verified",
"Only suggested TPE-OLD genes" = "suggested",
"Customize" = "custom"
choices = c(
"None",
"Random genes",
names(options$gene_sets),
"Customize"
)
),
conditionalPanel(
condition = sprintf(
"input['%s'] == 'custom'",
"input['%s'] == 'Customize'",
NS(id, "comparison_genes")
),
gene_selector_ui(NS(id, "custom_genes"))
@ -24,33 +25,32 @@ comparison_editor_ui <- function(id) {
)
}
# Create a server for the comparison editor.
#
# @param id ID for namespacing the inputs and outputs.
# @param preset A reactive containing the current preset.
#
# @return A reactive containing the comparison gene IDs.
comparison_editor_server <- function(id, preset) {
#' Create a server for the comparison editor.
#'
#' @param id ID for namespacing the inputs and outputs.
#' @param preset A reactive containing the current preset.
#' @param options Global application options
#'
#' @return A reactive containing the comparison gene IDs.
#'
#' @noRd
comparison_editor_server <- function(id, preset, options) {
moduleServer(id, function(input, output, session) {
custom_gene_ids <- gene_selector_server("custom_genes")
reactive({
if (input$comparison_genes == "none") {
if (input$comparison_genes == "None") {
NULL
} else if (input$comparison_genes == "random") {
} else if (input$comparison_genes == "Random genes") {
preset <- preset()
gene_pool <- preset$gene_ids
reference_gene_ids <- preset$reference_gene_ids
gene_pool <- gene_pool[!gene_pool %chin% reference_gene_ids]
gene_pool[sample(length(gene_pool), length(reference_gene_ids))]
} else if (input$comparison_genes == "tpeold") {
genes[verified | suggested == TRUE, id]
} else if (input$comparison_genes == "verified") {
genes[verified == TRUE, id]
} else if (input$comparison_genes == "suggested") {
genes[suggested == TRUE, id]
} else {
} else if (input$comparison_genes == "Customize") {
custom_gene_ids()
} else {
options$gene_sets[[input$comparison_genes]]
}
})
})