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Add options to configure default gene sets

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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
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118
R/preset_editor.R
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@ -1,88 +1,110 @@
#' Create the UI for a preset editor.
#'
#' @param id ID for namespacing.
#' @param options Global options for the application.
#'
#' @return The UI elements.
#'
#' @noRd
preset_editor_ui <- function(id) {
preset_editor_ui <- function(id, options) {
species_choices <- c("All species", names(options$species_sets))
gene_choices <- names(options$gene_sets)
if (!options$locked) {
species_choices <- c(species_choices, "Customize")
gene_choices <- c(gene_choices, "Customize")
}
verticalLayout(
h3("Inputs"),
selectInput(
NS(id, "species"),
"Species to include",
choices = list(
"All species" = "all",
"Known replicatively aging species" = "replicative",
"Customize" = "custom"
choices = species_choices
),
if (!options$locked) {
conditionalPanel(
condition = sprintf(
"input['%s'] == 'Customize'",
NS(id, "species")
),
selectizeInput(
inputId = NS(id, "custom_species"),
label = "Select input species",
choices = NULL,
multiple = TRUE
),
)
),
conditionalPanel(
condition = sprintf("input['%s'] == 'custom'", NS(id, "species")),
selectizeInput(
inputId = NS(id, "custom_species"),
label = "Select input species",
choices = NULL,
multiple = TRUE
),
),
},
selectInput(
NS(id, "reference_genes"),
"Reference genes",
choices = list(
"Verified or suggested TPE-OLD genes" = "tpeold",
"Only verified TPE-OLD genes" = "verified",
"Customize" = "custom"
)
choices = gene_choices
),
conditionalPanel(
condition = sprintf(
"input['%s'] == 'custom'",
NS(id, "reference_genes")
),
gene_selector_ui(
NS(id, "custom_genes"),
genes[suggested | verified == TRUE, id]
if (!options$locked) {
conditionalPanel(
condition = sprintf(
"input['%s'] == 'Customize'",
NS(id, "reference_genes")
),
gene_selector_ui(NS(id, "custom_genes"))
)
)
},
if (options$locked) {
HTML(
"This instance prohibits performing custom analyses ",
"to reduce resource usage. Normally, it is possible ",
"to use this web application for analyzing any set of ",
"reference genes to find patterns in their ",
"chromosomal positions. If you would like to apply ",
"this method for your own research, see ",
"<a href=\"https://code.johrpan.de/johrpan/tpeold\"",
"target=\"_blank\">this page</a> for more information."
)
}
)
}
#' Application logic for the preset editor.
#'
#' @param id ID for namespacing the inputs and outputs.
#' @param options Global application options.
#'
#' @return A reactive containing the preset or `NULL`, if the input data doesn't
#' result in a valid one.
#'
#' @noRd
preset_editor_server <- function(id) {
preset_editor_server <- function(id, options) {
moduleServer(id, function(input, output, session) {
species_choices <- geposan::species$id
names(species_choices) <- geposan::species$name
custom_gene_ids <- if (!options$locked) {
species_choices <- geposan::species$id
names(species_choices) <- geposan::species$name
updateSelectizeInput(
session,
"custom_species",
choices = species_choices,
server = TRUE
)
updateSelectizeInput(
session,
"custom_species",
choices = species_choices,
server = TRUE
)
custom_gene_ids <- gene_selector_server("custom_genes")
gene_selector_server("custom_genes")
} else {
NULL
}
reactive({
reference_gene_ids <- if (input$reference_genes == "tpeold") {
genes[verified | suggested == TRUE, id]
} else if (input$reference_genes == "verified") {
genes[verified == TRUE, id]
} else {
reference_gene_ids <- if (input$reference_genes == "Customize") {
custom_gene_ids()
} else {
options$gene_sets[[input$reference_genes]]
}
species_ids <- if (input$species == "replicative") {
species_ids_replicative
} else if (input$species == "all") {
species_ids <- if (input$species == "All species") {
geposan::species$id
} else {
} else if (input$species == "Customize") {
input$custom_species
} else {
options$species_sets[[input$species]]
}
tryCatch(