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Reindent code to use just two spaces

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This commit is contained in:
Elias Projahn 2022-05-26 12:44:09 +02:00
parent 47b8d7a1f0
commit 13b5efc1e3
10 changed files with 1000 additions and 999 deletions
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158
R/gene_selector.R
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@ -7,61 +7,61 @@
#'
#' @noRd
gene_selector_ui <- function(id, default_gene_ids = NULL) {
named_genes <- geposan::genes[name != ""]
named_genes <- unique(named_genes, by = "name")
gene_choices <- named_genes$id
names(gene_choices) <- named_genes$name
named_genes <- geposan::genes[name != ""]
named_genes <- unique(named_genes, by = "name")
gene_choices <- named_genes$id
names(gene_choices) <- named_genes$name
verticalLayout(
selectInput(
NS(id, "identifier_type"),
"Gene identifiers",
choices = list(
"Select from list" = "list",
"HGNC symbols" = "hgnc",
"Ensembl gene IDs" = "ensembl"
)
verticalLayout(
selectInput(
NS(id, "identifier_type"),
"Gene identifiers",
choices = list(
"Select from list" = "list",
"HGNC symbols" = "hgnc",
"Ensembl gene IDs" = "ensembl"
)
),
tabsetPanel(
id = NS(id, "custom_input"),
type = "hidden",
tabPanelBody(
"list",
shinyvs::virtualSelectInput(
NS(id, "selected_genes"),
label = "Select genes",
choices = gene_choices,
multiple = TRUE,
search = TRUE,
selectAllOnlyVisible = TRUE
),
tabsetPanel(
id = NS(id, "custom_input"),
type = "hidden",
tabPanelBody(
"list",
shinyvs::virtualSelectInput(
NS(id, "selected_genes"),
label = "Select genes",
choices = gene_choices,
multiple = TRUE,
search = TRUE,
selectAllOnlyVisible = TRUE
),
),
tabPanelBody(
"hgnc",
textAreaInput(
NS(id, "hgnc_names_raw"),
"Enter HGNC symbols",
value = paste(
geposan::genes[
id %chin% default_gene_ids & name != "",
name
],
collapse = "\n"
),
height = "250px"
)
),
tabPanelBody(
"ensembl",
textAreaInput(
NS(id, "gene_ids_raw"),
"Enter Ensembl gene IDs",
value = paste(default_gene_ids, collapse = "\n"),
height = "250px"
)
)
),
tabPanelBody(
"hgnc",
textAreaInput(
NS(id, "hgnc_names_raw"),
"Enter HGNC symbols",
value = paste(
geposan::genes[
id %chin% default_gene_ids & name != "",
name
],
collapse = "\n"
),
height = "250px"
)
),
tabPanelBody(
"ensembl",
textAreaInput(
NS(id, "gene_ids_raw"),
"Enter Ensembl gene IDs",
value = paste(default_gene_ids, collapse = "\n"),
height = "250px"
)
)
)
)
}
#' Application logic for the gene selector.
@ -72,33 +72,33 @@ gene_selector_ui <- function(id, default_gene_ids = NULL) {
#'
#' @noRd
gene_selector_server <- function(id) {
moduleServer(id, function(input, output, session) {
observe({
updateTabsetPanel(
session,
"custom_input",
selected = input$identifier_type
)
})
reactive({
gene_ids <- if (input$identifier_type == "list") {
input$selected_genes
} else if (input$identifier_type == "hgnc") {
inputs <- unique(strsplit(input$hgnc_names_raw, "\\s+")[[1]])
inputs <- inputs[inputs != ""]
geposan::genes[name %chin% inputs, id]
} else {
inputs <- unique(strsplit(input$gene_ids_raw, "\\s+")[[1]])
inputs <- inputs[inputs != ""]
geposan::genes[id %chin% inputs, id]
}
if (length(gene_ids > 100)) {
gene_ids[seq_len(100)]
} else {
gene_ids
}
})
moduleServer(id, function(input, output, session) {
observe({
updateTabsetPanel(
session,
"custom_input",
selected = input$identifier_type
)
})
reactive({
gene_ids <- if (input$identifier_type == "list") {
input$selected_genes
} else if (input$identifier_type == "hgnc") {
inputs <- unique(strsplit(input$hgnc_names_raw, "\\s+")[[1]])
inputs <- inputs[inputs != ""]
geposan::genes[name %chin% inputs, id]
} else {
inputs <- unique(strsplit(input$gene_ids_raw, "\\s+")[[1]])
inputs <- inputs[inputs != ""]
geposan::genes[id %chin% inputs, id]
}
if (length(gene_ids > 100)) {
gene_ids[seq_len(100)]
} else {
gene_ids
}
})
})
}