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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 12:42:19 +02:00
parent a1e6147466
commit c04b6337e9
17 changed files with 1583 additions and 1582 deletions
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22
scripts/chromosome_names.R
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@ -5,23 +5,23 @@ ensembl_api_url <- "https://rest.ensembl.org"
#' Perform a request to the Ensembl REST API.
ensembl_request <- function(api_path) {
content(stop_for_status(GET(
paste0(ensembl_api_url, api_path),
content_type_json()
)))
content(stop_for_status(GET(
paste0(ensembl_api_url, api_path),
content_type_json()
)))
}
#' Get IDs of all available vertebrates.
get_species_ids <- function() {
species <- ensembl_request("/info/species")$species
sapply(species, function(species) species$name)
species <- ensembl_request("/info/species")$species
sapply(species, function(species) species$name)
}
#' Get all chromosomes names for a species.
get_species_chromosomes <- function(species_id) {
chromosomes <- unlist(ensembl_request(
paste0("/info/assembly/", species_id)
)$karyotype)
chromosomes <- unlist(ensembl_request(
paste0("/info/assembly/", species_id)
)$karyotype)
}
#' Get a vector of all available unqiue chromosome names.
@ -29,6 +29,6 @@ get_species_chromosomes <- function(species_id) {
#' There are multiple names for mitochondrial DNA which have to be removed
#' manually, unfortunately.
get_all_chromosomes <- function() {
chromosomes <- sapply(get_species_ids(), get_species_chromosomes)
unique(unlist(chromosomes))
chromosomes <- sapply(get_species_ids(), get_species_chromosomes)
unique(unlist(chromosomes))
}