#' @title get_basic_genomes
#' @description a helper function for basic genomes,
#' obtains the genome codes (e.g. 'hg38')
#'
#' @rdname get_basic_genomes
#' @aliases get_basic_genomes
#'
#' @return an list of short genome codes, e.g., "hg38", "dm6"
#'
#' @examples
#' bs <- get_basic_genomes()
#'
#' @keywords utils
#' @export
#'
get_basic_genomes <- function() {
BASIC_GENOMES
} # get_basic_genomes
#-------------------------------------------------------------------------------
#' @title get_cas_genomes
#' @description a helper function for common always available stock genomes,
#' obtains the genome codes (e.g. 'hg38')
#'
#' @rdname get_cas_genomes
#' @aliases get_cas_genomes
#'
#' @return an list of short genome codes, e.g., "hg38", "dm6"
#'
#' @examples
#' cas <- get_cas_genomes()
#'
#' @keywords utils
#' @export
#'
get_cas_genomes <- function() {
CAS_GENOMES
} # get_cas_genomes
#-------------------------------------------------------------------------------
#' @title get_css_genomes
#' @description a helper function for mostly internal use,
#' obtains the genome codes (e.g. 'hg38') supported by igv.js
#'
#' @rdname get_css_genomes
#' @aliases get_css_genomes
#' @param test logical(1) defaults to FALSE
#'
#' @return an list of short genome codes, e.g., "hg38", "dm6", "tair10"
#'
#' @examples
#' css <- get_css_genomes(test = TRUE)
#'
#' @keywords utils
#' @export
#'
get_css_genomes <- function(test = FALSE) {
if (test)
return(get_basic_genomes())
current.genomes.file <-
"https://s3.amazonaws.com/igv.org.genomes/genomes.json"
if (!RCurl::url.exists(current.genomes.file))
return(get_basic_genomes())
current.genomes.raw <-
readLines(current.genomes.file, warn = FALSE, skipNul = TRUE)
tbl.genomes <- jsonlite::fromJSON(current.genomes.raw)
tbl.genomes$id
} # get_css_genomes
#-------------------------------------------------------------------------------
#' @title parseAndValidateGenomeSpec
#' @description a helper function for internal use by the igvShiny constructor,
#' but possible also of use to those building an igvShiny app,
#' to test their genome specification for validity
#'
#' @rdname parseAndValidateGenomeSpec
#' @aliases parseAndValidateGenomeSpec
#'
#' @param genomeName character usually one short code of a supported ("stock")
#' genome (e.g., "hg38") or for a user-supplied custom genome,
#' the name you wish to use
#' @param initialLocus character default "all", otherwise "chrN:start-end"
#' or a recognized gene symbol
#' @param stockGenome logical default TRUE
#' @param dataMode character either "stock", "localFile" or "http"
#' @param fasta character when supplying a custom (non-stock) genome,
#' either a file path or a URL
#' @param fastaIndex character when supplying a custom (non-stock) genome,
#' either a file path or a URL,
#' essential for all but the very small custom genomes.
#' @param genomeAnnotation character when supplying a custom (non-stock) genome,
#' a file path or URL pointing to a genome annotation file in
#' a gff3 format
#'
#' @examples
#' genomeSpec <-
#' parseAndValidateGenomeSpec("hg38", "APOE") # the simplest case
#' base.url <-
#' "https://gladki.pl/igvr/testFiles/sarsGenome"
#' fasta.file <-
#' sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.dna.toplevel.fa")
#' fastaIndex.file <-
#' sprintf("%s/%s",
#' base.url,
#' "Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai")
#' annotation.file <-
#' sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.101.gff3")
#' custom.genome.title <- "SARS-CoV-2"
#' genomeOptions <-
#' parseAndValidateGenomeSpec(
#' genomeName = custom.genome.title,
#' initialLocus = "all",
#' stockGenome = FALSE,
#' dataMode = "http",
#' fasta = fasta.file,
#' fastaIndex = fastaIndex.file,
#' genomeAnnotation = annotation.file
#' )
#'
#' @seealso [get_css_genomes()] for stock genomes we support.
#'
#' @return an options list directly usable by igvApp.js, and thus igv.js
#' @keywords igvShiny
#' @export
#'
parseAndValidateGenomeSpec <- function(genomeName,
initialLocus = "all",
stockGenome = TRUE,
dataMode = NA,
fasta = NA,
fastaIndex = NA,
genomeAnnotation = NA) {
options <- list()
options[["stockGenome"]] <- stockGenome
options[["dataMode"]] <- dataMode
options[["validated"]] <- FALSE
#--------------------------------------------------
# first: is this a stock genome? if so, we need
# only check if the genomeName is recognized
#--------------------------------------------------
if (stockGenome) {
if (!genomeName %in% get_cas_genomes()) {
supported.stock.genomes <- get_css_genomes()
if (!genomeName %in% supported.stock.genomes) {
s.1 <-
sprintf("Your genome '%s' is not currently supported",
genomeName)
s.2 <-
sprintf("Currently supported: %s",
paste(supported.stock.genomes, collapse = ","))
msg <- sprintf("%s\n%s", s.1, s.2)
stop(msg)
}
} # if not common & always available
options[["genomeName"]] <- genomeName
options[["initialLocus"]] <- initialLocus
options[["fasta"]] <- NA
options[["fastaIndex"]] <- NA
options[["annotation"]] <- NA
options[["validated"]] <- TRUE
}# stockGenome requested
if (!stockGenome) {
stopifnot(!is.na(dataMode))
stopifnot(!is.na(fasta))
stopifnot(!is.na(fastaIndex))
# genomeAnnotation is optional
# "direct" for an in-memory R data structure, deferred
recognized.modes <- c("localFiles", "http")
if (!dataMode %in% recognized.modes) {
msg <-
sprintf(
"dataMode '%s' should be one of %s",
dataMode,
paste(recognized.modes, collapse = ",")
)
stop(msg)
}
#---------------------------------------------------------------------
# dataMode determines how to check for the existence of each resource
#---------------------------------------------------------------------
exists.function <- switch(dataMode,
"localFiles" = file.exists,
"http" = RCurl::url.exists)
stopifnot(exists.function(fasta))
stopifnot(exists.function(fastaIndex))
if (!is.na(genomeAnnotation))
stopifnot(exists.function(genomeAnnotation))
options[["genomeName"]] <- genomeName
options[["fasta"]] <- fasta
options[["fastaIndex"]] <- fastaIndex
options[["initialLocus"]] <- initialLocus
options[["annotation"]] <- genomeAnnotation
options[["validated"]] <- TRUE
} # if !stockGenome
return(options)
} # parseAndValidateGenomeSpec
#-------------------------------------------------------------------------------
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.