#' Checks that the species names, i.e. "mouse" can be linked 1:1 to a species name from the MGI homolog table
#'
#' Returns the linked species name from the MGI homolog table, i.e. if you pass "mouse" it returns "mouse, laboratory".
#' Essentially it's a convenience function so you don't need to write out "mouse, laboratory". It's intended primarily
#' for use within the packages other functions and should not be generally called seperately.
#'
#' @param requestedSpecies String with the name of the first species, i.e. "mouse"
#' @param allSpecies String with the names of all species from the MGI homolog table
#'
#' @return The name of the species in the MGI homolog table.
#'
#' @examples
#' allHomologs = load.homologs()
#' species1 = check.species(requestedSpecies="mouse",allSpecies=allHomologs$`Common Organism Name`)
#'
#' @export
check.species <- function(requestedSpecies,allSpecies){
allSpecies = unique(allSpecies)
simpleSpecies = gsub(",.*","",allSpecies)
species = data.frame(all=allSpecies,simple=simpleSpecies)
# Check species only refers to one of the species listed
selectedSpecies = apply(species==requestedSpecies,1,sum)>0
if(sum(selectedSpecies==1)){
validSpecies=FALSE
selSpec = allSpecies[selectedSpecies]
print(sprintf("Selected species: %s",selSpec))
}else{
validSpecies=TRUE
print("Available species options:")
print(species)
stop("ERROR: species does not match available options")
}
return(selSpec)
}
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