R/taxa_id_dict.R

In neurogenomics/orthogene: Interspecies gene mapping

#' Taxa ID dictionary
#'
#' Dictionary of NCBI taxonomy IDs mapped to
#' Latin and common names of 20+ organisms.
#'
#' @param species Species to get dictionary for.
#' Can supply either Latin names (e.g. "Homo sapiens") or
#' common names (e.g, "human").
#'
#' @return Named list of taxa IDs to organism names.
#' @importFrom stats setNames
#' @keywords internal
taxa_id_dict <- function(species = c(
                             "human", "chimp", "monkey", "mouse", "rat",
                             "dog", "cow", "chicken",
                             "zebrafish", "frog", "fly", "worm",
                             "rice"
                         ),
                         include_common_names = TRUE) {
    dict <- setNames(
        homologene::taxData$tax_id,
        homologene::taxData$name_txt
    )
    ## Add some common names for ease of use
    if(include_common_names){
        dict <- c(
            dict,
            common_species_names_dict()
        )
    } 
    if (is.null(species)) {
        return(dict)
    } else {
        species <- tolower(species)
    }

    if (any(!species %in% names(dict))) {
        missing_species <- species[!(species %in% names(dict))]
        messager(
            paste0(
                "WARNING: Species '", paste(missing_species, collapse = ", "),
                "' not found in taxa dict."
            )
        )
        species <- species[species %in% names(dict)]
    }
    return(dict[species])
}