R/infer_ctd_species.R

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

#' Infer CellTypeDataset species
#' 
#' Infers species from from level 1 of a CellTypeDataset (CTD)
#' using either the metadata stored in the CTD
#'  (if the object has previously been standardised with 
#'  \link[EWCE]{standardise_ctd}) or using the gene names
#'   (via \link[orthogene]{infer_species}). 
#' If \code{ctd_species} is not \code{NULL}, 
#' this will be returned instead of inferring the species. 
#' @param verbose Message verbosity. 
#' \itemize{
#' \item{\code{0} or \code{FALSE} : }{
#' Don't print any messages.
#' }
#' \item{\code{1} or \code{TRUE} : }{
#' Only print messages from \pkg{MAGMA.Celltyping}.
#' }
#' \item{\code{2} or \code{c(TRUE,TRUE)} : }{
#' Print messages from \pkg{MAGMA.Celltyping} and 
#' the internal \pkg{orthogene} function.}
#' } 
#' @inheritParams celltype_associations_pipeline
#' @inheritDotParams orthogene::infer_species
#' @returns Inferred species name.
#' 
#' @export 
#' @importFrom orthogene infer_species
#' @examples   
#' ctd_species <- infer_ctd_species(ctd = ewceData::ctd())
infer_ctd_species <- function(ctd, 
                              ctd_species = NULL,
                              verbose = 2,
                              ...){
    #### Mainly for adjust_zstat_in_genesOut where ctd is optional ####
    if(is.null(ctd)) return(NULL)
    if(is.null(ctd_species)) {
        #### Infer from metadata ####
        if(!is.null(ctd[[1]]$species$output_species)){
            messager("ctd_species=NULL: Inferring species from ctd metadata.",
                     v=sum(verbose)>0)
            ctd_species <- ctd[[1]]$species$output_species
        #### Infer from genes #### 
        } else { 
            messager("ctd_species=NULL: Inferring species from gene names.",
                     v=sum(verbose)>0)
            ctd_species <- orthogene::infer_species(
                gene_df = ctd[[1]]$mean_exp,
                verbose = sum(verbose)>1,
                make_plot = FALSE,
                ...
            )$top_match
        } 
        #### Report ####
        messager("Inferred ctd species:",ctd_species,
                 v=sum(verbose)>0)
    }
    return(ctd_species)
}