R/utils.check.datatype.R

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

#' @name utils.check.datatype
#' @title Utility function to check the class of an object passed to a function
#' @description
#' Most functions require access to a genlight object, dist matrix, data matrix
#'  or fixed difference list (fd), and this function checks that a genlight
#'  object or one of the above has been passed, whether the genlight object is a
#'   SNP dataset or a SilicoDArT object, and reports back if verbosity is >=2.
#' @param x Name of the genlight object, dist matrix, data matrix, glPCA, or
#' fixed difference list (fd) [required].
#' @param accept Vector containing the classes of objects that are to be
#' accepted [default c('genlight','SNP','SilicoDArT'].
#' @param verbose Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
#' progress log; 3, progress and results summary; 5, full report
#' [default NULL, unless specified using gl.set.verbosity].
#' @details
#' This function checks the class of passed object and sets the datatype to
#' 'SNP', 'SilicoDArT', 'dist', 'mat', or class[1](x) as appropriate.
#'
#' Note also that this function checks to see if there are individuals or loci
#' scored as all missing (NA) and if so, issues the user with a warning.
#'
#' Note: One and only one of gl.check, fd.check, dist.check or mat.check can be
#'  TRUE.
#' @return datatype, 'SNP' for SNP data, 'SilicoDArT' for P/A data, 'dist' for a
#'  distance matrix, 'mat' for a data matrix, 'glPCA' for an ordination file, or
#'   class(x)[1].
#' @author Custodian: Arthur Georges -- Post to
#' \url{https://groups.google.com/d/forum/dartr}
#' @examples
#'  \donttest{
#' datatype <- utils.check.datatype(testset.gl)
#' datatype <- utils.check.datatype(as.matrix(testset.gl),accept='matrix')
#' fd <- gl.fixed.diff(testset.gl)
#' datatype <- utils.check.datatype(fd,accept='fd')
#' }
#' datatype <- utils.check.datatype(testset.gl)
#' 
#' @export

utils.check.datatype <- function(x,
                                 accept = c("genlight", "SNP", "SilicoDArT"),
                                 verbose = NULL) {
    #### SET VERBOSITY
    verbose <- gl.check.verbosity(verbose)
    
    #### CHECK THE TYPE OF OBJECT ####
    
    if (is(x, "genlight")) {
        if (is.null(ploidy(x))) {
            stop(
                error(
                    "Fatal Error: ploidy not set in the genlight object, run gl <- gl.compliance.check(gl)\n"
                )
            )
        }
        if (verbose >= 2) {
            cat(report("  Processing genlight object"))
        }
        if (all(ploidy(x) == 1)) {
            if (verbose >= 2) {
                cat(report(" with Presence/Absence (SilicoDArT) data\n"))
            }
            datatype <- "SilicoDArT"
        } else if (all(ploidy(x) == 2)) {
            if (verbose >= 2) {
                cat(report(" with SNP data\n"))
            }
            datatype <- "SNP"
        } else {
            stop(
                error(
                    "Fatal Error -- SNP or SilicoDArT coding misspecified, run gl <- gl.compliance.check(gl)"
                )
            )
        }
        # Check for individuals or loci scoring all missing values (NA)
        if (verbose > 1) {
            tmp <- gl.filter.allna(x, verbose = 0)
            if (nLoc(tmp) < nLoc(x)) {
                cat(
                    warn(
                        "  Warning: data include loci that are scored NA across all individuals.\n  Consider filtering using gl <- gl.filter.allna(gl)\n"
                    )
                )
            }
            if (nInd(tmp) < nInd(x)) {
                cat(
                    warn(
                        "  Warning: data include loci that are scored NA across all individuals.\n  Consider filtering using gl <- gl.filter.allna(gl)\n"
                    )
                )
            }
        }
    } else if (is(x, "fd")) {
        if (is(x$gl, "genlight")) {
            # if(is.null(ploidy(x$gl))){ stop(error('Fatal Error: ploidy not set in the genlight object, run gl <-
            # gl.compliance.check(gl)\n')) }
            if (verbose >= 2) {
                cat(report("  Processing a fixed difference (fd) object"))
            }
            if (all(ploidy(x$gl) == 1)) {
                if (verbose >= 2) {
                    cat(report(
                        " with Presence/Absence (SilicoDArT) data\n"
                    ))
                }
                type <- "SilicoDArT"
            } else if (all(ploidy(x$gl) == 2)) {
                if (verbose >= 2) {
                    cat(report(" with SNP data\n"))
                }
                type <- "SNP"
            }
        } else {
            stop(
                error(
                    "Fatal Error: Fixed Difference object expected! Check format of object\n"
                )
            )
        }
        datatype <- "fd"
        # if(verbose>=2 & type=='SilicoDArT'){ cat(report(' Processing a fixed difference (fd) object with Presence/Absence (SilicoDArT)
        # data\n')) } if(verbose>=2 & type=='SNP'){ cat(report(' Processing a fixed difference (fd) object with SNP data\n')) }
    } else if (is(x, "dist")) {
        if (verbose >= 2) {
            cat(report("  Processing a distance matrix\n"))
        }
        datatype <- "dist"
    } else if (is(x, "matrix")) {
        if (verbose >= 2) {
            cat(report("  Processing a data matrix\n"))
        }
        datatype <- "matrix"
    } else if (is(x, "glPca")) {
        if (verbose >= 2) {
            cat(report("  Processing an ordination file (glPca)\n"))
        }
        datatype <- "glPca"
    } else if (is.list(x)) {
        if (verbose >= 2) {
            cat(report("  Processing a list\n"))
        }
        datatype <- "list"
    } else {
        cat(warn("  Warning: Found object of class", class(x)[1], "\n"))
        datatype <- class(x)[1]
    }
    
    #### CHECK WHETHER TO THROW AN ERROR ####
    
    if (!(datatype %in% accept)) {
        stop(
            error(
                "Fatal Error: inappropriate object passed to function, found",
                datatype,
                "expecting",
                paste(accept, collapse = " or ")
            )
        )
    }
    
    invisible(datatype)
}