R/gl.plot.heatmap.r

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

#' @name gl.plot.heatmap
#' @title Represents a distance matrix as a heatmap
#' @description
#' The script plots a heat map to represent the distances in the distance or
#' dissimilarity matrix. This function is a wrapper for
#' \link[gplots]{heatmap.2} (package gplots).
#'
#' @param D Name of the distance matrix or class fd object [required].
#' @param palette_divergent A divergent palette for the distance values
#'  [default diverging_palette].
#' @param verbose Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
#' progress log; 3, progress and results summary; 5, full report
#' [default 2 or as specified using gl.set.verbosity]
#' @param ... Parameters passed to function
#' \link[gplots]{heatmap.2} (package gplots)
#' @return returns no value (i.e. NULL)
#' @export
#' @author Custodian: Luis Mijangos -- Post to
#' \url{https://groups.google.com/d/forum/dartr})
#' @examples
#' \dontrun{
#'    gl <- testset.gl[1:10,]
#'    D <- dist(as.matrix(gl),upper=TRUE,diag=TRUE)
#'    gl.plot.heatmap(D)
#'    D2 <- gl.dist.pop(possums.gl)
#'    gl.plot.heatmap(D2)
#'    D3 <- gl.fixed.diff(testset.gl)
#'    gl.plot.heatmap(D3)
#'    }
#'    if ((requireNamespace("gplots", quietly = TRUE))) {
#'    D2 <- gl.dist.pop(possums.gl)
#'    gl.plot.heatmap(D2)
#'    }

gl.plot.heatmap <- function(D,
                            palette_divergent = diverging_palette,
                            verbose = NULL,
                            ...) {
    # SET VERBOSITY
    verbose <- gl.check.verbosity(verbose)
    
    # FLAG SCRIPT START
    funname <- match.call()[[1]]
    utils.flag.start(func = funname,
                     build = "Jody",
                     verbosity = verbose)
    
    # CHECK DATATYPE
    datatype <-
        utils.check.datatype(D,
                             accept = c("dist", "fd", "matrix"),
                             verbose = verbose)
    
    # DO THE JOB
    
    if (datatype == "dist" | datatype == "matrix") {
        p3 <-
            gplots::heatmap.2(
                as.matrix(D),
                col = palette_divergent(255),
                dendrogram = "column",
                trace = "none",
                ...
            )
    }
    if (datatype == "fd") {
        p3 <-
            gplots::heatmap.2(
                as.matrix(D$fd),
                col = palette_divergent(255),
                dendrogram = "column",
                trace = "none",
                ...
            )
    }
    
    # FLAG SCRIPT END
    
    if (verbose > 0) {
        cat(report("Completed:", funname, "\n"))
    }
    
    invisible(p3)
    
}