R/coldiss.R

In CMET-UGent/CMETNGS: Convenience functions for CMET NGS automated pipeline

#' Color plots of a dissimilarity matrix, without and with ordering
#'
#' This function generates color plots of dissimilarity matrices, with our
#' without ordering. It was supplied as supplementary data to "Numerical
#' ecology with R" Boccard & Legendre, 2012. And authored by Francois Gillet.
#'
#' @param D dissimilarity matrix. If D is not a dissimilarity matrix (max(D)>1),
#' then D is divided by max(D)
#' @param nc number of colors (classes, defaults to 4)
#' @param byrank specifiy either equal-sized classes (TRUE) or equal-length
#' intervals (FALSE). Defaults to TRUE
#' @param diag print object labels on the diagonal (defaults to FALSE)
#' @importFrom gclus dmat.color plotcolors order.single
#' @importFrom graphics par
#' @importFrom grDevices cm.colors
#' @keywords heatmap
#' @examples
#' ## Short example
#'
#' # coldiss(spe.dj, nc=9, byrank=F, diag=T)
#' # Original author: Francois Gillet, 23 aug 2012
#'
#' @export


coldiss <- function(D, nc = 4, byrank = TRUE, diag = FALSE)
{
  #require(gclus)

  if (max(D)>1) D <- D/max(D)

  if (byrank) {
    spe.color <- dmat.color(1-D, cm.colors(nc))
  }
  else {
    spe.color <- dmat.color(1-D, byrank=FALSE, cm.colors(nc))
  }

  spe.o <- order.single(1-D)
  speo.color <- spe.color[spe.o, spe.o]

  op <- par(mfrow=c(1,2), pty="s")

  if (diag) {
    plotcolors(spe.color, rlabels=attributes(D)$Labels,
               main="Dissimilarity Matrix",
               dlabels=attributes(D)$Labels)
    plotcolors(speo.color, rlabels=attributes(D)$Labels[spe.o],
               main="Ordered Dissimilarity Matrix",
               dlabels=attributes(D)$Labels[spe.o])
  }
  else {
    plotcolors(spe.color, rlabels=attributes(D)$Labels,
               main="Dissimilarity Matrix")
    plotcolors(speo.color, rlabels=attributes(D)$Labels[spe.o],
               main="Ordered Dissimilarity Matrix")
  }
  par(op)
}