# Analysis of community ecology data in R

David Zelený

### Others

en:numecolr:coldiss

This script is part of supporting materials, coming with the book of Borcard et al. 2011.

To import the function definition directly into R, use the following:

This function needs to install the package gclus first!

coldiss
# coldiss()
# Color plots of a dissimilarity matrix, without and with ordering
#
# Author: Francois Gillet, 23 August 2012
#

"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)
}

# Usage:
# coldiss(D = dissimilarity.matrix, nc = 4, byrank = TRUE, diag = FALSE)
# If D is not a dissimilarity matrix (max(D) > 1), then D is divided by max(D)
# nc 							number of colours (classes)
# byrank= TRUE		equal-sized classes
# byrank= FALSE		equal-length intervals
# diag = TRUE			print object labels also on the diagonal

# Example:
# coldiss(spe.dj, nc=9, byrank=F, diag=T)