# coldiss() # Color plots of a dissimilarity matrix, without and with ordering # # License: GPL-2 # Author: Francois Gillet, August 2009 # "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 > 1), then D is divided by max(D) # Example: # coldiss(spe.dj, nc=9, byrank=F, diag=T) # byrank= TRUE equal-sized categories # byrank= FALSE equal-length intervals