random phylogenetic trees + multidimensional scaling

phylo.R

# generate a random phylogenetic tree, then apply multidimensional
# scaling to the distances and see what the 2D plot looks like

library(ape)

layout(matrix(1:12, 3, 4, byrow=TRUE))

for (i in 1:3){
  # generate a tree
  rr <- rtree(20)
  # get distances between nodes
  d <- cophenetic.phylo(rr)
  # do an MDS
  mds <- cmdscale(d, k=6)
  # plot that beside the tree
  plot(rr, main=i)
  plot(mds[,1:2], main=i, type="n")
  text(mds[,1:2], label=rr$tip.label)
  plot(mds[,3:4], main=i, type="n")
  text(mds[,3:4], label=rr$tip.label)
  plot(mds[,5:6], main=i, type="n")
  text(mds[,5:6], label=rr$tip.label)

}