Wednesday, June 5, 2013

Simple tree plotter

As I mentioned in a prior post I am writing a book chapter on visualization for phylogenetic comparative biology. As I component of this, I discuss the basics of plotting a couple of different types of phylogenetic trees, including some instruction on programming these methods.

For one component of this I wrote a simplified tree plotting function in R. This is what it looks like. Excluding annotation, the function code is less than 20 lines:

simpleTreePlot<-function(tree){
  n<-length(tree$tip.label)
  # reorder cladewise to assign tip positions
  cw<-reorder(tree,"cladewise")
  y<-vector(length=n+cw$Nnode)
  y[cw$edge[cw$edge[,2]<=n,2]]<-1:n
  # reorder pruningwise for post-order traversal
  pw<-reorder(tree,"pruningwise")
  nn<-unique(pw$edge[,1])
  # compute vertical position of each edge
  for(i in 1:length(nn)){
    yy<-y[pw$edge[which(pw$edge[,1]==nn[i]),2]]
    y[nn[i]]<-mean(range(yy))
  }
  # compute start & end points of each edge
  X<-nodeHeights(cw)
  # open & size a new plot
  plot.new(); par(mar=rep(0.1,4))
  plot.window(xlim=c(0,1.1*max(X)),ylim=c(0,max(y)+1))
  # plot horizontal edges
  for(i in 1:nrow(X))
    lines(X[i,],rep(y[cw$edge[i,2]],2),lwd=2,lend=2)
  # plot vertical relationships
  for(i in 1:tree$Nnode+n)
    lines(X[which(cw$edge[,1]==i),1],
    range(y[cw$edge[which(cw$edge[,1]==i),2]]),lwd=2,
    lend=2)
  # plot tip labels
  for(i in 1:n)
    text(X[which(cw$edge[,2]==i),2],y[i],tree$tip.label[i],
    pos=4,offset=0.1)
}

Try it out:

> require(phytools)
Loading required package: phytools
> tree<-pbtree(b=1,d=0.2,n=30)
> simpleTreePlot(tree)

Any suggestions?

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