Follow-up to plotting node labels on a co-phylogenetic tanglegram

Yesterday I wrote a post illustrating how to preserve node labels (such as bootstrap values) on a plotted "cophylo" object.

I meant to include a tutorial illustrating how to plot those bootstrap proportions as differently sized points: larger points for higher bootstrap support of each clade. Here’s how.

library(phytools)

Starting from the rooted MP & ML trees we obtained yesterday…

rooted.mp_tree

## 
## Phylogenetic tree with 47 tips and 46 internal nodes.
## 
## Tip labels:
##   Platypus, Wallaroo, Possum, Bandicoot, Opposum, Rabbit, ...
## Node labels:
##   Root, 1, 1, 0.89, 0.38, 0.39, ...
## 
## Rooted; no branch lengths.

rooted.ml_tree

## 
## Phylogenetic tree with 47 tips and 46 internal nodes.
## 
## Tip labels:
##   Platypus, Wallaroo, Possum, Bandicoot, Opposum, Rabbit, ...
## Node labels:
##   Root, 1, 1, 0.722, 0.986, 0.999, ...
## 
## Rooted; includes branch lengths.

Let’s create our "cophylo" object as follows:

obj<-cophylo(rooted.mp_tree,rooted.ml_tree)

## Rotating nodes to optimize matching...
## Done.

Finally, we plot it.

plot(obj,type=c("cladogram","phylogram"),fsize=0.8,part=0.48,
  mar=c(0.1,0.1,2.1,0.1),pts=FALSE,lwd=2,link.type="curved")
left<-get("last_plot.cophylo",envir=.PlotPhyloEnv)[[1]]
ind<-2:Nnode(obj$trees[[1]])+Ntip(obj$trees[[1]])
points(left$xx[ind],left$yy[ind],
  cex=2*as.numeric(obj$trees[[1]]$node.label[2:Nnode(obj$trees[[1]])]),
  pch=16,col=make.transparent(palette()[4],0.75))
right<-get("last_plot.cophylo",envir=.PlotPhyloEnv)[[2]]
ind<-2:Nnode(obj$trees[[2]])+Ntip(obj$trees[[2]])
points(right$xx[ind],right$yy[ind],
  cex=2*as.numeric(obj$trees[[2]]$node.label[2:Nnode(obj$trees[[2]])]),
  pch=16,col=make.transparent(palette()[4],0.75))
legend("bottomleft",
  legend=paste(seq(20,100,by=20),"%",sep=""),
  pt.cex=seq(0.4,2,by=0.4),
  pch=16,col=make.transparent(palette()[4],0.75),
  title="bootstrap support",bty="n")
mtext("a) Maximum Parsimony cladogram",at=-0.5,adj=0)
mtext("b) Maximum Likelihood phylogram",at=0.02,adj=0)

That’s it!