Preserving node & edge labels after optimizing node rotation in cophylo

A phytools user contacted me the other day about an issue in which her bootstrap values, stored as node labels in a Newick string, did not align with the correct edges when plotted using edgelabels.cophylo on a visualized "cophylo" object.

As it turns out, this had nothing to do with cophylo & everything to do with the fact that she wanted to plot node labels using edgelabels.

First, here is a demo showing that cophylo preserves the correct order of node labels.

A simulated tree with node labels:

library(phytools)
tree<-pbtree(n=26,tip.label=LETTERS)
tree$node.label<-letters[1:25]

Now I'll plot that tree labeling the nodes with their labels & node indices:

plotTree(tree)
nodelabels(tree$node.label,1:tree$Nnode+Ntip(tree))
nodelabels(adj=c(1.8,-1.8),frame="none",cex=0.5)

Next, I'm going to randomly rotate nodes on this tree to produce two new trees as follows:

t1<-tree
for(i in 1:100) t1<-untangle(rotate(t1,sample(1:t1$Nnode+Ntip(t1),1)),
    'read.tree')
t2<-tree
for(i in 1:100) t2<-untangle(rotate(t2,sample(1:t2$Nnode+Ntip(t2),1)),
    'read.tree')

Now I'm ready to make my "cophylo" object. First, without node rotation to maximize matching:

obj<-cophylo(t1,t2,rotate=FALSE)
plot(obj)
nodelabels.cophylo(obj$trees[[1]]$node.label,1:obj$trees[[1]]$Nnode+
    Ntip(obj$trees[[1]]))
nodelabels.cophylo(adj=c(1.8,-1.8),frame="none",cex=0.5)
nodelabels.cophylo(obj$trees[[2]]$node.label,1:obj$trees[[2]]$Nnode+
    Ntip(obj$trees[[2]]),which="right")
nodelabels.cophylo(adj=c(-0.8,-1.8),frame="none",cex=0.5,which="right")

We can see that the node indices (the little numbers that come from tree$edge have changed, but the node labels are still all associated with the right clades.

Now we can do the same thing, but in which we permit node rotation to be optimized as follows:

obj<-cophylo(t1,t2,rotate=TRUE)

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

plot(obj)
nodelabels.cophylo(obj$trees[[1]]$node.label,1:obj$trees[[1]]$Nnode+
    Ntip(obj$trees[[1]]))
nodelabels.cophylo(adj=c(1.8,-1.8),frame="none",cex=0.5)
nodelabels.cophylo(obj$trees[[2]]$node.label,1:obj$trees[[2]]$Nnode+
    Ntip(obj$trees[[2]]),which="right")
nodelabels.cophylo(adj=c(-0.8,-1.8),frame="none",cex=0.5,which="right")

So what was the problem with the edge labels in the user's inquiry? Well, basically, edgelabels (and edgelabels.cophylo, which just uses edgelabels internally) takes the labels in the order of the rows of tree$edge in the plotted phylogeny

• not in the number order of the node indices, as in nodelabels and tree$node.label. Thus, we have to match the two in order to visualize our node labels along each preceding edge. This might be done as follows:

obj<-cophylo(t1,t2,rotate=TRUE)

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

plot(obj)
edgelabels.cophylo(obj$trees[[1]]$node.label[2:obj$trees[[1]]$Nnode],
    edge=sapply(2:obj$trees[[1]]$Nnode+Ntip(obj$trees[[1]]),
    function(n,e) which(e==n),e=obj$trees[[1]]$edge[,2]),
    frame="none",adj=c(0.5,1))
edgelabels.cophylo(obj$trees[[2]]$node.label[2:obj$trees[[2]]$Nnode],
    edge=sapply(2:obj$trees[[2]]$Nnode+Ntip(obj$trees[[2]]),
    function(n,e) which(e==n),e=obj$trees[[2]]$edge[,2]),
    frame="none",adj=c(0.5,1),which="right")

Neat.