Tuesday, June 5, 2018

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)

plot of chunk unnamed-chunk-2

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")

plot of chunk unnamed-chunk-4

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")

plot of chunk unnamed-chunk-5

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")

plot of chunk unnamed-chunk-6

Neat.

3 comments:

  1. Hello Liam,

    Thank you for putting up this blog, it is very informative personally to me who is graduate student in bioinformatics who's just learning how to use R for phylogenetic studies.
    My major challenge here is knowing when, where and how to use these functions (for example nodelabels, edgelabels, Nnode, untagle, and many more). Do you have any tips that you can share on how to use them appropriately and not mixing them up.
    Cheers,
    ID.

    ReplyDelete
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  3. Hi Liam,

    When using cophylo with two rooted trees with node labels (bootstrap values), at least some of the node labels are at the wrong nodes in the output trees in the cophylo object. In the input trees tree$node.label[1]="Root" and tree$node.label[2]="", as they should be. After cophylo I extract the trees from the cophylo object. In these trees tree$node.label[1]= is still "Root", but tree$node.label[2]="100", and tree$node.label[79]="". Node 79 is nowhere near the root and clearly shouldn't be empty. When I compare other node labels with the input trees many do not match. This does not happen when I use cophylo with unrooted trees, but since I need my trees to be rooted, this is not an option. I have tried rooting both with the root and reroot functions, but the problem persists, and have also tried rerooting after cophylo, but this doesn't give the desired result. So is it possible to run cophylo with rooted trees, without scrambling the node labels, or is this function only meant to be run with unrooted trees?

    Cheers,
    ME

    ReplyDelete

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