Plotting with the leaves and edges to be dropped highlighted

An anonymous reader commented the following:

I am wondering, is it possible to give different colours to the taxa after pruning by using the drop.tip. I just want to show the locations of the used species in the whole tree. All the taxa in tree retains but with different colours? (e.g. used species blue or red and pruned ones grey)

Ok, I'm going to interpret this as meaning - can we paint the leaves and edges that we're going to drop from the tree a different color, plot these, then drop them? (Once we've dropped these tips and edges from the tree, they are really gone - so we definitely can't plot them any more at that point.)

The answer is, of course, yes - and I'm going to give a quick trick for doing this using functions from the packages phytools (my package, of course) and ape.

Here I go. For the purposes of illustration, I will use a simulated, 30-taxon ultrametric tree; and a random set of ten tips.

> # first simulate a tree > tree<-pbtree(n=30) > # choose a random set of tips to prune > tips<-sample(tree$tip.label)[1:10] > tips [1] "t20" "t8" "t17" "t9" "t15" "t2" "t13" "t14" "t16" [10] "t11" > # find the node numbers for those tips > nodes<-sapply(tips,function(x) which(x==tree$tip.label)) > # and the rows in our edge matrix for all terminal branches > # to be dropped > edges<-sapply(nodes,function(x) which(x==tree$edge[,2])) > # now let's shorten them by an imperceptible amount > tree$edge.length[edges]<-tree$edge.length[edges]- 0.0001*max(nodeHeights(tree)) > par(mfrow=c(2,1)) > # plot the tree using fancyTree in phytools > fancyTree(tree) > # drop tips and plot the pruned tree > tree<-drop.tip(tree,tips) > fancyTree(tree)

Pretty cool! The way this works is by identifying and then imperceptibly shortening the terminal edges leading to species that we plan to drop from the tree. We can then use the phytools function fancyTree(...,type="extinction") to automatically detect these species (as well as any internal branches leading to these species) as "extinct." It then plots all these edges with red dashed lines, instead of the standard black. (We could modify these color scheme - but as of now we'd have to change the function code).

That's it! Thanks for the suggestion.