Thursday, September 27, 2012

Modification to fancyTree(...,type="droptip") so that it works on non-ultrametric trees

In response to a phytools user comment I gave a trick (here) for plotting the leaves and edges to be dropped in a different color & style from the rest of the tree. I then incorporated this trick into the phytools function fancyTree (described here). What I failed to point out was that this trick will not work on non-ultrametric trees. (To be honest, it didn't even really occur to me to point this out, so jaded am I from working with simulated data and trees.) Well, I have fixed this now, so that fancyTree(...,type="droptip") no longer uses the trick I described here, although it does still, generally speaking, use the method of fancyTree(...,type="extinction").

Users can check out the updated code on my R phylogenetics page here; or just download the latest (non-CRAN) version of phytools (v0.1-98: here), and install from source.

Let's check out how it works:

> # install new version of phytools, if necessary
> install.packages("phytools_0.1-98.tar.gz",type="source", repos=NULL)
> # simulate non-ultrametric tree & drop tips
> set.seed(10)
> tree<-rtree(n=20)
> pruned<-fancyTree(tree,"drop",tip=sample(tree$tip)[1:5])

Well, that works great. The only thing I'm not satisfied with is that if pruning changes the total length of the tree, then the second panel will be automatically rescaled so that corresponding nodes in the two plotted trees no long have corresponding horizontal positions. For example:

> set.seed(100)
> tree<-rtree(n=20)
> tips<-c("t6","t8","t14","t12","t4","t20")
> pruned<-fancyTree(tree,"drop",tip=tips)

Still working on this. . . .

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