Thursday, October 4, 2012

Bug fix in xkcdTree; xkcd Caribbean anole phylogeny

I just realized that there was a bug in xkcdTree, my function for plotting xkcd style phylogenies. Basically, the argument lwd (line width) was not being transferred to the function for drawing xkcd style lines. Oops. Here is a link to a fixed version, which also allows control of the horizontal & vertical dimensions of the plotted tree. Also, for fun, an xkcd tree of 100 Greater Antillean anole species, from Mahler et al. (2010):
> library(phytools)
> source("xkcdTree.R")
> tree<-read.tree("anole.tre")
> xkcdTree(tree,"anoleTree.pdf",fsize=1.0,lwd=3, dim=c(5,13),waver=c(0.05,0.05),jitter=0.0005)


  1. Brilliant idea, the only problem is that it isn't future proof in that the function points to a specific version of GhostScript in a specific place. I guess a fix might be to make the filepath to the GhostScript .exe file an option in the function.