A recent
commenter pointed out something that I hadn't realized about the new phytools function,
plotBranchbyTrait - that is, that it can be used to plot different styles of tree and that the branch coloring works (mostly) for all of them. This
shouldn't have been a surprise - because, unlike most of my other tree plotting function,
plotBranchbyTrait is really just a wrapper around ape's versatile
plot.phylo function. Furthermore, I made a specific effort to migrate as much control of the operation of
plot.phylo out to the phytools user. Nonetheless, it did not occur to me that
plotBranchbyTrait(...,type="cladogram"),
type="unrooted", or
type="radial" would work or produce a nice looking result. In fact, they seem to work great - with one exception.... Here's a quick demo:
> tree<-pbtree(n=40)
> x<-fastBM(tree)
> plotBranchbyTrait(tree,x,mode="tips",type="cladogram", legend=F)
> plotBranchbyTrait(tree,x,mode="tips",type="unrooted", legend=F)
The only one that doesn't seem to work out quite right (as pointed out by
Jonathan) is
type="fan", where the 'horizontal' lines in the graph (actually, here circular lines) plot black:
> plotBranchbyTrait(tree,x,mode="tips",type="fan",legend=F)
Keep it up!
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