In my last post I demonstrated how the phytools function phenogram could be used to plot a slanted phylogram - at least most of the time. The ape phylogenetics package function plot.phylo can also plot slanted phylograms (by setting type="cladogram" for a tree with branch lengths assigned), but this phylogram has a fundamentally different style than the type created by phenogram. The effect in particular is one in which the branches of the tree plotted with phenogram slant much more gently from the root than the branches in plot.phylo(...,type="cladogram"). The following graphic contrasts the two styles:
While I was musing about yesterday's post this morning, it occurred to me that plot.phylo(...,type="cladogram") kind of looks like it uses the same method as phenogram, but with the positions of the internal nodes determined by computing the "ancestral state" (that is, of the y coordinate of the tip) for the root node of each subtree separately. This could be accomplished using ace(...,method="pic") in the ape package. Well, this is not, in fact, how plot.phylo(...,type="cladogram") works, but the two methods visually present as almost identical. For instance:
> x11(); phenogram(tree,c(x,a))
It turns out that both of these methods can sometimes result in lines that cross. For instance:
Post a Comment
Note: due to the very large amount of spam, all comments are now automatically submitted for moderation.