I love the ape phylogenetics package, but nothing is perfect for everything and I sometimes find myself messing around a . I’ve put many of those modifications up online, and written a quick ‘cartoon’ polytomy plotting script (cartoon.plot). The figure above shows off a few of the things (pretty polytomies, radially-spaced tiplabels) you can do with these functions.
It’s not very quick, but you can use it to automatically plot terminal polytomies as if they were just big ‘cartoon’ blocks, or you can specify tips and the function will find the monophyletic clade to group for you. The figure above uses the auto-detect feature, along with willeerd.tiplabel‘s radial.adj to put circles at distances around the phylogeny.
Maybe some of you are aware of this already, but you can use a line like
pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)
…to get information about the last phylogeny you plotted. This makes manually adding things to tips and nodes much easier, because you don’t have to reverse-engineer where you think ape put them! I found this nugget while poking around inside ape and it’s made my life much easier!