Arc-style phylogeny plotting now in phytools

Recently, I described a clever trick to plot a phylogenetic tree in a semi-circular “arc” format. This type of plot is popular in the literature, but I wasn’t aware of an R phylogenetics plotting method that could make plots of this style.

I’m still working out the bugs, but I have now added this feature to various phytools plotting methods. Where available, we can access it by setting the argument type to type="arc".

Let’s see.

library(phytools)

packageVersion("phytools")

## [1] '1.8.6'

First, let’s plot a phylogeny using plotTree. This phylogeny of Mycalesina butterflies comes from Halali et al. (2020).

data(butterfly.tree)
butterfly.tree

## 
## Phylogenetic tree with 287 tips and 286 internal nodes.
## 
## Tip labels:
##   Bra_peitho_gigas, Bra_decira, Bra_simonsii, Bra_perspicua, Bra_phaea, Tel_adolphei, ...
## 
## Rooted; includes branch lengths.

plotTree(ladderize(butterfly.tree),type="arc",fsize=0.3,
  lwd=1,ftype="i",arc_height=1.5)