Creating an "arc" style tree in R using phytools

I’ve been seeing quite a few phylogenies that one might best describe as “arc trees” – fan style trees, but plotted in an arc-like shape.

Here’s an example from Twitter:

New preprint with @HdzHdz_Lab, using phylogenetics and machine learning to rank the forces shaping the Cactus radiation, the coolest plant family 🏜️. Location and plant size are most powerful, followed by topographic, climatic and other biotic factors. Complexity is important https://t.co/C2QCS8uhTT pic.twitter.com/QkmYbZP2ch

— Jamie Thompson (@Jamie_T42) April 28, 2023

Note that this style is not just a half-fan style tree. To see that, let’s use a big phylogeny of scale insects from Hardy et al. (2016).

## load packages
library(phytools)
## read tree
scale_insects<-read.tree(
  file="http://www.phytools.org/Rbook/11/Coccoidea_phylogeny.tre")
## plot tree in half-fan
plotTree(scale_insects,type="fan",part=0.5,ftype="off",lwd=1)

Contrast that with the tweet above. See the differences?

Well, one can quite easily create a arc-style tree using phytools, but it requires a couple of tricks.

First, let’s add a root edge to the tree. This is straightforward. To maximize my arc, I’m going to make that edge 2 × the total depth of my original tree.

scale_insects$root.edge<-2*max(nodeHeights(scale_insects))

Next, I’ll turn this root edge into an unbranching node using rootedge.to.singleton in phytools.

scale_insects<-rootedge.to.singleton(scale_insects)

Finally, I’m going to paint two regimes on my tree – and then proceed to make one invisible!

scale_insects<-paintBranches(scale_insects,edge=scale_insects$edge[1,2],
  state="0")
cols<-setNames(c("transparent","black"),0:1)
plot(scale_insects,cols,type="fan",part=0.5,ftype="off",lwd=1)

What?! We did it!

OK, now let’s also throw some color on there – just for fun.

tmp<-collapse.singles(scale_insects)
x<-fastBM(tmp)
aa<-fastAnc(tmp,x)
aa<-setNames(c(aa[1],aa),1:(length(aa)+1)+Ntip(tmp))
obj<-contMap(scale_insects,x,method="user",anc.states=aa,plot=FALSE)
obj<-setMap(obj,viridisLite::viridis(n=10))
obj$tree<-paintBranches(obj$tree,edge=obj$tree$edge[1,2],
  state="0")
cols<-c("transparent",obj$cols)
names(cols)[1]<-"0"
plot(obj$tree,colors=cols,lwd=1,type="fan",part=0.5,ftype="off")
add.color.bar(max(nodeHeights(scale_insects)),obj$cols,subtitle="",
  title="observed or reconstructed trait value",lims=round(obj$lims,2),
  x=-0.5*max(nodeHeights(scale_insects)),y=0,prompt=FALSE,lwd=6,
  outline=FALSE)