Sunday, January 5, 2020

Slanted fan-style tree using phytools

Here at the SSB stand-alone meeting (aka. Systematics in the Swamp) in Gainesville, Florida I just saw a talk by Matt McGee in which he showed the following circular (aka. 'fan') slanted tree:

So far as I know, there is no option to create such a tree in R. It's not hard to do yourself, however. Let's see how. To do it, I will using plotTree and phylomorphospace. We will use plotTree to find compute the x, y coordinates of the nodes & tips, and then we'll use phylomorphospace to draw the lines between them!

library(phytools)
tree<-pbtree(n=200) ## simulated tree
## preliminaries
plotTree(tree,fsize=0.5,type="fan",lwd=1,
    ftype="off")

plot of chunk unnamed-chunk-1

obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
X<-cbind(obj$xx[1:Ntip(tree)],obj$yy[1:Ntip(tree)])
rownames(X)<-tree$tip.label
A<-cbind(obj$xx[1:tree$Nnode+Ntip(tree)],
    obj$yy[1:tree$Nnode+Ntip(tree)])
rownames(A)<-1:tree$Nnode+Ntip(tree)
## now let's create our plot
par(fg="transparent") ## to turn off axes
phylomorphospace(tree,X=X,A=A,ftype="off",
    node.size=c(0,0),xlim=obj$x.lim,
    ylim=obj$y.lim,axes=FALSE)

plot of chunk unnamed-chunk-1

par(fg="black")

If we'd like, we can also do this showing the topology only, as is often done with slanted trees. Here, I'll use an empirical tree from Near et al. (2011) that can be downloaded here.

darter.tree<-read.tree(file="http://www.phytools.org/blog/darter.tre")
plotTree(compute.brlen(darter.tree,power=0.5),
    fsize=0.5,type="fan",lwd=1,fsize=0.3,
    ftype="i")

plot of chunk unnamed-chunk-2

obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
X<-cbind(obj$xx[1:Ntip(darter.tree)],
    obj$yy[1:Ntip(darter.tree)])
rownames(X)<-darter.tree$tip.label
A<-cbind(obj$xx[1:darter.tree$Nnode+
    Ntip(darter.tree)],
    obj$yy[1:darter.tree$Nnode+
    Ntip(darter.tree)])
rownames(A)<-1:darter.tree$Nnode+
    Ntip(darter.tree)
par(fg="transparent")
phylomorphospace(darter.tree,X=X,A=A,ftype="off",
    node.size=c(0,0),xlim=obj$x.lim,
    ylim=obj$y.lim,xaxt="n")
par(fg="black")
## as a last step we can put our labels back on
plotTree(darter.tree,fsize=0.5,type="fan",lwd=1,
    fsize=0.3,ftype="i",add=TRUE,color="transparent")

plot of chunk unnamed-chunk-2

I personally find this visualization quite visually pleasing - but more difficult to read than a standard fan-style tree. Nonetheless, to each their own! Look for this to be automated in phytools soon.

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