Even more on plotting subtrees as triangles on a phylogenetic backbone tree

This is pretty much guaranteed to be the last post on this topic today, but I made some additional refinements of plot.backbonePhylo, my new plotting method to show subtrees as triangles.

The three main changes are as follows: (1) following Luke's suggestion, subtrees containing only 1 taxon are now plotted as a line (actually - a triangle with zero width, but I guarantee you won't be able to tell the difference), instead of as a triangle with unit width; (2) following Graham Slater's suggestion, I made a small change so that there is a space between adjacent triangles - the consequence is that clades with 2 taxa are of unit length, clades with 10 taxa are 9 units in width, etc., which actually lines up with tips containing 1 taxon, which now have unit width; and (3) I added the optional scaling factor vscale, which scales the vertical dimension so that large subtrees can be portrayed while still allowing singletons and spacing between triangles.

All of these updates are available here, but are also part of a new phytools build (phytools 0.3-51).

Here's a demo:

> library(phytools)
> packageVersion("phytools")
[1] ‘0.3.51’
> library(geiger) # to help us build our tree
> ## now let's create our backbone tree with
> ## random subtree diversities
> tree<-transform(pbtree(n=10),model="lambda",lambda=0.5)
> ## for old versions of geiger, use lambdaTree
>
> ## create a translation table
> ## leaving a couple of single-taxon clades for fun
> tip.label<-sample(tree$tip.label,8)
> clade.label<-LETTERS[1:8]
> N<-ceiling(runif(n=8,min=1,max=20))
> ## set crown node depth to 1/2 the maximum depth
> depth<-sapply(tip.label,function(x,y) 0.5*y$edge.length[which(tree$edge[,2]==which(y$tip.label== x))],y=tree)
> trans<-data.frame(tip.label,clade.label,N,depth)
> rownames(trans)<-NULL
> rm(tip.label,clade.label,N,depth)
>
> ## here's what trans looks like
> trans
  tip.label clade.label  N     depth
1        t4           A  3 1.0079214
2        t8           B 13 0.8367549
3        t1           C 15 1.1433276
4        t3           D  8 1.0129504
5        t6           E 12 0.9687320
6        t5           F  2 0.9687320
7        t9           G 14 0.7253729
8       t10           H 17 0.7253729
> 
> ## convert
> tt<-phylo.toBackbone(tree,trans)
>
> ## plot
> plot(tt)

> ## now let's make our clades much bigger
> trans$N<-trans$N*10
> trans
  tip.label clade.label   N     depth
1        t4           A  30 1.0079214
2        t8           B 130 0.8367549
3        t1           C 150 1.1433276
4        t3           D  80 1.0129504
5        t6           E 120 0.9687320
6        t5           F  20 0.9687320
7        t9           G 140 0.7253729
8       t10           H 170 0.7253729
> tt<-phylo.toBackbone(tree,trans)
> plot(tt)

> ## now let's use the new parameter vscale
> plot(tt,vscale=0.1)

Pretty cool.

We have to be careful with this, though, because if we adjust our clade widths such that any are less than 1 unit then we are going to get some really weird plots.