Plotting trick to connect aligned labels to the tips of a graphed non-ultrametric tree using phytools

I feel certain that I’ve shown this before, but the following is a simple ‘hack’ to plot a non-ultrametric rooted tree with aligned tip labels & dotted lines connecting each tip to the corresponding label.

To illustrate it, I’m going to quickly estimate an empirical tree using Maximum Likelihood with the excellent package phangorn.

library(phytools)
library(phangorn)
data("Laurasiatherian")
mammal.ML<-pml_bb(Laurasiatherian,model="GTR+G(4)+I",
  control=pml.control(trace=0))
mammal.ML

## model: GTR+G(4)+I 
## loglikelihood: -44565.74 
## unconstrained loglikelihood: -17300.92 
## Proportion of invariant sites: 0.292363 
## Model of rate heterogeneity: Discrete gamma model
## Number of rate categories: 4 
## Shape parameter: 0.5958122 
##         Rate Proportion
## 1 0.00000000  0.2923630
## 2 0.07383092  0.1769092
## 3 0.43798783  0.1769092
## 4 1.24239881  0.1769092
## 5 3.89839853  0.1769092
## 
## Rate matrix:
##           a          c          g         t
## a  0.000000  3.6283208 14.0268552  3.887259
## c  3.628321  0.0000000  0.4366659 25.447966
## g 14.026855  0.4366659  0.0000000  1.000000
## t  3.887259 25.4479659  1.0000000  0.000000
## 
## Base frequencies:  
##         a         c         g         t 
## 0.3321866 0.1990791 0.2040652 0.2646691

This dataset has a very clear outgroup, the platypus, so I’ll use that to root it as follows. Just for aesthetic purposes, I’ll root the tree 10% of the way along the edge leading to “Platypus” rather than at the node itself (but this is non-scientific – we don’t have any information about the real position of the root along the edge in this tree).

mammal_tree<-mammal.ML$tree
nn<-which(mammal_tree$tip.label=="Platypus")
mammal_tree<-reroot(mammal_tree,nn,
  position=0.1*mammal_tree$edge.length[which(mammal_tree$edge[,2]==nn)])
mammal_tree

## 
## Phylogenetic tree with 47 tips and 46 internal nodes.
## 
## Tip labels:
##   Platypus, Wallaroo, Possum, Bandicoot, Opposum, Armadillo, ...
## Node labels:
##   Root, 1, 0.999, 0.885, 1, 0.89, ...
## 
## Rooted; includes branch lengths.

Now I’m ready for my plotting routine.

par(lty="dotted")
plotTree(force.ultrametric(mammal_tree,method="extend",message=FALSE),
  lwd=1,fsize=0.7,offset=0.5)
xlim<-get("last_plot.phylo",envir=.PlotPhyloEnv)$x.lim
par(lty="solid")
plotTree(mammal_tree,xlim=xlim,lwd=3,add=TRUE,ftype="off")

The way this code chunk works is that I first plot my tree but with all tips extended to line up with a total length equal to the highest tip in the phylogeny. (This is accomplished by internally calling phytools::force.ultrametric.) Next, I pull out the x-axis limits using get("last_plot.phylo",envir=.PlotPhyloEnv). Finally, I overplot the ultrametric tree with my estimated phylogeny.

Having done this, it should be fairly evident that we can apply it to other plotting styles & cases as well. In the example below, I plot my tree upwards & also overplot in white to create a “outline” effect. Because I’m plotting upwards, I need to switch ylim for xlim.

par(lty="dotted")
plotTree(force.ultrametric(mammal_tree,method="extend",
  message=FALSE),lwd=1,fsize=0.8,offset=1,direction="upwards")
ylim<-get("last_plot.phylo",envir=.PlotPhyloEnv)$y.lim
par(lty="solid")
plotTree(mammal_tree,ylim=ylim,lwd=5,add=TRUE,ftype="off",
  direction="upwards",color="#000080")
plotTree(mammal_tree,ylim=ylim,lwd=3,add=TRUE,ftype="off",
  direction="upwards",color="white")

Unfortunately, the same approach didn’t work for phytools::sigmoidPhylogram, so I thought of this alternative hack.

plotTree(force.ultrametric(mammal_tree,method="extend",
  message=FALSE),lwd=1,fsize=0.8,offset=1,direction="upwards",
  color="transparent")
pp.1<-get("last_plot.phylo",envir=.PlotPhyloEnv)
plotTree(mammal_tree,lwd=1,fsize=0.8,offset=1,direction="upwards",
  ylim=pp.1$y.lim,add=TRUE,plot=FALSE)
pp.2<-get("last_plot.phylo",envir=.PlotPhyloEnv)
for(i in 1:Ntip(mammal_tree))
  lines(rep(pp.1$xx[i],2),c(pp.1$yy[i],pp.2$yy[i]),lty="dotted")
sigmoidPhylogram(mammal_tree,ftype="off",ylim=ylim,add=TRUE,
  direction="upwards",lwd=3,color="#000080")

Who can figure out what I did here?