Wednesday, March 5, 2014

Extracting a "phylo" object from the last plotted tree

I stumbled on this trick while working on something else. When plot.phylo in ape or plotTree or plotSimmap in phytools are used to plot a tree the environmental variable last_plot.phylo is created. This variable is used to by nodelabels, tiplabels, and other functions that are used to add elements to the plotted tree. This object contains mostly information about the plotted tree - coordinates of vertices, etc. Today I realized that (almost) the entire "phylo" object can be reconstructed from this variable.

Here's how that works:

> tree<-pbtree(n=26,tip.label=LETTERS)
> plotTree(tree)
> ## delete the tree from memory
> rm(tree)
> ## last plotted tree
> lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
> ## reconstruct the tree in memory
> tree<-list(edge=lastPP$edge,
  tip.label=1:lastPP$Ntip,
  Nnode=lastPP$Nnode)
> ## now get the edge lengths
> H<-matrix(lastPP$xx[tree$edge],nrow(tree$edge),2)
> tree$edge.length<-H[,2]-H[,1]
> class(tree)<-"phylo"
> plotTree(tree)

The only thing we've lost is the tip labels.

That's it on this.

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