Thursday, March 5, 2015

Splitting a tree over mutiple plotting devices or pages

An R-sig-phylo subscriber asked the following yesterday:

I'm searching for a way to plot a huge phylogenetic tree to multiple pages in one searchable pdf file from R…. Does anybody know if this is possible and an effective way of doing this?

Well, my first response was that phytools has a function, splitplotTree, that can be used to split a plotted tree across columns in a single plotting window, or across plotting devices. Consequently, I responded:

One option is to use the function splitplotTree in phytools. By default it plots the split tree in two columns, but there is an option to split it into two windows. Then each plotted tree could be saved as a PDF.

On further thought, I realized that there is a better way. plotSimmap in phytools (and, consequently, plotTree, which uses plotTree, which uses plotSimmap internally) allows the user to control the y-limits of the plot. As a result it would be straightforward to write a simple wrapper that split the tree using a moving window over the plotting area. It also allows us to relatively easily split our tree over more than two pages. The following is an example of what that might look like:

split.plotTree<-function(tree,splits=NULL,file=NULL,...){
    ef<-0.037037037037
    if(!is.null(file)) pdf(file,width=8.5,height=11)
    if(is.null(splits)) splits<-(floor(0.5*Ntip(tree))+0.5)/Ntip(tree)
    S<-matrix(c(0,splits,splits,1+1/Ntip(tree)),length(splits)+1,2)
    S<-cbind(S[,1]+ef*(S[,2]-S[,1]),S[,2]-ef*(S[,2]-S[,1]))
    for(i in nrow(S):1){
        if(is.null(file)&&i<nrow(S)) par(ask=TRUE)
        plotTree(tree,ylim=Ntip(tree)*S[i,],...)
    }
    if(!is.null(file)) oo<-dev.off()
}

Note that in order to avoid having the tips & edges near the bottom of each page plot at the top of the following page, I had to trim ~4% off of the top & bottom of each plot. This is because for a given y range, R will create a plotting area that is 4% on each size larger than the area specified.

OK, now let's try it:

library(phytools)
n<-100
## create realistic tip labels
foo<-function(i) paste(sample(LETTERS,1),"._",paste(sample(letters,round(runif(1,min=4,max=8))),
    collapse=""),sep="")
tree<-pbtree(n=n,tip.label=sapply(1:n,foo))
splits<-c(0.255,0.505,0.755)
split.plotTree(tree,splits,ftype="i",mar=rep(1.1,4),fsize=0.9,lwd=1)

plot of chunk unnamed-chunk-2 plot of chunk unnamed-chunk-2 plot of chunk unnamed-chunk-2 plot of chunk unnamed-chunk-2

The splits mark the proportions of the plotted graph that I want to be displayed on each page.

We can also send the output to a multi-page PDF:

split.plotTree(tree,splits,ftype="i",mar=rep(1,4),file="split.plotTree.pdf",lwd=1)

The output is here: split.plotTree.pdf.

That's it.

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