Wednesday, March 5, 2014

Drawing a line on a plotted tree to identify members of a clade

This is in response to a user request to the effect of I would like to place a vertical bar next to all the tips descended for a node that I specify. How do I do this?. Here's my answer:

First, here's our original tree. (Simulated, but generated to look like a realistic empirical tree).

plotTree(tree)
nodelabels()
## ok, let's say our node of interest is node 43
tree<-reorder(tree)
## get the tips numbers & thus their vertical
## positions
tips<-getDescendants(tree,43)
tips<-tips[tips<=length(tree$tip.label)]
## we're going to use these later!
## they assume cex=1, but could be adjusted otherwise
sw<-max(strwidth(tree$tip.label[tips]))
sh<-max(strheight(tree$tip.label))
## max height of the tips in our clade
## + their labels
h<-max(sapply(tips,function(x,tree)
    nodeHeights(tree)[which(tree$edge[,2]==x),2],
    tree=tree))+1.1*sw
## vertical line
lines(c(h,h),range(tips)+c(-sh,sh))
## upper & lower horizontal lines to demarcate the
## clade; their specific length is arbitrary
lines(c(h-0.5*sw,h),
    c(range(tips)[1]-sh,range(tips)[1]-sh))
lines(c(h-0.5*sw,h),
    c(range(tips)[2]+sh,range(tips)[2]+sh))
## label for the clade
text(h+0.5*strwidth("W"),mean(range(tips)),
    "clade of interest name",srt=90,pos=1)

That's pretty much it. Of course, the user should adapt this code to their specific tree and visualization goals.

1 comment:

  1. You may also need to adjust xlim in plotTree to allow space for the clade label to be plotted.

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