Friday, January 30, 2015

Arbitrary vertical spacing of the tips on a plotted tree

Today a R-sig-phylo reader asked the following:

I am looking for a way to manually specify varying vertical distance between the tips in a phylogeny (because i want to add several lines of text to some of the tips).

I.e. for the tree library(ape) TREE=read.tree(text=“((Tip_1:1,Tip_2:1):1,Tip_3:2);)”)

Is there a way for instance through plot phylo to print place the tips in the heights of c(1,2,6) as opposed to c(1,2,3) as they would be normally in plot.phylo.

This is not presently possible, but I realized immediately that this would be pretty straightforward to add to phytools plotSimmap because the way that functions works is by first assigning 1:N to the N tips of the tree, and then works backwards to assign the vertical position of all internal nodes via a post-order traversal.

I responded to the query, and now I have also posted code online that permits exactly this type of manipulation. The new phytools build with this update can be obtained here. Here's a demo using the code of the original query:

library(ape)
TREE=read.tree(text="((Tip_1:1,Tip_2:1):1,Tip_3:2);")
library(phytools)
packageVersion("phytools")
## [1] '0.4.43'
## normal vertical spacing
plotTree(TREE)

plot of chunk unnamed-chunk-1

## modified spacing
tips<-setNames(c(1,2,6),TREE$tip.label)
tips
## Tip_1 Tip_2 Tip_3 
##     1     2     6
plotTree(TREE,tips=tips)

plot of chunk unnamed-chunk-1

Note that there is nothing here to prevent us from plotting trees with line crossing! For instance:

tree<-pbtree(n=26,tip.label=LETTERS)
tips<-setNames(1:26,sample(LETTERS))
plotTree(tree,tips=tips)

plot of chunk unnamed-chunk-2

Yikes!

We can also do other weird stuff, like this:

plotTree(tree,tips=setNames(log(1:26),tree$tip.label),ftype="off")

plot of chunk unnamed-chunk-3

plotTree(tree,tips=setNames((1:26)^2,tree$tip.label),ftype="off")

plot of chunk unnamed-chunk-3

Well, you get the idea.

That's it.

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