cophylo: Creates a co-phylogenetic plot

Description

This function creates an object of class "cophylo" or, in the case of plot.cophylo, plots that object. The function can (optionally) first attempt to rotate the nodes of both trees to optimize vertical matching of tips.

Usage

cophylo(tr1, tr2, assoc=NULL, rotate=TRUE, ...)
## S3 method for class 'cophylo':
plot(x, ...)

Arguments

tr1

object of class "phylo".

tr2

object of class "phylo".

assoc

matrix containing the tip labels in tr1 to match to the tip labels in tr2. Note that not all labels in either tree need to be included; and, furthermore, one label in tr1 can be matched with more than one label in

rotate

logical argument indicating whether nodes on both trees should be rotated to attempt to match in vertical position.

in the case of plot.cophylo, an object of class "cophylo" to be plotted.

...

optional arguments to be passed to tipRotate, or, in the case of plot.cophylo, to the internally used tree plotting function, phylogram. phylogram takes similar argu

Value

An object of class "cophylo" which includes the following components or a pair of plotted facing phylogenies with links between tips as specified in assoc.

Details

If no matrix of associations, assoc, is provided, then cophylo will look for exact matches of tip labels between trees.

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Examples

Run this code

tr1<-pbtree(n=26,tip.label=LETTERS)
tr2<-pbtree(n=26,tip.label=sample(LETTERS))
obj<-cophylo(tr1,tr2)
plot(obj)

Run the code above in your browser using DataLab