phytools: cophylo – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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 `tr2`, or vice versa.
`rotate`	logical argument indicating whether nodes on both trees should be rotated to attempt to match in vertical position.
`x`	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 arguments to `plotSimmap`, such as `fsize`, `ftype`, `lwd`, and `pts`, though not all options from `plotSimmap` and `plotTree` are available. If `fsize` is supplied as a vector, different size fonts for the left & right facing trees may be used. In addition, the optional argument `scale.bar`, which should be a vector containing the lengths of the scale bars desired for the right & left trees, will add scale bars to the plot when supplied to `plot.cophylo`. If either tree contains polytomies, the `cophylo` argument `rotate.multi` should be set to `TRUE`. If curved linking lines are desired, the `plot.cophylo` argument `link.type` should be set to `"curved"`. Other arguments for the `plot` method include `link.col`, `link.lty`, and `link.lwd`, which can be supplied as a scalar or a vector in which the order of the elements corresponds to the order of the associations in `assoc`. Finally, `edge.col`, a list consisting of two vectors (`left` and `right`) can be used to specify the edge colors of the two left & right plotted trees. Note that the edge order is the same as in the rotated trees, assuming that a rotation has been performed on `x`.

Details

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

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.

Author(s)

Liam Revell liam.revell@umb.edu

References

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

Examples

## load data from Lopez-Vaamonde et al. (2001)
data(wasp.trees)
data(wasp.data)
## create co-phylogenetic object
wasp.cophylo<-cophylo(wasp.trees[[1]],wasp.trees[[2]],
    assoc=wasp.data)
## plot co-phylogenies
plot(wasp.cophylo,link.type="curved",link.lwd=4,
     link.lty="solid",link.col=make.transparent("red",
     0.25))
par(mar=c(5.1,4.1,4.1,2.1))

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19