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.
cophylo(tr1, tr2, assoc=NULL, rotate=TRUE, ...)
# S3 method for cophylo
object of class
object of class
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.
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 takes similar arguments to
plotSimmap, such as
pts, though not all options from
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
rotate.multi should be set to
TRUE. If curved linking lines are desired, the
link.type should be set to
"curved". Other arguments for the
plot method include
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
edge.col, a list consisting of two vectors (
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
An object of class
"cophylo" which includes the following components or a pair of plotted facing phylogenies with links between tips as specified in
If no matrix of associations,
assoc, is provided, then
cophylo will look for exact matches of tip labels between trees.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.