plotRegimes: Function to plot the regimes from a simmap tree

In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description

Function to plot the regimes from a simmap tree

Usage

plotRegimes(tree, col = NULL, lwd = 1, pal = rainbow, ...)

Arguments

tree	A simmap tree of class phylo or simmap with a tree$maps list
col	A named vector of colors to assign to character states, if NULL, then colors are generated from pal
lwd	A numeric value indicating the width of the edges
pal	A color palette function to generate colors if col=NULL
...	Optional arguments that are passed to plot.phylo

Details

This function uses plot.phylo to generate coordinates and plot the tree, but plots the 'maps' element of phytools' simmap format. This provides much of the functionality of plot.phylo from the ape package. Currently, only types 'phylogram', 'unrooted', 'radial', and 'cladogram' are allowed. Phylogenies must have branch lengths.

bayou documentation built on May 2, 2019, 2:46 a.m.