cartoon.plot: 'cartoon.plot' Plot phylogenies with cartoon-ised polytomies

In willpearse/willeerd: Will's Eco-Evo R coDe

Description

cartoon.plot Plot phylogenies with cartoon-ised polytomies

Usage

cartoon.plot(tree, tip.groups = vector("list", 0), clade.col = NULL,
  br.clade.col = NULL, auto.polies = FALSE, ...)

Arguments

tree	ape::phylo object
tip.groups	list where each element are the tip *numbers* that should be in a cartoon polytomy (see auto.polies below)
clade.col	a vector of length tip.groups with colours for each polytomy OR a single colour for all polytomies OR NULL (the default) to make all polytomies rainbow-coloured
br.clade.col	the colours of the branches inside the cartoon. If NULL (the default, which you probably want), they don't show up in the plot.
auto.polies	generate tip.groups by making a cartoon polytomy for all terminal polytomies. Setting this to TRUE (default is FALSE) will over-ride any tip.groups information. Note the function's return values is you want to set up a weird interaction of polytomies
...	additional arguments to pass to ape::plot.phylo

Details

Makes a simple 'cartoon' phylogeny where polytomies are joined together in a big triangle. Could cause problems if you're outputting to PDF, sorry!

Value

A list containing the tip.groups plotted, the clade colours they were plotted under, the edges that were obscured by the cartoon printing, and a list of the number of the node that each polytomy started under

Author(s)

Will Pearse

Examples

## Not run: 
require(ape)
tree <- read.tree(text="(((((A,B,C,D,E),(F,G,H,I,J)),H),K),L);")
cartoon.plot(tree, auto.polies=TRUE)
cartoon.plot(tree, list(1:5, 6:10), clade.col="grey30")
cartoon.plot(tree, list(1:5, 6:10), clade.col=c("blue", "red"))

## End(Not run)

willpearse/willeerd documentation built on May 4, 2019, 6:27 a.m.