phytools (version 0.4-45)

phylomorphospace: Creates phylomorphospace plot

Description

This function creates a phylomorphospace plot (a projection of the tree into morphospace) for two characters following Sidlauskas (2008; Evolution). It will also plot a discrete character mapped on tree.

Usage

phylomorphospace(tree, X, A=NULL, label=c("radial","horizontal","off"),
	control=list(), ...)

Arguments

tree

a phylogenetic tree in "phylo" format, or a modified "phylo" object with a mapped discrete character.

X

an n x 2 matrix of tip values for two characters in n species.

A

an optional m x 2 matrix (for m nodes) of values for two taits at internal nodes in the tree - if not supplied, these values will be estimated using fastAnc.

label

string indicating whether to plot the tip labels in the same direction as the terminal edge (label="radial"), horizontally label="horizontal", or not at all "off". label=TRUE and label=FALSE

control

a list containing the following optional control parameters: col.edge: a vector of edge colors; and col.node: a vector of node colors.

...

optional arguments for plotting, including xlim, ylim, xlab, ylab, lwd, colors, fsize, and node.by.map. colors is only used when there is

Value

• This function creates a phylomorphospace plot

References

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-90. Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223. Sidlauskas, B. (2008) Continuous and arrested morphological diversification in sister clades of characiform fishes: A phylomorphospace approach. Evolution, 62, 3135-3156.

Examples

tree<-pbtree(n=25)
X<-fastBM(tree,nsim=2)
phylomorphospace(tree,X,xlab="trait 1",ylab="trait 2")