phytools (version 0.2-40)

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=TRUE, 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

logical value indicating whether to print tip labels next to terminal nodes in the plot.

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, and fsize. colors is only used when there is a mapped discrete characte

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--290. 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")