phytools: phylomorphospace – R documentation

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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.

project.phylomorphospace animates the phylomorphospace projection.

Usage

phylomorphospace(tree, X, A=NULL, label=c("radial","horizontal","off"),
   control=list(), ...)
project.phylomorphospace(tree, X, nsteps=200, sleep=0,
	direction=c("to","from","both"), ...)

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` are also acceptable, for compatibility with phytools <= 0.3-03.
`control`	a list containing the following optional control parameters: `col.edge`: a vector of edge colors; and `col.node`: a vector of node colors.
`nsteps`	for `project.phylomorphospace` the number of frames in the animation between the phylogeny & the phylomorphospace or vice versa.
`sleep`	for `project.phylomorphospace` the time between frames.
`direction`	for `project.phylomorphospace` whether to morph `"to"` a phylomorphospace, `"from"` a phylomorphospace, or there & back again (`"both"`).
`...`	optional arguments for plotting, including `xlim`, `ylim`, `xlab`, `ylab`, `lwd`, `colors`, `fsize`, and `node.by.map`. `colors` is only used when there is a mapped discrete character on the tree, in which case `control$col.edge` is ignored. `fsize` is relative to the default, which is `textxy(...,cx=0.75)`. `node.by.map` is a logical value (defaults to `FALSE` which tells the function whether or not to plot the node colors using the colors of the mapped discrete character. Setting this option to `TRUE` will cause `control$col.node` to be ignored. `node.size` is a vector containing the point size relative to the default (see `par` for plotted internal nodes and tips, respectively. Defaults to `node.size=c(1,1.3)`. If only one number is provided it will be recycled. `axes` is a logical value indicating whether or not axes should be plotted (see `plot.default`. Finally, `add` indicates whether to add the phylmorphospace to the current plot.

Value

This function creates a phylomorphospace plot

Author(s)

Liam Revell liam.revell@umb.edu

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

## load tree & data from Revell & Collar (2009)
data(sunfish.tree)
data(sunfish.data)
## set colors for mapped discrete character
cols<-setNames(c("blue","red"),
    levels(sunfish.data$feeding.mode))
phylomorphospace(sunfish.tree,sunfish.data[,3:2],
    colors=cols,bty="l",ftype="off",node.by.map=TRUE,
    node.size=c(0,1.2),xlab="relative buccal length",
    ylab="relative gape width")
title(main="Phylomorphospace of buccal morphology in Centrarchidae",
    font.main=3)

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19