phylomorphospace {phytools}R Documentation

Creates phylomorphospace plot


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.


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



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


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


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.


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.


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 colors is only used when there is a mapped discrete character on the tree, in which case control$col.edge is ignored. fsize is relative to the default, which is textxy(...,cx=0.75). is a logical value (defaults to FALSE which tells the function whether or not to plot the node colors using the colors of the mapped discrete character. Setting this option to TRUE will cause control$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.


This function creates a phylomorphospace plot


Liam Revell


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.


phylomorphospace(tree,X,xlab="trait 1",ylab="trait 2")

[Package phytools version 0.4-60 Index]