phytools (version 0.2-40)

phenogram: Plot phenogram (traitgram)

Description

Function plots a traitgram, that is, a projection of the phylogenetic tree in a space defined by phenotype (on the y axis) and time (on the x). If a discrete character is mapped on the tree this will also be plotted.

Usage

phenogram(tree, x, fsize=1.0, ftype="reg", colors=NULL, axes=list(), add=FALSE, ...)

Arguments

tree

an object of class "phylo", with or without a mapped discrete character.

x

a vector containing the states at the tips or the states at all the tips and the internal nodes of the tree.

fsize

relative font size for tip labels.

ftype

font type - options are "reg", "i" (italics), "b" (bold), or "bi" (bold-italics).

colors

colors for plotting the mapped character (if available) in tree. If no character is mapped on the tree, then a single color for all the branches of the tree can be provided.

axes

list of axis dimensions. Items are time and trait.

add

optional logical value indicating whether to add to an open plot. If TRUE, then new axes will not be plotted.

...

optional arguments including xlim, ylim, log, main, sub, xlab, ylab, asp, type, lty, lwd, offset, <

Value

• plots a traitgram, optionally with a mapped discrete character.

Details

For spread.labels=TRUE numerical optimization is performed to optimize the distribution of the labels vertically, where the solution depends on the vector spread.cost containing the cost of overlap (first) and the cost of deviation from the vertical position of the tip. Because this is done via numerical optimization, plotting may hang briefly while the best solution is found (especially for large trees).

Examples

tree<-pbtree(n=20,scale=2)
	x<-fastBM(tree)
	phenogram(tree,x)
	# or, simulate a discrete character history
	tree<-sim.history(tree,Q=matrix(c(-1,1,1,-1),2,2),anc="1")
	# simulate in which the rate depends on the state
	x<-sim.rates(tree,c(1,10))
	phenogram(tree,x)
	# now use spread.labels
	tree<-pbtree(n=40)
	x<-fastBM(tree)
	phenogram(tree,x,spread.labels=TRUE,spread.cost=c(1,0))