R: Plot stochastic character mapped tree

plotSimmap {phytools}

R Documentation

Plot stochastic character mapped tree

Description

Function plots one or multiple stochastic character mapped trees.

Usage

plotSimmap(tree, colors=NULL, fsize=1.0, ftype="reg", lwd=2, pts=FALSE, 
	node.numbers=FALSE, mar=NULL, add=FALSE, offset=NULL, direction="rightwards",
	type="phylogram", setEnv=TRUE, part=1.0, xlim=NULL, ylim=NULL, 
	nodes="intermediate", tips=NULL, maxY=NULL, hold=TRUE)

Arguments

`tree`	a modified object of class "phylo" or "multiPhylo" containing a stochastic mapping or set of mappings (e.g., see `read.simmap` & `make.simmap`).
`colors`	a vector with names translating the mapped states to colors - see `Examples`.
`fsize`	relative font size for tip labels.
`ftype`	font type - options are `"reg"`, `"i"` (italics), `"b"` (bold), or `"bi"` (bold-italics).
`lwd`	line width for plotting.
`pts`	logical value indicating whether or not to plot filled circles at each vertex of the tree, as well as at transition points between mapped states. Default is `FALSE`.
`node.numbers`	a logical value indicating whether or not node numbers should be plotted.
`mar`	vector containing the margins for the plot to be passed to `par`. If not specified, the default margins are [0.1,0.1,0.1,0.1].
`add`	a logical value indicating whether or not to add the plotted tree to the current plot (`TRUE`) or create a new plot (`FALSE`, the default).
`offset`	offset for the tip labels. Primarily to be used internally by `densityMap`.
`direction`	plotting direction. Options are `"rightwards"` (the default) and `"leftwards"`. Note that for some reason that is not totally clear, `node.numbers=TRUE` does not work for `direction="leftwards"`.
`type`	plot type. Can be `"phylogram"` or `"fan"`. Only a subset of options are presently available for `type="fan"`.
`setEnv`	logical value indicating whether or not to set the environment `.PlotPhyloEnv`. Setting this to `TRUE` will allow (so far, only for `type="phylogram"` compatibility with ape function `nodelabels`.
`part`	value between 0 and 1 for `type="fan"` indicating what fraction of the full circular tree to use as plotting area. For instance, `part=0.5` will plot a half fan phylogeny. It also affects the axis scaling used.
`xlim`	x-limits for the plot.
`ylim`	y-limits for the plot.
`nodes`	node placement following Felsenstein (2004; pp. 574-576). Can be `"intermediate"`, `"centered"`, `"weighted"`, or `"inner"`. So far only works for `type="phylogram"`.
`tips`	labeled vector containing the vertical position of tips. Normally this will be `1:N` for `N` tips in the tree.
`maxY`	maximum value of y to use before rotating a tree into fan configuration. This will only make a difference if different from `Ntip(tree)`.
`hold`	logical argument indicating whether or not to hold the output to the graphical device before plotting. Defaults to `hold=TRUE`.

Details

The underscore character "_" is automatically swapped for a space in tip labels, as in plot.phylo.

Value

Plots a tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.

Felsenstein, J. (2004) Inferring Phylogenies. Sinauer.

Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback. (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Examples

# simulate a mapped tree
Q<-matrix(c(-2,1,1,1,-2,1,1,1,-2),3,3)
rownames(Q)<-colnames(Q)<-letters[1:3]
tree<-sim.history(pbtree(n=100,scale=1),Q)
cols<-setNames(c("blue","red","green"),letters[1:3])
# plot the mapping
plotSimmap(tree,cols,ftype="i",fsize=0.7)

[Package phytools version 0.4-60 Index]