phytools (version 0.2-40)

plotSimmap: 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=TRUE, 
     node.numbers=FALSE, mar=NULL, add=FALSE, offset=NULL, direction="rightwards")

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 TRUE.

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".

Value

• plots a tree.

Details

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

References

Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138. Bollback, J. P. 2006. Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.

See Also

densityMap, make.simmap, read.simmap

Examples

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])
	plotSimmap(tree,cols,ftype="i",fsize=0.7)