densityMap: Plot posterior density of stochastic mapping on a tree

Description

Function plots a tree with the posterior density for a mapped character from stochastic character mapping on the tree. Since the mapped value is the probability of being in state "1", only binary [0,1] characters are allowed.

Usage

densityMap(trees, res=100, fsize=NULL, ftype=NULL, lwd=3, check=FALSE,
     legend=NULL, outline=FALSE)

Arguments

trees

set of phylogenetic trees in a modified "multiPhylo" object. Values for a discrete character are mapped on the tree. See make.simmap and read.simma

res

resolution for gradient plotting. Larger numbers indicate a finer (smoother) gradient.

fsize

relative font size - can be a vector with the second element giving the font size for the legend.

ftype

font type - see options in plotSimmap. As with fsize, can be a vector with the second element giving font type for the legend.

lwd

line width for branches.

check

check to make sure that the topology and branch lengths of all phylogenies in trees are equal.

legend

if FALSE no legend is plotted; if a numeric value, it gives the length of the legend in units of branch length. Default is 0.5 times the total tree length.

outline

logical value indicating whether or not to outline the branches of the tree in black.

Value

plots a tree.

References

Revell, L. J. Submitted. Two new graphical methods for mapping trait evolution on phylogenies. 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.

Description

Usage

Arguments

Value

References

See Also