densiTree: Plots a densiTree.

Description

An R function to plot trees similar to those produced by DensiTree.

Usage

densiTree(x, type = "cladogram", alpha = 1/length(x), consensus = NULL, optim = FALSE, 
    scaleX = FALSE, col = 1, width = 1, cex = 0.8, ...)

Arguments

an object of class multiPhylo.

type

a character string specifying the type of phylogeny, so far "cladogram" (default) or "phylogram" (the default) are supported.

alpha

parameter for semi-transparent colors.

consensus

A tree which is used to define the order of the tip labels.

optim

not yet used.

scaleX

scale trees to have identical heights.

col

edge color.

width

edge width.

cex

a numeric value giving the factor scaling of the tip labels.

...

further arguments to be passed to plot.

Details

If no consensus tree is provided densiTree computes a rooted mrp.supertree as a backbone. This should avoid too many unnecessary crossings of edges. Trees should be rooted, other wise the output may not make sense.

References

densiTree is inspired from the great www.cs.auckland.ac.nz/~remco/DensiTree{DensiTree} program of Remco Bouckaert.

Remco R. Bouckaert (2010) DensiTree: making sense of sets of phylogenetic trees Bioinformatics, 26 (10), 1372-1373.

Examples

Run this code

data(Laurasiatherian)
set.seed(1)
bs <- bootstrap.phyDat(Laurasiatherian, FUN = 
   function(x)upgma(dist.hamming(x)), bs=25)
# cladogram nice to show topological differences
densiTree(bs, optim=TRUE, type="cladogram", col="blue")
densiTree(bs, optim=TRUE, type="phylogram", col="green")
# phylogram are nice to show different age estimates
require(PhyloOrchard)
data(BinindaEmondsEtAl2007)
BinindaEmondsEtAl2007 <- .compressTipLabel(BinindaEmondsEtAl2007) 
densiTree(BinindaEmondsEtAl2007, type="phylogram", col="red")