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 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")
## Not run: 
# # phylograms are nice to show different age estimates
# require(PhyloOrchard)
# data(BinindaEmondsEtAl2007)
# BinindaEmondsEtAl2007 <- .compressTipLabel(BinindaEmondsEtAl2007) 
# densiTree(BinindaEmondsEtAl2007, type="phylogram", col="red")
# ## End(Not run)