phangorn (version 2.12.1)

densiTree: Plots a densiTree.

Description

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

Usage

densiTree(x, type = "phylogram", ..., alpha = 1/length(x),
  consensus = NULL, direction = "rightwards", optim = FALSE,
  scaleX = FALSE, col = 1, width = 1, lty = 1, cex = 0.8, font = 3,
  tip.color = 1, adj = 0, srt = 0, underscore = FALSE,
  label.offset = 0, scale.bar = TRUE, jitter = list(amount = 0, random =
  TRUE), tip.dates = NULL, xlim = NULL, ylim = NULL)

Value

densiTree returns silently x.

Arguments

x

an object of class multiPhylo.

type

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

...

further arguments to be passed to plot.

alpha

parameter for semi-transparent colors.

consensus

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

direction

a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards".

optim

not yet used.

scaleX

scale trees to have identical heights.

col

a scalar or vector giving the colours used to draw the edges for each plotted phylogeny. These are taken to be in the same order than input trees x. If fewer colours are given than the number of trees, then the colours are recycled.

width

edge width.

lty

line type.

cex

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

font

an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic).

tip.color

color of the tip labels.

adj

a numeric specifying the justification of the text strings of the labels: 0 (left-justification), 0.5 (centering), or 1 (right-justification).

srt

a numeric giving how much the labels are rotated in degrees.

underscore

a logical specifying whether the underscores in tip labels should be written as spaces (the default) or left as are (if TRUE).

label.offset

a numeric giving the space between the nodes and the tips of the phylogeny and their corresponding labels.

scale.bar

a logical specifying whether add scale.bar to the plot.

jitter

allows to shift trees. a list with two arguments: the amount of jitter and random or equally spaced (see details below)

tip.dates

A named vector of sampling times associated with the tips.

xlim

the x limits of the plot.

ylim

the y limits of the plot.

Author

Klaus Schliep

Details

If no consensus tree is provided densiTree computes a consensus tree, and if the input trees have different labels a mrp.supertree as a backbone. This should avoid too many unnecessary crossings of edges. Trees should be rooted, other wise the output may not be visually pleasing. jitter shifts trees a bit so that they are not exactly on top of each other. If amount == 0, it is ignored. If random=TRUE the result of the permutation is runif(n, -amount, amount), otherwise seq(-amount, amount, length=n), where n <- length(x).

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.

See Also

plot.phylo, plot.networx, jitter, rtt

Examples

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, type="cladogram", col="blue")
densiTree(bs, type="phylogram", col="green", direction="downwards", width=2)
# plot five trees slightly shifted, no transparent color
densiTree(bs[1:5], type="phylogram", col=1:5, width=2, jitter=
    list(amount=.3, random=FALSE), alpha=1)
if (FALSE) {
# phylograms are nice to show different age estimates
require(PhyloOrchard)
data(BinindaEmondsEtAl2007)
BinindaEmondsEtAl2007 <- .compressTipLabel(BinindaEmondsEtAl2007)
densiTree(BinindaEmondsEtAl2007, type="phylogram", col="red")
}