bullseye: Fan-like phylogeny with possible representation of traits on tips

Description

This function represents a phylogeny as a fan, using circles to provide a legend for distances and optionally colored symbols to represent traits associated to the tips of the tree. This function uses and is compatible with ape's plot.phylo.

Usage

bullseye(
  phy,
  traits = NULL,
  col.tips.by = NULL,
  col.pal = spectral,
  circ.n = 6,
  circ.bg = transp("royalblue", 0.1),
  circ.unit = NULL,
  legend = TRUE,
  leg.posi = "bottomleft",
  leg.title = "",
  leg.bg = "white",
  traits.inset = 1.1,
  traits.space = 0.05,
  traits.pch = 19,
  traits.cex = 1,
  alpha = 1,
  axis = TRUE,
  ...
)

Value

No return value, function produces only a plot.

The phylo4d class for storing phylogeny+data.

plot.phylo from the ape package.

dotchart.phylog.

Arguments

phy: a tree in phylo, phylo4 or phylo4d format.
traits: an optional data.frame of traits.
col.tips.by: an optional vector used to define colors for tip labels; if unamed, must be ordered in the same order as phy$tip.label.
col.pal: a function generating colors according to a given palette; several palettes can be provided as a list, in the case of several traits; the first palette is always reserved for the tip colors; this argument is recycled.
circ.n: the number of circles for the distance annotations.
circ.bg: the color of the circles.
circ.unit: the unit of the circles; if NULL, determined automatically from the data.
legend: a logical specifying whether a legend should be plotted; only one legend is displayed, with priority to tip colors first, and then to the first trait.
leg.posi, leg.title, leg.bg: position, title and background for the legend.
traits.inset: inset for positioning the traits; 1 corresponds to the circle crossing the furthest tip, 0 to the center of the plot.
traits.space: a coefficient indicating the spacing between traits.
traits.pch, traits.cex: type and size of the symbols used for the traits; recycled if needed.
alpha: alpha value to be used for the color transparency, between 0 (invisible) and 1 (plain).
axis: a logical indicating whether an axis should be displayed.
...: further arguments to be passed to plot methods from ape. See plot.phylo.

Author

Thibaut Jombart tjombart@imperial.ac.uk

Examples

Run this code


if(require(ape) && require(phylobase) && require(adegenet)){

data(lizards)
tre <- read.tree(text=lizards$hprA) # make a tree

## basic plots
bullseye(tre)
bullseye(tre, lizards$traits)

## customized
oldpar <- par(mar=c(6,6,6,6))
bullseye(tre, lizards$traits, traits.cex=sqrt(1:7), alpha=.7,
         legend=FALSE, circ.unit=10, circ.bg=transp("black",.1),
         edge.width=2)
par(oldpar)
}