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

Description Usage Arguments Author(s) See Also Examples

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

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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, ...)

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(s)

Thibaut Jombart tjombart@imperial.ac.uk

See Also

table.phylo4d for non-radial plots.

The phylo4d class for storing phylogeny+data.

plot.phylo from the ape package.

dotchart.phylog.

Examples

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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
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)

}

adephylo documentation built on May 1, 2019, 7:21 p.m.