adephylo: bullseye – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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, ...)

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

Examples

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

Exploratory Analyses for the Phylogenetic Comparative Method

v1.1-11

GPL (>= 2)

Authors

Thibaut Jombart <t.jombart@imperial.ac.uk>, Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anders Ellern Bilgrau <abilgrau@math.aau.dk>

Initial release

2017-12-18