EXPERIMENTAL: plotting members of communities (or plots) on a phylogeny

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Description

phy.dotplot is used to visually display species membership in communities, generating one plot per community

Usage

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phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outfile=NULL,...)

Arguments

sp.plot

a community dataset in spacodiR format (see as.spacodi)

phy

a phylogenetic tree of class phylo; see read.tree

edge.width

a value specifying the thickness of branches on the plotted phylogen(ies)

lab.adj

a vector of two values, adjusting plotted group names, with respect to the x- and y-axes

tips.adj

a vector of two values, adjusting the position of plotted symbols (referencing the x- and y-axes)

tips.cex

a value for character expansion of plotted symbols for present species

pch

a value for the plotting character for species-presence symbols: see par

print.labs

Boolean; returns array of tip labels, group membership of species, and tree to the console

outfile

an optional .pdf file to which to write output

...

additional plotting options to be specified

Details

For several groups (fewer than sixteen, for optimal visibility), this function will generate a plot of phylogenies, group labels for each tree, and symbols demarcating a particular species that is present within the group. This may be useful in visual representations of phylogenetic overdispersion or underdispersion within plots (or other groups). Particularly the tips.adj option may require fiddling in order for symbols to appear precisely where they should.

Value

A collection of trees (or a single tree), where species present within a predefined group are represented with a dark circle at the tip (if pch=21).

Author(s)

Jonathan Eastman

Examples

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data(sp.example)
attach(sp.example)

phy.dotplot(sp.plot=spl[,1:9], phy=phy, tips.adj=c(0.50,0.55), lab.adj=c(0,1))

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