iteRates (version 3.1)

color.tree.plot: color.tree.plot

Description

This function plots phylogenetic trees on the current graphical device and indicates potential regions of the tree that might have undergone a shift in diversification rate.

Usage

color.tree.plot(out, tree, p.thres = 1, evid.thres=0, PorE=1, show.node.label = FALSE, 
NODE = TRUE, PADJ = NULL, scale = 1, col.rank = TRUE, breaks = 50, ...)

Arguments

out

the output object from comp.subs.

tree

an object of class "phylo" used in the comp.subs analysis.

p.thres

a numeric between 0 and 1 setting the threshold to plot rate-shifts with p-value<=p.thres. Default is 1.0.

evid.thres

a numeric setting the threshold to plot rate-shifts with evidence ratio >=evid.thres. Default is 0.

PorE

a switch to indicate whether rate-shifts are indicated based on the p-value (PorE=1) or the evidence ratio (PorE=1).

show.node.label

a logical indicating whether the node labels need to be plotted with the tree. Default is FALSE.

NODE

a logical switch between identifying rate-shifts on trees by coloring "nodes" or "branches". Default is TRUE.

PADJ

a character vector to adjust p-values from comp.subs for multiple comparison. Options are identical to the ones in p.adjust in the stats package including "holm","hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default is NULL.

scale

a numeric that controls the size of the colored nodes or thickness of colored branch lengths used to indicate rate-shifts. Default is 1.

col.rank

a logical indicating whether various instances of potential rate-shifts should be colored based on the rank of the p-value or the absolute magnitude of the rate-shift. Default is TRUE indicating use of ranks instead of magnitude.

breaks

a numeric indicating the range of colors to be used for plotting. Choosing a smaller value will lead to big differences in colors while a bigger value will lead to finer variations in colors.

...

additional arguments to be passed to plot.phylo in the ape package.

Value

color.tree.plot returns only a graphical device output.

Details

When passing an object of class "phylo" (tree) follow the guidelines in plot.phylo in the ape package. Also make sure that the tree passed to color.tree.plot is the same as the one used to generate out from comp.subs.

References

Shah, P., B. M. Fitzpatrick, and J. A. Fordyce. 2013. A parametric method for assessing diversification rate variation in phylogenetic trees. Evolution 67:368-377.

See Also

comp.subs, plot.phylo

Examples

Run this code

data(geospiza)
attach(geospiza)

output.geospiza <- comp.subs(geospiza.tree)

color.tree.plot(out=output.geospiza, tree= geospiza.tree)	
color.tree.plot(out=output.geospiza, tree= geospiza.tree, NODE=FALSE)	
color.tree.plot(out=output.geospiza, tree= geospiza.tree, p.thres=1)	
color.tree.plot(out=output.geospiza, tree= geospiza.tree, scale=2)	

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