color.plot.phylo {picante}R Documentation

Color tip labels based on trait

Description

Plots a phylogeny with tip labels colored to indicate continuous or discrete trait values

Usage

  color.plot.phylo(phylo, df, trait, taxa.names,
        num.breaks = ifelse(is.factor(df[, trait]), length(levels(df[,trait])), 12),
        col.names = rainbow(ifelse(is.vector(num.breaks), length(num.breaks) - 1, num.breaks)),
        cut.labs = NULL, leg.title = NULL, main = trait, leg.cex = 1,
        tip.labs = NULL, ...)

Arguments

phylo An object of class phylo
df A dataframe containing the traits to be plotted
trait A string representing the name of column in the dataframe to be plotted
taxa.names A string representing the name of column in the dataframe that contains the names of the taxa
num.breaks For continuous traits, the number of bins to separate the data into
col.names A vector of colors to use for tip labels
leg.title A title for the tip color legend
main A main title for the plot
cut.labs A main title for the plot
leg.cex A main title for the plot
tip.labs A main title for the plot
... Additional argument to pass to the plot.phylo function

Details

If if trait is a factor then each level of the factor is plotted with the corresponding col.names value (if length(num.breaks) > length(col.names) colors are recycled.) If trait is not a factor then it is assumed to be continuous and trait is evenly divided into num.breaks levels.

Value

The command is invoked for its side effect, a plot of the phylo with tips colored based on trait

Author(s)

Peter Cowan <pdc@berkeley.edu>


[Package picante version 0.4-0 Index]