Color tip labels based on trait
Plots a phylogeny with tip labels colored to indicate continuous or discrete trait values
color.plot.phylo(phylo, df, trait, taxa.names,
num.breaks = ifelse(is.factor(df[,trait]),
length(levels(df[,trait])), 12),
col.names = rainbow(ifelse(length(num.breaks) > 1,
length(num.breaks) - 1, num.breaks)),
cut.labs = NULL,
leg.title = NULL,
main = trait,
leg.cex = 1,
tip.labs = NULL,
...)phylo |
An object of class |
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 |
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.
The command is invoked for its side effect, a plot of the phylo with tips colored based on trait
Peter Cowan <pdc@berkeley.edu>
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