color.plot.phylo: Color tip labels based on trait
In picante: Integrating Phylogenies and Ecology

Description Usage Arguments Details Value Author(s)

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 `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

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>

picante documentation built on July 1, 2020, 10:57 p.m.