color.tips.by.element: Color the tip labels of a tree according to elements of the...

In andrew-hipp/morton: Tools for manipulation of phylogenetic, genetic, and other biodiversity data

Color the tip labels of a tree according to elements of the tip labels

Description

Takes a tree with tip labels structured in a consistent manner, and colors according to unique elements

Usage

color.tips.by.element(tr, element = 6, delim = "|", fixed = TRUE, whiteOut = "NA", addLegend = T,
colorIt = FALSE, byLabels = TRUE, tip.cex = 0.1, dot.pch = 1, blank.tips = T, ...)

Arguments

tr	a phylo object
element	which element of the delimited labels to use for coloring
delim	label delimters
fixed	boolean: should strsplit use fixed = TRUE or not
whiteOut	a character vector identifying labels that should be whited out; defaults to NA
addLegend	boolean
colorIt	boolean: if TRUE, colored dots are added at the tips
byLabels	boolean: if TRUE, tip labels are reassigned the label element, and colored
tip.cex	cex for tip labels
dot.pch	character code for colorIt option
blank.tips	boolean: if TRUE, tip labels are not plotted
...	additional arguments to plot.phylo

Details

The default assumes tips are pipe-delimited. If tips are species|country|subcountry|collectorNumber, for example, use element = 2 to color by country.

Value

the plot.phylo value, returned invisibly

Author(s)

Andrew Hipp

See Also

section.coloring label.elements

andrew-hipp/morton documentation built on April 7, 2024, 12:15 p.m.