section.coloring: Color Tree Tips by Section

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

Color Tree Tips by Section

Description

Plot a circular tree with tips colored by section to a PDF file. Assumes that section is the sixth pipe-delimited part of a tip label.

Usage

section.coloring(tr, tipChar = "-", tiplty = 0, 
                 pdfTitle = paste("trial.", paste(sample(letters, 3), collapse = ""), ".pdf", sep = ""), 
				 dist.cats = rep(1, length(tr$tip.label)), whiteOut = "NA", 
				 xy.multiplier = 1.5, offset.proportion = 0.03, writeLabels = 0.1, 
				 vectorToColorBy = label.elements(tr, "|", returnNum = 6, fixed = T),
				 ...)

Arguments

tr	The tree to be plotted, an object of class phylo.
tipChar	Optional. The character with which to replace the full tip label.
tiplty
pdfTitle
dist.cats
whiteOut
xy.multiplier
offset.proportion
writeLabels
...

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