plotPhyloWithClassification: Plot Phylogentic Tree with Clade Highlighting

In heibl/viper: VIsualitaion of Phylogenetics and Evolution with R

Description

Plots a phylogenetic tree together with color highlighting of the underlying taxonomic classification.

Usage

plotPhyloWithClassification(phy, tax, outgroup = "dont.show",
  min.support, collapse.unsupported = TRUE, genus.monophyly = TRUE,
  genus.col = "grey95", edges, higher.rank, higher.rank.cex = 0.85,
  tags, xex = 1.25, pdf.height = "auto", pdf.width = 20, title, file)

Arguments

phy	An object of class phylo.
tax	An object of class megapteraProj or a taxonomic table in parent-child format; if missing, the taxonomy is taken from the tip labels.
outgroup	A vector of mode "character". Outgroup will not be shown, if outgroup = "dont.show".
min.support	An integer giving a threshold for support values. Edges with lower support values will be collapsed into polytomies, if collapes.unsupported = TRUE.
collapse.unsupported	Logical
genus.monophyly	Logical indicating if monophyletic genera should be highlighted.
genus.col	A vector of mode "character" giving a color for the filling of boxes drawn around monophyletic genera.
edges	A vector of mode "character".
higher.rank	A vector of mode "character".
tags	A data frame with two columns: the first column contains tip labels as contained in phy, the second columns contains the labels with will be appended (within square bracket) to the corresponding tip labels.
xex	A numeric, the x.lim extension; try larger values if parts of the plot are truncated at the right side of the plot.
pdf.height	An integer ...
pdf.width	An integer ...
title	A vector of mode "character".
file	A vector of mode "character".

Details

collapse.unsupported assumes that the support values are found in phy$node.label; no edges will be collapsed, if this list element does not exist.

heibl/viper documentation built on May 21, 2019, 10:47 a.m.