barMonophyletic: barMonophyletic

Description Usage Arguments Details Value Author(s)

Description

puts vertical bars next to monophyletic clades in a tree.

Usage

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barMonophyletic(groupLabel, groupMatch, tree, cex.plot, cex.text = 0.8,
  include.tip.label = FALSE, extra.space = 0, coef.space = 1,
  draw = TRUE, text.offset = 1.02, font = 1, font.col = 1,
  seg.col = 1, srt = 0, bar.at.tips = FALSE)

Arguments

groupLabel

a vector of mode character that indicates the labels for each of the monophyletic group.

groupMatch

a vector of mode character that contains a way to identify each of the monophyletic clade. The function grep is used for this process.

tree

a phylogenetic tree a phylo object.

cex.plot

the cex (in par) value for plotting the tree.

cex.text

the cex (in par) value for the text next to the vertical bars.

include.tip.label

should the tip labels be displayed on the tree? (default is FALSE)

extra.space

amount of extra space (additive)

coef.space

amount of space (multiplicative)

draw

should a plot be produce? (default is TRUE)

text.offset

how much space to add between the vertical bar and the text.

font

type of font to be used for the text next to the vertical bars.

font.col

color of the font to be used for the text next to the vertical bars.

seg.col

color of the vertical bar.

srt

the string rotation in degrees (see see srt in par) of the text next to the vertical bars.

bar.at.tips

should the vertical bars be plotted right next to the tips? (default FALSE)

Details

Based on a tree (as a phylo object) and a character-vector, this function draws vertical bars next to each monophyletic group. Each element of the vector must contain a character string that matches (through grep) all the tips that are included in each of the monophyletic group. In other words, this function does not identify the monophyletic groups for you. Also, the length of the vector should be of the same length as the number of monophyletic groups in your tree.

The element of the vector are considered labels and will be displayed next to the vertical bars.

Value

Function mostly used for its side effect of plotting a phylogeny but it also returns invisibly the total width of the tree.

Author(s)

Francois Michonneau


fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.