Description Usage Arguments Details Value Author(s)
puts vertical bars next to monophyletic clades in a tree.
1 2 3 4 | 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)
|
groupLabel |
a vector of mode |
groupMatch |
a vector of mode |
tree |
a phylogenetic tree a |
cex.plot |
the |
cex.text |
the |
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 |
bar.at.tips |
should the vertical bars be plotted right next to the tips? (default FALSE) |
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.
Function mostly used for its side effect of plotting a phylogeny but it also returns invisibly the total width of the tree.
Francois Michonneau
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