prettyTree {clstutils} | R Documentation |
Extends plot.phylo
to draw a
phylogenetic tree with additional annotation.
prettyTree(x, groups, fill, X, O, indices, labels, show = rep(TRUE, length(x)), largs = list(cex = 0.75, bty = "n", yjust = 0.5), parargs = list(mar = c(bottom = 5, left = 2, top = 2, right = ifelse(is.null(largs), 2, 8)), xpd = NA), pointargs = list(), glyphs, shuffleGlyphs = NA, ...)
x |
an object of class phylo, eg |
groups |
a factor (or object coercible) to a factor assigning group identity to leaf nodes in x |
fill |
vector (logical or indices) of points to fill |
X |
vector of points to mark with an X |
O |
vector of points to mark with a circle |
indices |
label points with indices (all points if 'yes', or a subset indicated by a vector) |
labels |
character vector of tip labels in the same order as
|
show |
boolean vector of points to show |
largs |
arguments controlling appearance of the legend or NULL for no legend |
parargs |
arguments to pass par() |
pointargs |
arguments to pass points() (other than pch, col, bg) |
glyphs |
a |
shuffleGlyphs |
NA or an integer (argument to |
... |
passed to |
prettyTree
adds to a plot drawn by plot.phylo
Vectors specifying annotation should be in the order of row or column
labels of the distance matrix used to generate x
.
Plots to the active device; no return value.
See package vignette for additional examples.
Noah Hoffman
library(ape) data(seqs) data(seqdat) prettyTree(nj(dist.dna(seqs)), groups=seqdat$tax_name)