prettyTree: Draw an annotated phylogenetic tree.

In clstutils: Tools for performing taxonomic assignment.

Description

Extends plot.phylo to draw a phylogenetic tree with additional annotation.

Usage

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, ...)

Arguments

x	an object of class phylo, eg x <- nj(ddist)
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 x$tip.label
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 data.frame with columns named 'col' and 'pch' corresponding to elements of unique(groups)
shuffleGlyphs	NA or an integer (argument to set.seed)
...	passed to plot.phylo

Details

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.

Value

Plots to the active device; no return value.

Note

See package vignette for additional examples.

Author(s)

Noah Hoffman

See Also

plot.phylo

Examples

library(ape)
data(seqs)
data(seqdat)
prettyTree(nj(dist.dna(seqs)), groups=seqdat$tax_name)

clstutils documentation built on Nov. 8, 2020, 5:23 p.m.