prettyTree {clstutils} | R Documentation

## Draw an annotated phylogenetic tree.

### 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)

[Package clstutils version 1.42.0 Index]