R: Extra Fuctions to Plot and Annotate Phylogenies

plot.phylo.extra {ape} | R Documentation

## Extra Fuctions to Plot and Annotate Phylogenies

### Description

These are extra functions to plot and annotate phylogenies, mostly calling basic graphical functions in ape.

### Usage

    plotBreakLongEdges(phy, n = 1, ...)
    drawSupportOnEdges(value, ...)

### Arguments

`phy` | an object of class `"phylo"`.
`n` | the numner of long branches to be broken.
`value` | the values to be printed on the internal branches of the tree.
`...` | further arguments to be passed to `plot.phylo` or to `edgelabels`.

### Details

`drawSupportOnEdges` assumes the tree is unrooted, so the vector `value` should have as many values than the number of internal branches (= number of nodes - 1). If there is one additional value, it is assumed that it relates to the root node and is dropped (see examples).

### Value

NULL

### Author(s)

Emmanuel Paradis

### See Also

`plot.phylo`, `edgelabels`, `boot.phylo`, `plotTreeTime`

### Examples

    tr <- rtree(10)
    tr$edge.length[c(1, 18)] <- 100
    op <- par(mfcol = 1:2)
    plot(tr); axisPhylo()
    plotBreakLongEdges(tr, 2); axisPhylo()

    ## from ?boot.phylo:
    f <- function(x) nj(dist.dna(x))
    data(woodmouse)
    tw <- f(woodmouse) # NJ tree with K80 distance
    set.seed(1)
    ## bootstrap with 100 replications:
    (bp <- boot.phylo(tw, woodmouse, f, quiet = TRUE))
    ## the first value relates to the root node and is always 100
    ## it is ignored below:
    plot(tw, "u")
    drawSupportOnEdges(bp)
    ## more readable but the tree is really unrooted:
    plot(tw)
    drawSupportOnEdges(bp)
    par(op)

[Package ape version 4.1 Index]