R: Plot Mutations on Networks

mutations {pegas} | R Documentation

## Plot Mutations on Networks

### Description

`mutations` draws annotations about mutations related to the link of a haplotype network.

### Usage

    mutations(haploNet, link, x, y, data = NULL, style = "table", POS, SEQLEN, ...)

### Arguments

`haploNet` | an object of class `"haploNet"` which should be plotted beforehand.
`link` | the link number; can be left missing in which case the list of links in the network is printed and the function exits.
`x, y` | the coordinates where to draw the annotations; can be left missing: the user is then asked to click where to draw them and the chosen coordinates are printed.
`data` | the sequence data; can be left missing if the data are attached to the network (for a MJN network output by `mjn`.)
`style` | the type annotations. There two possible choices: `"table"` (default) and `"sequence"` (can be abbreviated).
`POS, SEQLEN` | a vector of genomic positions and the sequence length in case `data` is of class `"haplotype.loci"`.
`...` | options

### Details

The easiest way to use this function is with an output from `mjn` since the data are attached to the network. In other cases, the sequence data must given to the argument `data` or attached to the network as an attribute named `"data"`.

### Value

none

### Author(s)

Emmanuel Paradis

### See Also

`plot.haploNet`, `haplotype.loci`

### Examples

    ## simple example
    x <- as.DNAbin(matrix(c("a", "g"), 2, 1))
    rownames(x) <- paste("Ind", 1:2, sep = "_")
    nt <- mst(dist.dna(x, "N"))
    plot(nt)
    mutations(nt, link = 1, x = 2, y = 2, data = x)

    example(mjn)
    plot(ntz, xlim = c(-5, 20))
    mutations(ntz, 6, 10, 0, style = "s")
    mutations(ntz, 8, 10, -2, style = "s")

[Package pegas version 1.1 Index]