R: Plot Networks With MDS Layout

plotNetMDS {pegas} | R Documentation

## Plot Networks With MDS Layout

### Description

This function plots a haplotype network using a layout calculated from an MDS performed on the pairwise distance matrix. The haplotypes have always the same positions for different networks.

### Usage

    plotNetMDS(net, d, k = 2, show.mutation = FALSE, col = NULL, font = 2, cex = 1)

### Arguments

`net` | an object of class `"haploNet"`.
`d` | an object of class `"dist"` (or a matrix).
`k` | the number of dimensions of the plot (2 or 3).
`show.mutation` | a logical value: if `TRUE`, the number of steps is printed on the links.
`col` | the colours of the links; by default, semi-transparent green.
`font` | the font used to print the labels; bold by default.
`cex` | the character expansion of the labels.

### Value

NULL

### Author(s)

Emmanuel Paradis

### References

Paradis, E. (2017) Analysis of haplotype networks: the randomized minimum spanning tree method. Manuscript.

### See Also

`haploNet`

### Examples

    data(woodmouse)
    d <- dist.dna(woodmouse, "n")
    net <- rmst(d)
    plotNetMDS(net, d)

[Package pegas version 0.13 Index]