pegas: plotNetMDS – R documentation

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plotNetMDS

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.

Examples

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

pegas

Population and Evolutionary Genetics Analysis System

v1.0

GPL (>= 2)

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut, cph] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut, cph] (<https://orcid.org/0000-0003-1665-4343>), Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut, cph] (<https://orcid.org/0000-0003-0919-7279>), David Winter [aut, cph] (<https://orcid.org/0000-0002-6165-0029>)

Initial release

2021-04-08