gl.evanno: Creates an Evanno plot from a STRUCTURE run object
In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

gl.evanno

R Documentation

Creates an Evanno plot from a STRUCTURE run object

Description

This function takes a genlight object and runs a STRUCTURE analysis based on functions from strataG

Usage

gl.evanno(sr, plot.out = TRUE)

Arguments

`sr`	structure run object from `gl.run.structure` [required].
`plot.out`	TRUE: all four plots are shown. FALSE: all four plots are returned as a ggplot but not shown [default TRUE].

Details

The function is basically a convenient wrapper around the beautiful strataG function evanno (Archer et al. 2016). For a detailed description please refer to this package (see references below).

Value

An Evanno plot is created and a list of all four plots is returned.

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

References

Pritchard, J.K., Stephens, M., Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
Archer, F. I., Adams, P. E. and Schneiders, B. B. (2016) strataG: An R package for manipulating, summarizing and analysing population genetic data. Mol Ecol Resour. doi:10.1111/1755-0998.12559
Evanno, G., Regnaut, S., and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611-2620.

Examples

## Not run: 
#CLUMPP and STRUCTURE need to be installed to be able to run the example
#bc <- bandicoot.gl[,1:100]
#sr <- gl.run.structure(bc, k.range = 2:5, num.k.rep = 3, exec = './structure.exe')
#ev <- gl.evanno(sr)
#ev
#qmat <- gl.plot.structure(sr, k=3, CLUMPP='d:/structure/')
#head(qmat)
#gl.map.structure(qmat, bc, scalex=1, scaley=0.5)

## End(Not run)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.