| gl.evanno {dartR} | 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 |
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.
See Also
gl.run.structure, clumpp,
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)