This function takes a genlight object and runs a STRUCTURE analysis based on
functions from strataG
Usage
gl.run.structure(
x,
...,
exec = ".",
plot.out = TRUE,
plot_theme = theme_dartR(),
save2tmp = FALSE,
verbose = NULL
)
Arguments
- x
Name of the genlight object containing the SNP data [required].
- ...
Parameters to specify the STRUCTURE run (check
structureRun
within strataG. for more details). Parameters are passed to thestructureRun
function. For example you need to set the k.range and the type of model you would like to run (noadmix, locprior) etc. If those parameter names do not tell you anything, please make sure you familiarize with the STRUCTURE program (Pritchard 2000).- exec
Full path and name+extension where the structure executable is located. E.g.
'c:/structure/structure.exe'
under Windows. For Mac and Linux it might be something like'./structure/structure'
if the executable is in a subfolder 'structure' in your home directory [default working directory "."].- plot.out
Create an Evanno plot once finished. Be aware k.range needs to be at least three different k steps [default TRUE].
- plot_theme
Theme for the plot. See details for options [default theme_dartR()].
- save2tmp
If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].
- verbose
Set verbosity for this function (though structure output cannot be switched off currently) [default NULL]
Value
An sr object (structure.result list output). Each list entry is a
single structurerun output (there are k.range * num.k.rep number of runs).
For example the summary output of the first run can be accessed via
sr[[1]]$summary
or the q-matrix of the third run via
sr[[3]]$q.mat
. To conveniently summarise the outputs across runs
(clumpp) you need to run gl.plot.structure on the returned sr object. For
Evanno plots run gl.evanno on your sr object.
Details
The function is basically a convenient wrapper around the beautiful
strataG function structureRun
(Archer et al. 2016). For a detailed
description please refer to this package (see references below).
To make use of this function you need to download STRUCTURE for you system
(non GUI version) from here
STRUCTURE.
Format note
For this function to work, make sure that individual and population names
have no spaces. To substitute spaces by underscores you could use the R
function gsub
as below.
popNames(gl) <- gsub(" ","_",popNames(gl))
indNames(gl) <- gsub(" ","_",indNames(gl))
It's also worth noting that Structure truncates individual names at 11
characters. The function will fail if the names of individuals are not unique
after truncation. To avoid this possible problem, a number sequence, as
shown in the code below, might be used instead of individual names.
indNames(gl) <- as.character(1:length(indNames(gl)))
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
Author
Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)