R/gl.evanno.r

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

#' @name gl.evanno
#' @title 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 \code{strataG}
#' @param sr structure run object from \code{\link{gl.run.structure}} [required].
#' @param 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 \code{evanno} (Archer et al. 2016). For a detailed
#' description please refer to this package (see references below).
#' @return An Evanno plot is created and a list of all four plots is returned.
#' @author Bernd Gruber (Post to \url{https://groups.google.com/d/forum/dartr})
#' @examples
#' \dontrun{
#' #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)
#' }
#' @import patchwork
### @importFrom strataG genind2gtypes structureRun
#' @export
#' @seealso \code{\link{gl.run.structure}},  \code{clumpp},
#' @references
#' \itemize{
#' \item Pritchard, J.K., Stephens, M., Donnelly, P. (2000) Inference of
#' population structure using multilocus genotype data. Genetics 155, 945-959.
#' \item 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
#' \item 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.
#' }

gl.evanno <- function(sr, plot.out = TRUE) {
        evno <- utils.structure.evanno(sr, plot = plot.out)
        # for (i in 1:4) evno$plots[[i]] <- evno$plots[[i]]+theme_dartR()
        
        return(evno)
}