A single function to analyse STRUCTURE, TESS, BAPS or BASIC text runs. Converts runs to a qlist, tabulates, summarises, runs evanno method (for STRUCTURE runs), aligns clusters and plots all runs.
analyseQ(files = NULL, evannomethod = TRUE, align = TRUE,
plotruns = TRUE, imgoutput = "sep", grplab = NA, clustercol = NA,
writetable = TRUE, sorttable = TRUE)A character or character vector of one or more STRUCTURE, TESS,
BAPS or BASIC run files. Use choose.files(multi=TRUE) to choose
interactively.
A logical indicating if evanno method should be performed. Applies only to STRUCTURE runs.
A logical indicating if clusters must be aligned within and across K.
A logical indicating if selected files should be exported as barplots.
A character indicating if files are plotted as separate image files ("sep") or joined into a single image ("join").
A dataframe with one or more columns (group label sets), and rows equal to the number of individuals.
A character vector of colours for colouring clusters. If
NA, colours are automatically generated. K 1 to 12 are custom unique colours
while K>12 are coloured by function rich.color().
A logical T or F. Setting to TRUE writes the output table to the working directory.
A logical indicating if the output table must be sorted. Sorts table by loci, ind and K when available.
A qlist (list of data.frames) is returned.
The function analyseQ is a wrapper around several other
pophelper functions. All arguments for all sub-functions are
not available. If more arguments/options are required, consider running the functions separately.
See the vignette for more details.
# NOT RUN {
# structure files
sfiles <- list.files(path=system.file("files/structure",package="pophelper"),
full.names=TRUE)
analyseQ(sfiles)
# }
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