pophelper (version 2.0.0)

analyseQ: Analyse STRUCTURE, TESS or BASIC text runs. Wrapper around several smaller functions.

Description

A single function to analyse STRUCTURE, TESS or BASIC text runs. Converts runs to a qlist, then tabulate, summarise, perform evanno method, export clumpp and plots runs.

Usage

analyseQ(files = NULL, evannomethod = TRUE, clumppexport = TRUE,
  plotruns = TRUE, imgoutput = "sep", grplab = NA, clustercol = NA,
  writetable = TRUE, sorttable = TRUE)

Arguments

files

A character or character vector of one or more STRUCTURE, TESS or BASIC run files. Use choose.files(multi=TRUE) to choose interactively.

evannomethod

A logical indicating if evanno method should be performed. Applies only to STRUCTURE runs.

clumppexport

A logical indicating if files must be exported for clumpp.

plotruns

A logical indicating if selected files should be exported as barplots.

imgoutput

A character indicating if files are plotted as separate image files ("sep") or joined into a single image ("join").

grplab

A named list of one or more group label sets. The length of each group label vector must be equal to the length of individuals.

clustercol

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().

writetable

A logical T or F. Setting to TRUE writes the output table to the working directory.

sorttable

A logical indicating if the output table must be sorted. Sorts table by loci, ind and K when available.

Value

If a single file is selected, a single dataframe is returned. If multiple files are selected, a list with multiple dataframes is returned.

Details

The function analyseQ is a wrapper around several other pophelper functions. All arguments for all these other functions are not available. If more arguments/options are required, consider running the functions separately.

See the vignette for more details.

Examples

# NOT RUN {
#structure files
sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE)
analyseQ(sfiles)

#tess files
tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE)
analyseQ(tfiles)

#admixture files
afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE)
analyseQ(afiles)
# }