pophelper v2.3.0

Tabulate, analyse and visualise admixture proportions from STRUCTURE, TESS, BAPS, ADMIXTURE and tab-delimited q-matrices files

A set of useful functions for processing admixture proportion files from the population structure analysis softwares STRUCTURE, TESS, ADMIXTURE, BAPS, fastSTRUCTURE etc. The package contains functions to read runs, tabulate runs, summarise runs, plot runs, estimate K using Evanno method, export clumpp files, export distruct files and generate barplots.

Readme

pophelper

pophelper is an R package and web app to analyse and visualise population structure. See the project website for more details.

Disclaimer

The pophelper R package is offered free and without warranty of any kind, either expressed or implied. I will not be held liable to you for any damage arising out of the use, modification or inability to use this program. pophelper R package can be used, redistributed and/or modified freely for non-commercial purposes subject to the original source being properly cited. Licensed under GPL-3. Please make sure you verify all your results.

Contact

If you have an comments, suggestions, corrections or ideas on ways to improve or extend this package, feel free to contact me. Submit a report on the Github issues page.

2019 | Roy M Francis

Functions in pophelper

Name Description
readQ Convert run files (q-matrices) to qlist.
mergeQ Merge replicate runs of the same K
joinQ Combine two or more qlist objects into one
readQClumpp Convert CLUMPP format numeric text files to qlist.
readQBasic Convert delimited text files to qlist.
readQTess3 Convert TESS3 R object to pophelper qlist.
readQStructure Convert STRUCTURE run files to qlist.
readQTess Convert TESS cluster files to qlist.
sortQ Sort runs in a qlist based on an attribute
clumppExport Generate CLUMPP output from a qlist
plotQ Generate barplots from qlists.
splitQ Split a qlist into sublists by attribute
summariseQ Summarise a tabulated dataframe
plotQMultiline Plot a qlist as individual-level multiline barplot
tabulateQ Tabulate runs from a qlist
verifyGrplab Verify a grplab dataframe
readQBaps Convert BAPS cluster files to qlist.
distructColours Vector of 90 Distruct colours
is.qlist Verify if a qlist is formatted correctly.
collectClumppOutput Collect CLUMPP output files from multiple folders
distructExport Generate files for DISTRUCT.
as.qlist Convert a qlist or qlist-like list to a valid qlist.
collectRunsTess Collect TESS cluster run files from multiple folders
analyseQ Analyse STRUCTURE, TESS, BAPS or BASIC text runs. Wrapper around several smaller functions.
evannoMethodStructure Perform the Evanno method for STRUCTURE runs.
alignK Align clusters
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Vignettes of pophelper

Name
Joined2Files-20180501215308.png
Joined2Files-20180501215347.png
Joined2Files-20180501215348.png
Joined2Files-20180501215620.png
Joined2Files-20180501215631.png
Joined2Files-20180501220336.png
Joined3Files-20180501215152.png
Joined3Files-20180501215331.png
Joined3Files-20180501215333.png
Joined3Files-20180501220420.png
Joined3Files-20180501220655.png
STRUCTUREpop_K4-combined-1.png
STRUCTUREpop_K4-combined-2.png
STRUCTUREpop_K4-combined-3.png
STRUCTUREpop_K4-combined-aligned-1.png
STRUCTUREpop_K4-combined-aligned-2.png
STRUCTUREpop_K4-combined-aligned-3.png
STRUCTUREpop_K4-combined-merged-1.png
clumpp-aligned.png
clumpp-folder.png
clumpp-format.png
clumpp-output.png
destruct-structure.png
evanno-plot.png
index.Rmd
index.html
input-preview.png
plotq-overview.png
plotq.png
plotqmultiline-colours.png
plotqmultiline-overview.png
plotqmultiline.png
structure-files.png
structure_01.pdf
structure_01.png
structure_01.tiff
structure_02.png
structure_03.png
structure_04.png
workflow.svg
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Details

Type Package
Date 2019-08-15
URL https://github.com/royfrancis/pophelper
License GPL-3
Encoding UTF-8
BugReports https://github.com/royfrancis/pophelper/issues
VignetteBuilder knitr
RoxygenNote 6.1.1

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