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