pophelper 2.1.0

pophelper is an R package and web app to analyse and visualise population structure. pophelper curently supports output run files generated from population analysis programs such as STRUCTURE, TESS and numeric delimited formats such as ADMIXTURE or fastSTRUCTURE. The pophelper package can be used to read run files to R, tabulate runs, summarise runs, estimate K using the Evanno method, export files for CLUMPP, export files for DISTRUCT and generate barplot figures.

For a detailed demonstration and walkthrough, refer the online vignette. A quick intro video is available here. New versions and updates are shown only on this GitHub page.

Latest version

This version 2.1.0 no longer supports any of the functions deprecated in version <2.0.0. ggplot2 version must be 2.2.0 or above. Some of the important changes from the previous version 2.0.0 are listed below:

• Order of arguments have changed in plotQ(),plotQMultiline() and evannoMethodStructure()
• plotQMultiline(): Group labels, sorting within groups, subsetting groups, reordering groups etc
• plotQMultiline(): Sorting by individual labels
• plotQ(): Sorting by individual labels
• More plot customisation arguments added to evannoMethodStructure()
• tiff export added to all export functions
• Argument 'barwidth' replaced with 'barsize'
• Argument 'linethick' replaced with 'linesize'
• Argument 'divthick' replaced with 'divsize'
• Argument 'res' replaced with 'dpi'

For full list of changes, refer to the NEWS.

Installation

You need to have R (> 3.3.0) statistical package installed on your system. R is open-source and freely available to download for Windows, Mac and other OS. Then, install the devtools and other dependency packages. Then, you can install pophelper from github using the devtools package.

# install dependencies and devtools
install.packages(c("Cairo","ggplot2","gridExtra","gtable","tidyr","devtools"),dependencies=T)

# load package
library(devtools)

# install pophelper package from GitHub
install_github('royfrancis/pophelper')

# load library for use
library(pophelper)

Note that pophelper 1.2.0 and later includes binary executables for CLUMPP and DISTRUCT. This is experimental and may not work on all OS and versions.

pophelper 2.1.0 has been tested on the following systems:

• Windows 10 64bit, R 3.3.3
• Windows 7 64bit, R 3.3.3 (DISTRUCT is unstable)
• Scientific Linux 6.8 (Carbon) 64bit, R 3.3.2

Web App

An online interactive version of pophelper is available at pophelper.com. Not all features of the R package is supported in the online app.

List of Functions

For help on any function, use
?tabulateQ
?evannoMethodStructure

readQ()                   # Read q-matrix run files to R qlist
tabulateQ()               # Tabulate a qlist
summariseQ()              # Summarise an output from tabulateQ()
clumppExport()            # Generate CLUMPP input/output files
collectClumppOutput()     # Collect CLUMPP output into a common directory
plotQ()                   # Create single-line barplots from qlist
PlotQMultiline()          # Create multi-line barplots from qlist
distructExport()          # Export files for DISTRUCT from qlist

evannoMethodStructure()   # Perform the Evanno method for STRUCTURE data
collectRunsTess()         # Collect TESS output from multiple directories into one

analyseQ()                # A wrapper function to quickly tabulate, summarise, 
                          # perform evanno method, clumpp output and generate
                          # barplots from filenames/paths.

Workflow

Fig: Workflow for all filetypes.

Fig: Plots from Evanno method.

Fig: Barplots from q-matrices.

For detailed demonstration and description, refer the vignette.

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.

2017 Roy M Francis