openmendel / mendelplots.jl

Julia package for plotting results from GWAS

MendelPlots

Documentation	Build Status	Code Coverage	Citation

MendelPlots.jl is a Julia package for generating common plots from results of genome-wide association studies (GWAS). It can currently create Manhattan Plots and QQ Plots.

MendelPlots is a plotting and data visualization system written in Julia. It uses Gadfly as the backend, which is influenced by Grammar of Graphics Style programming and Hadley Wickham's ggplot2

This package is registered in the default Julia package registry, and can be installed through standard package installation procedure: e.g., running the following code in Julia REPL.

using Pkg
pkg"add MendelPlots"

Citation

If you use OpenMendel analysis packages in your research, please cite the following reference in the resulting publications:

Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. OPENMENDEL: a cooperative programming project for statistical genetics. Hum Genet. 2020 Jan;139(1):61-71. doi: 10.1007/s00439-019-02001-z. Epub 2019 Mar 26. PMID: 30915546; PMCID: PMC6763373.

Acknowledgments

This project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.

Package features

• Creates publication quality plots in PNG format

Contributing and Request Plots

The software is relatively new. File an issue to report a bug or request a feature.

mendelplots.jl's Issues

QQ plot looks weird

On a particular list of p-values (attached below), I get

Code to reproduce:

using MendelPlots, CSV, DataFrames, DelimitedFiles
pvals = vec(readdlm("pvals.txt"))
qq(pvals)
display("image/png", read("qqplot.png"))

Did I do something wrong?

pvals.txt

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Is there a DOI for this package?

I'd like to cite this package since I used it in my paper. I can do so if there's a DOI.

You can get one at https://zenodo.org/