Q-Q and Manhattan Plots for GWAS Data

Create Q-Q and manhattan plots for GWAS data from PLINK results.




If you'd like to cite qqman (appreciated but not required), please cite the pre-print below:

Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165.


Install the stable release from CRAN:


Or install directly from github using devtools


Or install the most recent development release with devtools (note, there be dragons here):


Load the package each time you use it:



See the online package vignette for more examples:


Take a look at the built-in data:


Basic manhattan plot using built-in data:


Basic Q-Q plot using built-in data:


Get help:



  • This release is substantially simplified for the sake of maintainability and creating an R package. The old code that allows confidence intervals on the Q-Q plot and allows more flexible annotation and highlighting is still available at the version 0.0.0 tag.
  • Special thanks to Dan Capurso and Tim Knutsen for useful contributions and bugfixes.
  • Thanks to all the blog commenters for pointing out bugs and other issues.


qqman 0.1.4

  • Minor fix to location to referenced image for pandoc self-contained README.html generation.

qqman 0.1.3

  • Annotate SNPs below a p-value threshold with the annotatePval= option. See vignette for details.
  • Annotate the top SNP on each chromosome with the annotateTop= option. See vignette for details.

qqman 0.1.2

  • Does not assume that SNPs are evenly distributed across chromosomes when deciding where to place the tick in the center of the chromosome.
  • Changed single chromosome x-axis notation to use Mb instead of raw pos
  • qq() accepts graphical parameters the same way as manhattan()
  • Removed default xlim
  • Citation details on package load
  • Added axis label options
  • Removed ymax argument in favor of allowing user to set ylim in ...
  • Option to not take log of p-value

qqman 0.1.1

  • Fixed a bunch of typos in the vignette

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


0.1.8 by Stephen Turner, 8 months ago


Report a bug at https://github.com/stephenturner/qqman/issues

Browse source code at https://github.com/cran/qqman

Authors: Stephen Turner <[email protected]>

Documentation:   PDF Manual  

GPL-3 license

Imports calibrate

Suggests knitr, rmarkdown

Imported by MAGNAMWAR, gwsem.

Suggested by polyRAD, rehh.

See at CRAN