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qqman

ANALYTICS
Velocity0.0

Q-Q and Manhattan Plots for GWAS Data

github.com/stephenturner/qqman ↗

The Manhattan-plot package for GWAS results, finished and dormant since 2017.

gwasgenomicsmanhattan-plotvisualizationbioinformatics
◆Current state
qqman does two things: manhattan() and qq() plots for genome-wide association study results. Its six visible releases run from 2014 to a single 2017 packaging fix, and the last release with any user-facing change shipped in 2015. The archive is non-monotonic — a 0.0.0 tag published after 0.1.1 archives the pre-package standalone script — so version order and publication order disagree.
◆Where it's heading
The real development window was 2014 to 2015. The 0.1.2 release did the substantive work, replacing the assumption that SNPs are evenly distributed across chromosomes and handing users control of axis limits, labels and log transformation; 0.1.3 then added annotation by p-value threshold and top-SNP-per-chromosome. After that the package stops. Notably, the archival 0.0.0 entry records that the original script had confidence intervals on QQ plots and richer highlighting than the released package ever regained.
◆Prediction
With one packaging fix in the last decade, these entries support no prediction of further releases. The package reads as complete for its narrow purpose rather than abandoned mid-arc.

◆Recent moves

  1. 9y ago

    README image path fix for pandoc

    A path correction so pandoc can generate a self-contained README.html. Packaging housekeeping, and the last thing the project shipped.

    View source ↗
  2. 11y ago

    Annotate SNPs by p-value threshold or per-chromosome top hit

    Adds annotatePval= to label SNPs below a p-value threshold and annotateTop= to label the leading SNP on each chromosome. Real plotting capability, and the last functional change the package made.

    View source ↗
  3. 11y ago

    Chromosome ticks stop assuming even SNP spacing; axis control opens up

    The package's substantive release. Chromosome tick placement no longer assumes SNPs are evenly distributed, which corrects the x-axis on every real dataset, and single-chromosome axes switch to Mb. Alongside that, control moves to the user: qq() takes graphical parameters like manhattan(), ymax gives way to ylim, default xlim is dropped, axis labels are configurable, and the p-value log transform can be skipped.

    View source ↗
  4. 12y ago

    Archival tag for the pre-package standalone script

    An archival tag for the pre-package standalone script, published five days after 0.1.1 despite its 0.0.0 number. Its note is the more interesting part: the original script supported QQ-plot confidence intervals and richer highlighting than the packaged 0.1.x releases carried forward.

    View source ↗
  5. 12y ago

    Vignette touch-up

    Minor vignette changes on the way to CRAN. No functional change.

    View source ↗
  6. 12y ago

    Zenodo archival tag, no code change

    Identical in content to the preceding release, tagged only to create a Zenodo archive record. A citation artifact rather than a release.

    View source ↗