[manhattan-gwas] Manhattan Plot for GWAS

[MarkusNeusinger]

A Manhattan plot displaying genome-wide association study (GWAS) results. Shows -log10 p-values across chromosomal positions, with alternating colors per chromosome and a genome-wide significance threshold line.

[claude]

✅ Spec ID: manhattan-gwas

Rationale: Manhattan plot is a specialized scatter/point plot for genome-wide association studies (GWAS) - the ID reflects both the plot type and its specific genomics application.

No duplicate exists. This is a well-established bioinformatics visualization with clear requirements: chromosomal positions on x-axis, -log10(p-value) on y-axis, alternating chromosome colors, and significance threshold line.

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[github-actions]

✅ Specification Ready: manhattan-gwas

PR: #2929

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specification.md

manhattan-gwas: Manhattan Plot for GWAS

Description

A Manhattan plot visualizes genome-wide association study (GWAS) results by displaying -log10 transformed p-values across chromosomal positions. Points are arranged by genomic position along the x-axis with alternating colors for each chromosome, making it easy to identify significant associations. A horizontal threshold line indicates genome-wide significance (typically p < 5×10⁻⁸). This plot is essential for identifying genetic variants associated with traits or diseases.

Applications

• Identifying significant SNPs in genome-wide association studies for complex diseases
• Visualizing genetic association results across the entire genome in pharmacogenomics research
• Presenting GWAS findings in scientific publications and research presentations
• Screening for candidate loci in agricultural genomics and breeding programs

Data

• chromosome (categorical) - Chromosome identifier (1-22, X, Y, or MT)
• position (integer) - Base pair position along the chromosome
• p_value (float) - P-value from association test (will be -log10 transformed)
• snp_id (string, optional) - SNP identifier for labeling significant hits
• Size: 100,000 - 1,000,000+ variants typical for GWAS
• Example: Simulated GWAS data with random p-values and some significant peaks

Notes

• X-axis should show cumulative genomic position with chromosome labels centered below their region
• Use alternating colors (e.g., blue/gray) for adjacent chromosomes for visual distinction
• Include horizontal dashed line at -log10(5×10⁻⁸) ≈ 7.3 for genome-wide significance threshold
• Optionally include suggestive threshold line at -log10(1×10⁻⁵) = 5
• Consider point size reduction for dense datasets to prevent overplotting
• Significant SNPs above threshold may be labeled or highlighted with different color

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Next: Add approved label to merge this specification to main.

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[github-actions]

🚀 Specification Merged!

Specification: manhattan-gwas
PR: #2929 (merged)

The specification is now in main and synced to PostgreSQL.

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Available libraries: matplotlib, seaborn, plotly, bokeh, altair, plotnine, pygal, highcharts, letsplot

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