spec: add manhattan-gwas specification (#2929)

## New Specification: `manhattan-gwas`

Related to #2925

---

### 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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plots/manhattan-gwas/specification.md

@@ -0,0 +1,30 @@
+# 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

plots/manhattan-gwas/specification.yaml

@@ -0,0 +1,32 @@
+# Specification-level metadata for manhattan-gwas
+# Auto-synced to PostgreSQL on push to main
+
+spec_id: manhattan-gwas
+title: Manhattan Plot for GWAS
+
+# Specification tracking
+created: 2025-12-31T05:13:06Z
+updated: null
+issue: 2925
+suggested: MarkusNeusinger
+
+# Classification tags (applies to all library implementations)
+# See docs/concepts/tagging-system.md for detailed guidelines
+tags:
+  plot_type:
+    - scatter
+    - manhattan
+    - point
+  data_type:
+    - numeric
+    - categorical
+    - genomic
+  domain:
+    - science
+    - bioinformatics
+    - genetics
+    - healthcare
+  features:
+    - threshold-line
+    - color-mapped
+    - chromosome-segmented