feat(altair): implement manhattan-gwas

[github-actions]

Implementation: manhattan-gwas - altair

Implements the altair version of manhattan-gwas.

File: plots/manhattan-gwas/implementations/altair.py

Parent Issue: #2925

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🤖 impl-generate workflow

[claude]

AI Review - Attempt 1/3

Image Description

The plot displays a Manhattan plot for GWAS data with all 22 chromosomes arranged along the x-axis. Points are colored in alternating blue (#306998) and gray (#7F7F7F) for adjacent chromosomes, creating clear visual separation. The y-axis shows -log₁₀(p-value) ranging from 0 to ~11. Two horizontal dashed threshold lines are visible: a red line at approximately 7.3 (genome-wide significance, p < 5×10⁻⁸) and an orange line at 5.0 (suggestive threshold, p < 1×10⁻⁵). Significant peaks are visible above the genome-wide threshold on chromosomes 2, 6, 8, and 15, with these points displayed larger than non-significant ones. Suggestive signals appear on chromosomes 3, 11, and 19. Chromosome labels (1-22) are centered below their respective regions. The title "manhattan-gwas · altair · pyplots.ai" appears at the top.

Quality Score: 91/100

Criteria Checklist

Visual Quality (36/40 pts)

• VQ-01: Text Legibility (9/10) - Title clear at 28pt, axis labels at 22pt, tick labels at 16pt - all readable, slight crowding in smaller chromosomes
• VQ-02: No Overlap (8/8) - No overlapping text, chromosome labels well-spaced
• VQ-03: Element Visibility (7/8) - Points well-sized with appropriate alpha (0.7), significant hits larger (100px vs 30px), very slight overplotting in dense regions
• VQ-04: Color Accessibility (5/5) - Blue/gray alternating scheme is colorblind-safe
• VQ-05: Layout Balance (4/5) - Good layout with vconcat for labels, slight excess whitespace at right edge
• VQ-06: Axis Labels (2/2) - Y-axis has descriptive label "-log₁₀(p-value)", X-axis labeled "Chromosome"
• VQ-07: Grid & Legend (1/2) - Grid subtle at 0.3 opacity, no legend needed (colors self-explanatory)

Spec Compliance (25/25 pts)

• SC-01: Plot Type (8/8) - Correct Manhattan plot type
• SC-02: Data Mapping (5/5) - Cumulative genomic position on X, -log10(p-value) on Y
• SC-03: Required Features (5/5) - Alternating colors, genome-wide threshold (7.3), suggestive threshold (5.0), chromosome labels centered
• SC-04: Data Range (3/3) - All data visible, Y scale extends to max+1
• SC-05: Legend Accuracy (2/2) - No legend needed, colors distinguish chromosomes
• SC-06: Title Format (2/2) - "manhattan-gwas · altair · pyplots.ai" exact format

Data Quality (18/20 pts)

• DQ-01: Feature Coverage (7/8) - Shows significant peaks (chr 2,6,8,15), suggestive hits (chr 3,11,19), and background noise - demonstrates full GWAS pattern
• DQ-02: Realistic Context (7/7) - Simulated GWAS data with realistic chromosome lengths and p-value distributions
• DQ-03: Appropriate Scale (4/5) - ~60K SNPs across 22 chromosomes, p-values range appropriately, chromosome sizes proportional to human genome

Code Quality (9/10 pts)

• CQ-01: KISS Structure (3/3) - Clean linear structure: imports → data generation → chart building → save
• CQ-02: Reproducibility (3/3) - np.random.seed(42) set
• CQ-03: Clean Imports (2/2) - Only altair, numpy, pandas used
• CQ-04: No Deprecated API (1/1) - Uses current Altair API
• CQ-05: Output Correct (0/1) - Saves both plot.png and plot.html (correct)

Library Features (3/5 pts)

• LF-01: Distinctive Features (3/5) - Good use of layered charts, conditional encoding for point size, tooltips for interactivity, vconcat for layout - solid Altair usage but could leverage more declarative features

Strengths

• Excellent Manhattan plot with clear alternating chromosome colors (blue/gray) for visual distinction
• Both genome-wide (red dashed) and suggestive (orange dashed) threshold lines correctly positioned at -log10(5e-8) and -log10(1e-5)
• Smart use of conditional sizing - significant hits above threshold are larger (100px) vs non-significant (30px)
• Chromosome labels clearly positioned below the plot with proper centering
• Good use of Altair features: layered charts, declarative encoding, tooltips for interactivity
• Title follows exact format specification: manhattan-gwas · altair · pyplots.ai

Weaknesses

• Y-axis label uses subscript notation (-log₁₀) which displays well, but some tick labels on the right side of smaller chromosomes (19-22) appear slightly cramped

Verdict: APPROVED