feat(pygal): implement manhattan-gwas

[github-actions]

Implementation: manhattan-gwas - python/pygal

Implements the python/pygal version of manhattan-gwas.

File: plots/manhattan-gwas/implementations/python/pygal.py

Parent Issue: #2925

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🤖 impl-generate workflow

[claude]

AI Review - Attempt 1/3

Image Description

Light render (plot-light.png): The Manhattan plot displays a warm off-white background (#FAF8F1) with the title "manhattan-gwas · pygal · anyplot.ai" in dark text at the top. The y-axis is labeled "-log₁₀(p-value)" with tick marks visible from 0–16. The x-axis shows chromosome labels (1-22) centered below their genomic regions. The plot exhibits the characteristic Manhattan plot structure: a dense band of points near the baseline (non-significant variants), with prominent peaks rising above two horizontal threshold lines (dashed, at ~7.3 and ~5). The data points use alternating colors—green (#009E73, the brand color, representing odd chromosomes) and orange (#D55E00, representing even chromosomes)—creating clear visual separation. A third series ("Significant (p<5×10⁻⁸)") marks the tallest peaks. All text is clearly readable against the light background with no contrast issues.

Dark render (plot-dark.png): The dark render uses a warm near-black background (#1A1A17) with light text throughout. The title, axis labels, and tick marks are all rendered in light colors (#F0EFE8 for primary text) and remain fully readable against the dark surface. The data colors are identical to the light render—green and orange points maintain perfect visual consistency, confirming that only the chrome (background, text, grid) has adapted to the theme while data identity is preserved. The two threshold lines are clearly visible as dashed lines. No "dark-on-dark" failures are present; all elements have sufficient contrast. The plot structure and data representation are identical to the light version, proving successful theme adaptation.

Score: 89/100

Category	Score	Max
Visual Quality	30	30
Design Excellence	13	20
Spec Compliance	15	15
Data Quality	14	15
Code Quality	10	10
Library Mastery	7	10
Total	89	100

Visual Quality (30/30)

• VQ-01: Text Legibility (8/8) - All text sizes explicitly set (title=28px, labels=22px, ticks=18px). Fully readable in both themes.
• VQ-02: No Overlap (6/6) - Point density expected at lower y-values. Readable regions have no text collisions.
• VQ-03: Element Visibility (6/6) - Marker size (dots_size=4) appropriate for 11,000-point dataset.
• VQ-04: Color Accessibility (2/2) - Okabe-Ito palette is colorblind-safe.
• VQ-05: Layout & Canvas (4/4) - 4800×2700 landscape with appropriate margins.
• VQ-06: Axis Labels & Title (2/2) - Title matches spec. Axes labeled with units.
• VQ-07: Palette Compliance (2/2) - First color #009E73. Backgrounds match (#FAF8F1 light / #1A1A17 dark).

Design Excellence (13/20)

• DE-01: Aesthetic Sophistication (5/8) - Custom Style with explicit font sizing and theme-adaptive tokens. Professional polish.
• DE-02: Visual Refinement (3/6) - Clean spacing. Pygal's API limitations prevent advanced spine control.
• DE-03: Data Storytelling (5/6) - Clear focal points. Color alternation guides the eye. Thresholds emphasize significance.

Spec Compliance (15/15)

• SC-01: Plot Type (5/5) - Correct Manhattan plot (XY scatter).
• SC-02: Required Features (4/4) - Cumulative position, -log10 transform, alternating colors, both thresholds.
• SC-03: Data Mapping (3/3) - X-axis cumulative position, Y-axis -log10 p-values, all 22 chromosomes.
• SC-04: Title & Legend (3/3) - Title format correct, legend placement appropriate.

Data Quality (14/15)

• DQ-01: Feature Coverage (5/6) - Shows all aspects: baseline, peaks, thresholds, three data series.
• DQ-02: Realistic Context (5/5) - Plausible GWAS simulation with accurate chromosome representation.
• DQ-03: Appropriate Scale (4/4) - Y-axis range covers -log10 values; X-axis spans genome.

Code Quality (10/10)

• CQ-01: KISS Structure (3/3) - Direct script, no unnecessary functions.
• CQ-02: Reproducibility (2/2) - Seeded random number generator.
• CQ-03: Clean Imports (2/2) - Only necessary imports.
• CQ-04: Code Elegance (2/2) - Clean logic, appropriate complexity.
• CQ-05: Output & API (1/1) - Renders to plot-{THEME}.png and .html correctly.

Library Mastery (7/10)

• LM-01: Idiomatic Usage (4/5) - Proper pygal.XY() usage. Style object for theming. Custom x_value_formatter demonstrates beyond-basic API.
• LM-02: Distinctive Features (3/5) - Good use of interactive tooltips and HTML export, but limited distinctive techniques.

Score Caps Applied

• None

Strengths

• Excellent theme adaptation: both light and dark renders are equally readable with no contrast issues
• Correct palette usage: Okabe-Ito colors applied correctly; green (#009E73) dominates
• Comprehensive data: 11,000 points across 22 chromosomes with realistic GWAS distribution
• Proper typography: All font sizes follow the 4800×2700 scale guide
• Clear visual hierarchy: Threshold lines and color alternation create effective focal points

Weaknesses

• Design Excellence limited by pygal's API constraints (cannot customize spines/grid as granularly as matplotlib)
• Only 2 of 7 Okabe-Ito colors utilized (green, orange) — limitation of the plot type, not implementation

Verdict: APPROVED

[github-actions]

🔧 Repair Attempt 1/4

Applied fixes based on AI review feedback.

Status: Repair completed, re-triggering review...

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🤖 impl-repair

[claude]

AI Review - Attempt 2/3

Image Description

Light render (plot-light.png): The manhattan plot displays GWAS results on a warm off-white background (#FAF8F1) with excellent readability. The title "manhattan-gwas · pygal · anyplot.ai" is clearly visible at the top in dark text. The y-axis label "-log₁₀(p-value)" with subscript is readable, and the x-axis shows chromosome numbers (1-22) centered at their region midpoints. Data points are colored with alternating teal/green (#009E73 - Okabe-Ito position 1) and orange (#D55E00 - position 2) for odd and even chromosomes respectively, creating clear visual distinction. Two dashed threshold lines are visible at y≈5 (suggestive) and y≈7.3 (genome-wide significance). Significant peaks are highlighted in blue. The legend at the bottom clearly lists all series. All text, gridlines, and data elements are distinctly readable against the light background with no contrast issues.

Dark render (plot-dark.png): The same plot rendered on a warm near-black background (#1A1A17) maintains perfect readability with light text for title and axis labels. The data colors are identical to the light render—the same greens and oranges, confirming proper theme-adaptive chrome. Secondary text uses the muted light tone, providing appropriate contrast. The threshold lines remain clearly visible. No "dark-on-dark" failures are present; all text is readable against the dark surface. The grid lines are subtle in both renders. Critically, the Okabe-Ito data colors remain constant between themes, with only chrome (background, text, grid) adapting appropriately.

Score: 89/100

Category	Score	Max
Visual Quality	30	30
Design Excellence	13	20
Spec Compliance	15	15
Data Quality	15	15
Code Quality	10	10
Library Mastery	6	10
Total	89	100

Visual Quality (30/30)

• VQ-01: Text Legibility (8/8) — All text elements clearly readable at full size in both themes
• VQ-02: No Overlap (6/6) — Chromosome labels centered without collisions, legend positioned cleanly
• VQ-03: Element Visibility (6/6) — All markers visible even in dense regions, significant peaks stand out clearly
• VQ-04: Color Accessibility (2/2) — Okabe-Ito palette (colorblind-safe), no red-green as sole signal
• VQ-05: Layout & Canvas (4/4) — Balanced proportions, generous margins, nothing cut off
• VQ-06: Axis Labels & Title (2/2) — Title correct format, axes labeled with units
• VQ-07: Palette Compliance (2/2) — First series #009E73, backgrounds correct (#FAF8F1/#1A1A17), both themes work perfectly

Design Excellence (13/20)

• DE-01: Aesthetic Sophistication (4/8) — Professional with theme adaptation, meaningful color choices
• DE-02: Visual Refinement (4/6) — Clean appearance, threshold lines appropriately dashed
• DE-03: Data Storytelling (5/6) — Effectively guides viewer through genome, thresholds provide context

Spec Compliance (15/15)

• SC-01: Plot Type (5/5) — XY scatter correctly implements manhattan plot
• SC-02: Required Features (4/4) — All features present: alternating colors, both thresholds, significant peaks
• SC-03: Data Mapping (3/3) — Axes correct, all data shown
• SC-04: Title & Legend (3/3) — Title format correct, legend labels match

Data Quality (15/15)

• DQ-01: Feature Coverage (6/6) — Full manhattan plot with all GWAS elements
• DQ-02: Realistic Context (5/5) — Realistic GWAS-like data, neutral domain context
• DQ-03: Appropriate Scale (4/4) — Realistic p-value range and standard thresholds

Code Quality (10/10)

• CQ-01: KISS Structure (3/3) — Straightforward, no unnecessary abstraction
• CQ-02: Reproducibility (2/2) — Fixed seed for deterministic output
• CQ-03: Clean Imports (2/2) — Only necessary imports
• CQ-04: Code Elegance (2/2) — Appropriate complexity, no fake functionality
• CQ-05: Output & API (1/1) — Correct output format and current API

Library Mastery (6/10)

• LM-01: Idiomatic Usage (4/5) — Good XY chart and Style usage, follows pygal conventions
• LM-02: Distinctive Features (2/5) — Limited showcase of distinctive pygal features

Strengths

• Proper theme adaptation with all required theme tokens
• Correct Okabe-Ito color palette with first series as brand green
• Both light and dark renders fully readable with no legibility failures
• Clean visualization with effective alternating chromosome coloring
• Both significance thresholds properly marked at correct p-value levels
• Data colors remain identical between themes; only chrome adapts appropriately
• Reproducible output with fixed random seed

Weaknesses

• None identified — implementation is correct and complete

Verdict: APPROVED