feat(plotly): implement volcano-basic

[github-actions]

Implementation: volcano-basic - plotly

Implements the plotly version of volcano-basic.

File: plots/volcano-basic/implementations/plotly.py

Parent Issue: #2924

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🤖 impl-generate workflow

[claude]

AI Review - Attempt 1/3

Image Description

The plot displays a volcano plot with approximately 500 data points representing simulated gene expression data. The x-axis shows "log₂ Fold Change" ranging from approximately -4 to 6, and the y-axis shows "-log₁₀(p-value)" ranging from 0 to about 3.5. Points are colored in three categories: gray for "Not Significant" (majority of points clustered in the center), blue (#306998) for "Down-regulated" genes (left side, above thresholds), and orange (#D35400) for "Up-regulated" genes (right side, above thresholds). Dashed threshold lines are clearly visible: horizontal line at p = 0.05 (~1.3 on y-axis) and vertical lines at log2FC = ±1. Three top significant genes are labeled with arrows (Gene_374, Gene_346, Gene_236). The legend is positioned in the upper-left with a semi-transparent white background. The overall layout uses the plotly_white template with subtle gridlines.

Quality Score: 92/100

Criteria Checklist

Visual Quality (37/40 pts)

• VQ-01: Text Legibility (10/10) - Title at 28pt, axis labels at 22pt, ticks at 18pt - all perfectly readable
• VQ-02: No Overlap (8/8) - No overlapping text elements; gene annotations well-positioned with arrows
• VQ-03: Element Visibility (7/8) - Marker sizes appropriate (10-12px), opacity levels good (0.5-0.8), though some central overlap in gray points
• VQ-04: Color Accessibility (5/5) - Blue/orange/gray palette is colorblind-safe (no red-green only distinction)
• VQ-05: Layout Balance (5/5) - Plot fills canvas well, balanced margins, legend well-placed
• VQ-06: Axis Labels (2/2) - Descriptive labels with proper subscript notation (log₂, log₁₀)
• VQ-07: Grid & Legend (0/2) - Grid is subtle but legend entries for threshold lines add clutter; could be simplified

Spec Compliance (25/25 pts)

• SC-01: Plot Type (8/8) - Correct volcano plot visualization
• SC-02: Data Mapping (5/5) - X = log2 fold change, Y = -log10(p-value) correctly mapped
• SC-03: Required Features (5/5) - All spec features present: horizontal threshold at p=0.05, vertical thresholds at ±1, color-coded significance, top gene labels
• SC-04: Data Range (3/3) - All data visible within axis ranges
• SC-05: Legend Accuracy (2/2) - Legend labels correctly describe each category
• SC-06: Title Format (2/2) - Correct format: "volcano-basic · plotly · pyplots.ai"

Data Quality (18/20 pts)

• DQ-01: Feature Coverage (7/8) - Shows up-regulated, down-regulated, and non-significant genes; good spread of significance values; could show more extreme p-values
• DQ-02: Realistic Context (7/7) - Gene expression scenario is realistic and neutral; appropriate for differential expression analysis
• DQ-03: Appropriate Scale (4/5) - log2FC range (-4 to 6) and p-value range reasonable, though p-values could extend lower for more dramatic top hits

Code Quality (9/10 pts)

• CQ-01: KISS Structure (3/3) - Clean imports → data → plot → save structure, no functions/classes
• CQ-02: Reproducibility (3/3) - np.random.seed(42) set
• CQ-03: Clean Imports (2/2) - Only numpy and plotly.graph_objects used
• CQ-04: No Deprecated API (1/1) - Uses current Plotly API
• CQ-05: Output Correct (0/0) - Saves as plot.png at correct resolution (4800×2700 via scale=3)

Library Features (3/5 pts)

• LF-01: Uses distinctive library features (3/5) - Good use of hover templates with custom formatting, interactive HTML export, but could leverage more Plotly-specific features like custom hover data or range sliders

Strengths

• Excellent implementation of volcano plot with all required threshold lines and color coding
• Proper use of Plotly hover templates showing gene name, fold change, and p-value
• Clean three-color scheme (gray/blue/orange) that is colorblind accessible
• Appropriate marker sizing and alpha transparency for the data density
• Gene annotations with arrows for top significant hits
• Both PNG and HTML outputs generated correctly

Weaknesses

• Legend includes threshold line entries (p = 0.05, log2FC = 1.0) which adds visual clutter; threshold lines are self-explanatory from context
• Some overlap in the dense central gray point cluster could benefit from slightly smaller markers or more transparency
• Could utilize more Plotly-specific features like updatemenus or rangeslider for enhanced interactivity

Verdict: APPROVED