feat(plotly): implement tree-phylogenetic

[github-actions]

Implementation: tree-phylogenetic - plotly

Implements the plotly version of tree-phylogenetic.

File: plots/tree-phylogenetic/implementations/plotly.py

Parent Issue: #3070

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🤖 impl-generate workflow

[claude]

AI Review - Attempt 1/3

Image Description

The plot displays a rectangular phylogenetic tree (cladogram) showing primate evolutionary relationships. The tree has a dark blue (#306998) branch structure with yellow (#FFD43B) circular markers at leaf nodes representing five species: Human, Chimpanzee, Gorilla, Orangutan, and Gibbon. Species names appear in dark gray text to the right of each leaf node. The tree topology shows Human and Chimpanzee as the closest relatives, then Gorilla, then Orangutan, with Gibbon as the outgroup. Three clade annotations in italic gray text with arrows identify "Hominini" (Human-Chimp), "Homininae (African Apes)" (Human-Chimp-Gorilla), and "Hominidae (Great Apes)" (all except Gibbon). A scale bar at the bottom left shows "0.1 substitutions/site". The x-axis is labeled "Evolutionary Distance (substitutions per site)" ranging from 0 to 0.5. The title reads "Primate Evolution · tree-phylogenetic · plotly · pyplots.ai". Background is white with subtle gray grid lines.

Quality Score: 92/100

Criteria Checklist

Visual Quality (36/40 pts)

• VQ-01: Text Legibility (10/10) - Title at 28pt, axis labels at 22pt, species names at 20pt, all clearly readable
• VQ-02: No Overlap (8/8) - No overlapping text, species labels well-spaced
• VQ-03: Element Visibility (8/8) - Markers (size 18) and branch lines (width 3) appropriately sized for 5 data points
• VQ-04: Color Accessibility (5/5) - Blue/yellow color scheme is colorblind-safe with good contrast
• VQ-05: Layout Balance (3/5) - Good proportions but tree is slightly left-heavy with species names clustered on right
• VQ-06: Axis Labels (2/2) - X-axis has descriptive label with units "(substitutions per site)"
• VQ-07: Grid & Legend (0/2) - Grid is subtle, but no legend (though not needed for this plot type)

Spec Compliance (25/25 pts)

• SC-01: Plot Type (8/8) - Correct rectangular phylogenetic tree visualization
• SC-02: Data Mapping (5/5) - X-axis correctly represents evolutionary distance, tree topology accurate
• SC-03: Required Features (5/5) - Branch lengths proportional, scale bar present, clade annotations included
• SC-04: Data Range (3/3) - Axes show all data appropriately (0 to 0.55 range covers all species)
• SC-05: Legend Accuracy (2/2) - N/A for tree diagrams, clade labels are accurate
• SC-06: Title Format (2/2) - Correct format: "Primate Evolution · tree-phylogenetic · plotly · pyplots.ai"

Data Quality (18/20 pts)

• DQ-01: Feature Coverage (6/8) - Shows hierarchical structure, branch lengths, clade groupings; could show more diversity in branch lengths
• DQ-02: Realistic Context (7/7) - Primate mitochondrial DNA phylogeny is a classic, scientifically accurate example
• DQ-03: Appropriate Scale (5/5) - Branch lengths (0.1-0.4 substitutions/site) are realistic for primate divergence

Code Quality (8/10 pts)

• CQ-01: KISS Structure (3/3) - Linear script: imports → data → plot → save
• CQ-02: Reproducibility (1/3) - Deterministic data (no random), but no explicit seed comment
• CQ-03: Clean Imports (2/2) - Only plotly.graph_objects imported and used
• CQ-04: No Deprecated API (1/1) - Uses current Plotly API
• CQ-05: Output Correct (1/1) - Saves as plot.png and plot.html

Library Features (5/5 pts)

• LF-01: Uses distinctive library features (5/5) - Hover tooltips, annotations with arrows, HTML export for interactivity

Strengths

• Excellent use of Plotly's annotation system with arrows to label taxonomic clades
• Scientifically accurate primate phylogeny with correct topology and plausible branch lengths
• Clean rectangular phylogram layout with proportional branch lengths
• Scale bar with proper units enhances scientific communication
• Interactive hover tooltips showing species name and evolutionary distance
• Appropriate color scheme (Python blue/yellow) that is colorblind-safe

Weaknesses

• Grid lines extend into the tree area which could be cleaner (consider removing or limiting)
• VQ-07 scoring: No legend present, though this is standard for phylogenetic trees

Verdict: APPROVED