bokeh.yaml

library: bokeh
specification_id: dendrogram-basic
created: '2025-12-23T10:01:43Z'
updated: '2026-04-05T20:00:00+00:00'
generated_by: claude-opus-4-6
workflow_run: 20457532402
issue: 0
python_version: '3.14.3'
library_version: 3.8.2
preview_url: https://storage.googleapis.com/pyplots-images/plots/dendrogram-basic/bokeh/plot.png
preview_html: https://storage.googleapis.com/pyplots-images/plots/dendrogram-basic/bokeh/plot.html
quality_score: null
impl_tags:
  dependencies:
    - scipy
  techniques:
    - html-export
  patterns:
    - data-generation
    - iteration-over-groups
  dataprep:
    - hierarchical-clustering
  styling: []
review:
  strengths:
  - Excellent manual implementation of dendrogram structure using Bokeh primitives
    (line glyphs)
  - Two-color scheme effectively distinguishes cluster levels with colorblind-safe
    palette
  - Biologically accurate iris data clustering with proper species separation
  - Clean KISS code structure with proper seed for reproducibility
  - Rotated labels prevent overlap and maintain readability
  - Generates both PNG and interactive HTML output leveraging Bokeh web capabilities
  weaknesses:
  - X-axis label Sample is generic; could be more descriptive like Iris Samples
  - No legend or annotation explaining the blue/yellow color threshold meaning
  - Could use ColumnDataSource for more idiomatic Bokeh code
  image_description: 'The plot displays a hierarchical dendrogram visualizing clustering
    of 15 iris flower samples across three species (Setosa, Versicolor, Virginica).
    The tree structure uses a two-color scheme: blue (#306998) for high-level merges
    above the color threshold and yellow/gold (#FFD43B) for lower-level within-cluster
    merges. The Y-axis shows "Distance (Ward)" ranging from 0 to approximately 10,
    with dashed grid lines. The X-axis is labeled "Sample" with 15 rotated labels
    (45°) showing sample names like "Setosa-1", "Versicolor-4", "Virginica-3", etc.
    The title "dendrogram-basic · bokeh · pyplots.ai" appears at the top left. The
    dendrogram correctly shows Setosa samples clustering separately on the left, while
    Versicolor and Virginica samples intermix on the right before merging at a higher
    distance level - biologically accurate for iris data.'
  criteria_checklist:
    visual_quality:
      score: 36
      max: 40
      items:
      - id: VQ-01
        name: Text Legibility
        score: 9
        max: 10
        passed: true
        comment: Title, axis labels, and tick labels are readable; rotated sample
          labels are slightly small but legible
      - id: VQ-02
        name: No Overlap
        score: 8
        max: 8
        passed: true
        comment: No overlapping text elements; rotated labels fit well
      - id: VQ-03
        name: Element Visibility
        score: 8
        max: 8
        passed: true
        comment: Line width of 4 makes dendrogram branches clearly visible
      - id: VQ-04
        name: Color Accessibility
        score: 5
        max: 5
        passed: true
        comment: Blue and yellow provide excellent contrast and are colorblind-safe
      - id: VQ-05
        name: Layout Balance
        score: 4
        max: 5
        passed: true
        comment: Good proportions, slight extra whitespace on right side
      - id: VQ-06
        name: Axis Labels
        score: 1
        max: 2
        passed: true
        comment: '"Distance (Ward)" is descriptive but "Sample" is generic'
      - id: VQ-07
        name: Grid & Legend
        score: 1
        max: 2
        passed: true
        comment: Dashed grid is subtle (alpha 0.3), no legend needed but color meaning
          unexplained
    spec_compliance:
      score: 25
      max: 25
      items:
      - id: SC-01
        name: Plot Type
        score: 8
        max: 8
        passed: true
        comment: Correct dendrogram/tree visualization
      - id: SC-02
        name: Data Mapping
        score: 5
        max: 5
        passed: true
        comment: Samples on X-axis, merge distances on Y-axis
      - id: SC-03
        name: Required Features
        score: 5
        max: 5
        passed: true
        comment: Hierarchical structure, branch heights proportional to merge distances,
          labels present
      - id: SC-04
        name: Data Range
        score: 3
        max: 3
        passed: true
        comment: Y-axis shows full range from 0 to max distance
      - id: SC-05
        name: Legend Accuracy
        score: 2
        max: 2
        passed: true
        comment: No legend required for this plot type
      - id: SC-06
        name: Title Format
        score: 2
        max: 2
        passed: true
        comment: Uses correct format "dendrogram-basic · bokeh · pyplots.ai"
    data_quality:
      score: 18
      max: 20
      items:
      - id: DQ-01
        name: Feature Coverage
        score: 7
        max: 8
        passed: true
        comment: Shows hierarchical merging at multiple levels, cluster separation
          visible; could show more diversity in merge distances
      - id: DQ-02
        name: Realistic Context
        score: 7
        max: 7
        passed: true
        comment: Iris flower species is a classic, real-world clustering example
      - id: DQ-03
        name: Appropriate Scale
        score: 4
        max: 5
        passed: true
        comment: 15 samples is within recommended 10-50 range; Ward distances are
          realistic
    code_quality:
      score: 9
      max: 10
      items:
      - id: CQ-01
        name: KISS Structure
        score: 3
        max: 3
        passed: true
        comment: 'Linear script: imports → data → linkage → plot → save'
      - id: CQ-02
        name: Reproducibility
        score: 3
        max: 3
        passed: true
        comment: np.random.seed(42) set
      - id: CQ-03
        name: Clean Imports
        score: 2
        max: 2
        passed: true
        comment: All imports are used
      - id: CQ-04
        name: No Deprecated API
        score: 1
        max: 1
        passed: true
        comment: Uses current Bokeh API
      - id: CQ-05
        name: Output Correct
        score: 0
        max: 1
        passed: false
        comment: Saves both plot.png and plot.html (minor issue, but PNG is correct)
    library_features:
      score: 3
      max: 5
      items:
      - id: LF-01
        name: Uses distinctive library features
        score: 3
        max: 5
        passed: true
        comment: Manual rendering with Bokeh figure and line glyphs; generates HTML
          output for interactivity; however, could use ColumnDataSource pattern more
  verdict: APPROVED