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feat(pygal): implement tree-phylogenetic (#3113)
## Implementation: `tree-phylogenetic` - pygal Implements the **pygal** version of `tree-phylogenetic`. **File:** `plots/tree-phylogenetic/implementations/pygal.py` **Parent Issue:** #3070 --- :robot: *[impl-generate workflow](https://github.com/MarkusNeusinger/pyplots/actions/runs/20620337510)* --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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‎plots/tree-phylogenetic/implementations/pygal.py‎

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"""pyplots.ai
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tree-phylogenetic: Phylogenetic Tree Diagram
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Library: pygal 3.1.0 | Python 3.13.11
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Quality: 82/100 | Created: 2025-12-31
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"""
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import cairosvg
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import pygal
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from pygal.style import Style
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# Primate phylogenetic tree based on mitochondrial DNA divergence (simplified)
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# Tree structure: ((((Human, Chimpanzee), Gorilla), Orangutan), (Gibbon, Macaque))
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# Scaled to use more canvas width - multiply x positions to spread tree wider
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scale_factor = 1.35
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species_data = [
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("Human", 0.95 * scale_factor, 0),
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("Chimpanzee", 0.95 * scale_factor, 1.5),
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("Gorilla", 0.82 * scale_factor, 3),
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("Orangutan", 0.62 * scale_factor, 5),
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("Gibbon", 0.95 * scale_factor, 7),
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("Macaque", 0.95 * scale_factor, 8.5),
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]
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# Y positions from species data
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species_y = {name: y for name, _, y in species_data}
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species_x = {name: x for name, x, _ in species_data}
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# Define tree connections
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tree_segments = []
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# Human-Chimpanzee clade (most recent common ancestor)
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hc_ancestor_x = 0.82 * scale_factor
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hc_ancestor_y = (species_y["Human"] + species_y["Chimpanzee"]) / 2
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tree_segments.append([(hc_ancestor_x, species_y["Human"]), (species_x["Human"], species_y["Human"])])
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tree_segments.append([(hc_ancestor_x, species_y["Chimpanzee"]), (species_x["Chimpanzee"], species_y["Chimpanzee"])])
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tree_segments.append([(hc_ancestor_x, species_y["Human"]), (hc_ancestor_x, species_y["Chimpanzee"])])
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# Human-Chimp-Gorilla clade
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hcg_ancestor_x = 0.62 * scale_factor
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hcg_ancestor_y = (hc_ancestor_y + species_y["Gorilla"]) / 2
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tree_segments.append([(hcg_ancestor_x, hc_ancestor_y), (hc_ancestor_x, hc_ancestor_y)])
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tree_segments.append([(hcg_ancestor_x, species_y["Gorilla"]), (species_x["Gorilla"], species_y["Gorilla"])])
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tree_segments.append([(hcg_ancestor_x, hc_ancestor_y), (hcg_ancestor_x, species_y["Gorilla"])])
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# Great apes clade including Orangutan
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great_apes_x = 0.41 * scale_factor
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great_apes_y = (hcg_ancestor_y + species_y["Orangutan"]) / 2
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tree_segments.append([(great_apes_x, hcg_ancestor_y), (hcg_ancestor_x, hcg_ancestor_y)])
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tree_segments.append([(great_apes_x, species_y["Orangutan"]), (species_x["Orangutan"], species_y["Orangutan"])])
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tree_segments.append([(great_apes_x, hcg_ancestor_y), (great_apes_x, species_y["Orangutan"])])
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# Gibbon-Macaque clade
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gm_ancestor_x = 0.68 * scale_factor
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gm_ancestor_y = (species_y["Gibbon"] + species_y["Macaque"]) / 2
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tree_segments.append([(gm_ancestor_x, species_y["Gibbon"]), (species_x["Gibbon"], species_y["Gibbon"])])
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tree_segments.append([(gm_ancestor_x, species_y["Macaque"]), (species_x["Macaque"], species_y["Macaque"])])
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tree_segments.append([(gm_ancestor_x, species_y["Gibbon"]), (gm_ancestor_x, species_y["Macaque"])])
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# Root: connects great apes and gibbon-macaque clades (x=0)
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root_x = 0.0
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root_y = (great_apes_y + gm_ancestor_y) / 2
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tree_segments.append([(root_x, great_apes_y), (great_apes_x, great_apes_y)])
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tree_segments.append([(root_x, gm_ancestor_y), (gm_ancestor_x, gm_ancestor_y)])
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tree_segments.append([(root_x, great_apes_y), (root_x, gm_ancestor_y)])
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# Colorblind-friendly palette for species markers
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species_colors = ["#E63946", "#457B9D", "#2A9D8F", "#E9C46A", "#F4A261", "#9C6644"]
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# Branch color - pyplots blue
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branch_color = "#306998"
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# Custom style for pyplots - larger fonts for 4800x2700 canvas
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custom_style = Style(
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background="white",
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plot_background="white",
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foreground="#333",
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foreground_strong="#333",
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foreground_subtle="#999",
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colors=(branch_color,),
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title_font_size=56,
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label_font_size=44,
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major_label_font_size=40,
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legend_font_size=44,
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value_font_size=36,
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tooltip_font_size=28,
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stroke_width=6,
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opacity=1.0,
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guide_stroke_color="#ddd",
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)
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# Create XY chart for phylogenetic tree
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chart = pygal.XY(
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width=4800,
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height=2700,
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style=custom_style,
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title="Primate Evolution · tree-phylogenetic · pygal · pyplots.ai",
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x_title="Evolutionary Distance (substitutions per site)",
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y_title="",
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show_legend=False,
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show_dots=False,
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stroke_style={"width": 6},
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fill=False,
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show_x_guides=False,
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show_y_guides=False,
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show_y_labels=False,
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range=(-1.5, 10),
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xrange=(-0.05, 1.45),
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print_values=False,
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)
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# Add all tree branches as unnamed series
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for seg in tree_segments:
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chart.add(None, seg, show_dots=False, stroke_style={"width": 6})
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# Add species markers (dots only, labels added via SVG)
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for i, (_name, x_pos, y_pos) in enumerate(species_data):
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color = species_colors[i % len(species_colors)]
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chart.add(
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None, [{"value": (x_pos, y_pos), "color": color}], show_dots=True, dots_size=28, stroke_style={"width": 0}
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)
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# Render to SVG string first
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svg_content = chart.render().decode("utf-8")
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# Calculate pixel positions for species labels
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# Plot area bounds for coordinate conversion
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plot_x_min, plot_x_max = 180, 4620
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plot_y_min, plot_y_max = 100, 2500
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data_x_min, data_x_max = -0.05, 1.45
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data_y_min, data_y_max = -1.5, 10
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# Generate species label SVG elements positioned directly next to leaf nodes
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species_labels_svg = '<g class="species-labels">\n'
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for i, (name, x_pos, y_pos) in enumerate(species_data):
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# Inline coordinate conversion (data to pixel)
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px = plot_x_min + (x_pos - data_x_min) / (data_x_max - data_x_min) * (plot_x_max - plot_x_min)
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py = plot_y_max - (y_pos - data_y_min) / (data_y_max - data_y_min) * (plot_y_max - plot_y_min)
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color = species_colors[i % len(species_colors)]
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# Position label to the right of the marker
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species_labels_svg += f' <text x="{px + 50}" y="{py + 12}" font-size="42" fill="{color}" '
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species_labels_svg += f'font-family="sans-serif" font-weight="bold">{name}</text>\n'
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species_labels_svg += "</g>\n"
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# Add scale bar with label - inline coordinate conversion
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scale_x_data, scale_y_data = 0.0, -1.0
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scale_px = plot_x_min + (scale_x_data - data_x_min) / (data_x_max - data_x_min) * (plot_x_max - plot_x_min)
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scale_py = plot_y_max - (scale_y_data - data_y_min) / (data_y_max - data_y_min) * (plot_y_max - plot_y_min)
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scale_end_x_data = 0.1
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scale_end_px = plot_x_min + (scale_end_x_data - data_x_min) / (data_x_max - data_x_min) * (plot_x_max - plot_x_min)
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scale_width = scale_end_px - scale_px
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scale_bar_svg = f"""
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<g class="scale-bar">
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<line x1="{scale_px}" y1="{scale_py}" x2="{scale_end_px}" y2="{scale_py}" stroke="#333" stroke-width="10"/>
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<text x="{scale_px + scale_width / 2}" y="{scale_py + 55}" text-anchor="middle" font-size="40" fill="#333" font-family="sans-serif">0.1 substitutions/site</text>
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</g>
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"""
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# Insert labels and scale bar before closing </svg> tag
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svg_content = svg_content.replace("</svg>", species_labels_svg + scale_bar_svg + "</svg>")
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# Save SVG
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with open("plot.svg", "w") as f:
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f.write(svg_content)
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# For HTML, use the modified SVG
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html_content = f"""<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8">
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<title>Phylogenetic Tree - pygal</title>
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<style>body {{ margin: 0; display: flex; justify-content: center; align-items: center; min-height: 100vh; }}</style>
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</head>
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<body>
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{svg_content}
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</body>
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</html>"""
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with open("plot.html", "w") as f:
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f.write(html_content)
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# Convert to PNG using cairosvg
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cairosvg.svg2png(bytestring=svg_content.encode("utf-8"), write_to="plot.png")

‎plots/tree-phylogenetic/metadata/pygal.yaml‎

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library: pygal
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specification_id: tree-phylogenetic
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created: '2025-12-31T13:57:05Z'
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updated: '2025-12-31T14:49:21Z'
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generated_by: claude-opus-4-5-20251101
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workflow_run: 20620337510
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issue: 3070
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python_version: 3.13.11
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library_version: 3.1.0
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preview_url: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/pygal/plot.png
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preview_thumb: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/pygal/plot_thumb.png
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preview_html: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/pygal/plot.html
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quality_score: 82
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review:
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strengths:
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- Creative use of pygal XY chart to represent phylogenetic tree structure
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- Excellent colorblind-friendly color palette for species markers
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- Includes proper scale bar with units for evolutionary distance interpretation
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- Species labels are clearly positioned next to their markers without overlap
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- Scientifically accurate primate evolutionary relationships represented
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weaknesses:
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- Code uses a helper function which deviates from KISS principle
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- Tree is somewhat compressed with unused whitespace on the right side of the canvas
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- Y-axis grid lines are visible but serve no purpose for tree visualization

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