--- name: bio-phylo-tree-visualization description: Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib. Use when creating publication-quality tree figures, customizing colors and labels, or exporting to image formats. tool_type: python primary_tool: Bio.Phylo measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- # Tree Visualization Draw phylogenetic trees using matplotlib integration. ## Required Import ```python from Bio import Phylo import matplotlib.pyplot as plt ``` ## ASCII Tree Display ```python tree = Phylo.read('tree.nwk', 'newick') # Quick text representation print(tree) # ASCII art diagram Phylo.draw_ascii(tree) ``` ## Basic Tree Drawing ```python tree = Phylo.read('tree.nwk', 'newick') # Simple plot (opens interactive window) Phylo.draw(tree) plt.show() # Save to file fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(tree, axes=ax) plt.savefig('tree.png', dpi=300, bbox_inches='tight') plt.close() ``` ## Customizing Tree Appearance ```python fig, ax = plt.subplots(figsize=(12, 10)) Phylo.draw(tree, axes=ax, do_show=False, branch_labels=lambda c: f'{c.branch_length:.2f}' if c.branch_length else '', label_func=lambda c: c.name if c.is_terminal() else '') ax.set_title('Phylogenetic Tree') plt.savefig('custom_tree.png', dpi=300, bbox_inches='tight') plt.close() ``` ## Label Customization ```python # Custom label function def custom_labels(clade): if clade.is_terminal(): return clade.name elif clade.confidence: return f'{clade.confidence:.0f}' return '' fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(tree, axes=ax, label_func=custom_labels) plt.savefig('labeled_tree.png', dpi=300) plt.close() ``` ## Branch Labels (Bootstrap, Lengths) ```python # Show branch lengths def branch_length_labels(clade): if clade.branch_length: return f'{clade.branch_length:.3f}' return '' fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(tree, axes=ax, branch_labels=branch_length_labels) plt.savefig('with_lengths.png', dpi=300) plt.close() # Show bootstrap values (stored in clade.confidence or clade.name for internal nodes) def bootstrap_labels(clade): if not clade.is_terminal() and clade.confidence: return f'{clade.confidence:.0f}' return '' Phylo.draw(tree, axes=ax, branch_labels=bootstrap_labels) ``` ## Coloring Trees ```python # Color specific clades before drawing tree = Phylo.read('tree.nwk', 'newick') # Set colors for specific clades (PhyloXML trees support this natively) for clade in tree.find_clades(): if clade.name and 'Human' in clade.name: clade.color = 'red' elif clade.name and 'Mouse' in clade.name: clade.color = 'blue' fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(tree, axes=ax) plt.savefig('colored_tree.png', dpi=300) plt.close() ``` ## Highlighting Clades ```python from Bio.Phylo.PhyloXML import BranchColor # Convert to PhyloXML for color support phyloxml_tree = tree.as_phyloxml() # Color a clade and its descendants target = phyloxml_tree.find_any(name='Human') if target: target.color = BranchColor.from_name('red') fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(phyloxml_tree, axes=ax) plt.savefig('highlighted.png', dpi=300) plt.close() ``` ## Multiple Output Formats ```python tree = Phylo.read('tree.nwk', 'newick') tree.ladderize() fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(tree, axes=ax, do_show=False) # PNG (raster, good for presentations) plt.savefig('tree.png', dpi=300, bbox_inches='tight') # PDF (vector, good for publications) plt.savefig('tree.pdf', bbox_inches='tight') # SVG (vector, good for web) plt.savefig('tree.svg', bbox_inches='tight') plt.close() ``` ## Figure Size and Layout ```python # Adjust figure size based on tree size n_taxa = len(tree.get_terminals()) height = max(8, n_taxa * 0.3) # Scale with number of taxa fig, ax = plt.subplots(figsize=(10, height)) Phylo.draw(tree, axes=ax, do_show=False) plt.tight_layout() plt.savefig('scaled_tree.png', dpi=300) plt.close() ``` ## Phylo.draw() Parameters | Parameter | Type | Description | |-----------|------|-------------| | `tree` | Tree | Tree object to draw | | `axes` | Axes | Matplotlib axes (optional) | | `label_func` | callable | Function to generate tip labels | | `branch_labels` | callable/dict | Function or dict for branch labels | | `do_show` | bool | Call plt.show() automatically (default True) | ## Pre-Processing for Better Visualization ```python tree = Phylo.read('tree.nwk', 'newick') # Ladderize for cleaner appearance tree.ladderize(reverse=True) # Set missing branch lengths to small value for clade in tree.find_clades(): if clade.branch_length is None: clade.branch_length = 0.001 fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(tree, axes=ax) plt.savefig('clean_tree.png', dpi=300) plt.close() ``` ## Side-by-Side Tree Comparison ```python tree1 = Phylo.read('tree1.nwk', 'newick') tree2 = Phylo.read('tree2.nwk', 'newick') fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(16, 8)) Phylo.draw(tree1, axes=ax1, do_show=False) ax1.set_title('Tree 1') Phylo.draw(tree2, axes=ax2, do_show=False) ax2.set_title('Tree 2') plt.tight_layout() plt.savefig('comparison.png', dpi=300) plt.close() ``` ## Hide Axis and Frame ```python fig, ax = plt.subplots(figsize=(10, 8)) Phylo.draw(tree, axes=ax, do_show=False) ax.axis('off') # Remove axis ax.set_frame_on(False) # Remove frame plt.savefig('clean_tree.png', dpi=300, bbox_inches='tight', transparent=True) plt.close() ``` ## Deprecated Functions | Function | Status | Alternative | |----------|--------|-------------| | `draw_graphviz()` | Removed (1.79) | Use `Phylo.draw()` for rectangular trees | For radial (circular) tree layouts, use external tools like ETE3 or DendroPy. ## Common Issues | Issue | Cause | Solution | |-------|-------|----------| | Labels overlap | Too many taxa | Increase figure height | | No branch lengths | Missing in file | Set defaults or use cladogram | | Colors not showing | Wrong tree format | Convert to PhyloXML first | | Figure not saving | `do_show=True` | Set `do_show=False` before savefig | ## Related Skills - tree-io - Read and write tree files - tree-manipulation - Ladderize and reroot before visualization - distance-calculations - Build trees from alignments for visualization