ReddRadar
Agent skill
bio-phylo-tree-visualization
Install this agent skill to your Project
npx add-skill https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-phylo-tree-visualization
SKILL.md
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
from Bio import Phylo
import matplotlib.pyplot as plt
ASCII Tree Display
tree = Phylo.read('tree.nwk', 'newick')
# Quick text representation
print(tree)
# ASCII art diagram
Phylo.draw_ascii(tree)
Basic Tree Drawing
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
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
# 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)
# 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
# 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
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
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
# 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
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
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
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
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