#!/usr/bin/env python3
"""
Quick tree visualization script with common customization options.
Provides command-line interface for rapid tree visualization with
customizable styles, layouts, and output formats.
"""
import argparse
import sys
from pathlib import Path
try:
from ete3 import Tree, TreeStyle, NodeStyle
except ImportError:
print("Error: ete3 not installed. Install with: pip install ete3")
sys.exit(1)
def create_tree_style(args):
"""Create TreeStyle based on arguments."""
ts = TreeStyle()
# Basic display options
ts.show_leaf_name = args.show_names
ts.show_branch_length = args.show_lengths
ts.show_branch_support = args.show_support
ts.show_scale = args.show_scale
# Layout
ts.mode = args.mode
ts.rotation = args.rotation
# Circular tree options
if args.mode == "c":
ts.arc_start = args.arc_start
ts.arc_span = args.arc_span
# Spacing
ts.branch_vertical_margin = args.vertical_margin
if args.scale_factor:
ts.scale = args.scale_factor
# Title
if args.title:
from ete3 import TextFace
title_face = TextFace(args.title, fsize=16, bold=True)
ts.title.add_face(title_face, column=0)
return ts
def apply_node_styling(tree, args):
"""Apply styling to tree nodes."""
for node in tree.traverse():
nstyle = NodeStyle()
if node.is_leaf():
# Leaf style
nstyle["fgcolor"] = args.leaf_color
nstyle["size"] = args.leaf_size
else:
# Internal node style
nstyle["fgcolor"] = args.internal_color
nstyle["size"] = args.internal_size
# Color by support if enabled
if args.color_by_support and hasattr(node, 'support') and node.support:
if node.support >= 0.9:
nstyle["fgcolor"] = "darkgreen"
elif node.support >= 0.7:
nstyle["fgcolor"] = "orange"
else:
nstyle["fgcolor"] = "red"
node.set_style(nstyle)
def visualize_tree(tree_file, output, args):
"""Load tree, apply styles, and render."""
try:
tree = Tree(str(tree_file), format=args.format)
except Exception as e:
print(f"Error loading tree: {e}")
sys.exit(1)
# Apply styling
apply_node_styling(tree, args)
# Create tree style
ts = create_tree_style(args)
# Render
try:
# Determine output parameters based on format
output_path = str(output)
render_args = {"tree_style": ts}
if args.width:
render_args["w"] = args.width
if args.height:
render_args["h"] = args.height
if args.units:
render_args["units"] = args.units
if args.dpi:
render_args["dpi"] = args.dpi
tree.render(output_path, **render_args)
print(f"Tree rendered successfully to: {output}")
except Exception as e:
print(f"Error rendering tree: {e}")
sys.exit(1)
def main():
parser = argparse.ArgumentParser(
description="Quick tree visualization with ETE toolkit",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="""
Examples:
# Basic visualization
%(prog)s tree.nw output.pdf
# Circular tree
%(prog)s tree.nw output.pdf --mode c
# Large tree with custom sizing
%(prog)s tree.nw output.png --width 1200 --height 800 --units px --dpi 300
# Hide names, show support, color by support
%(prog)s tree.nw output.pdf --no-names --show-support --color-by-support
# Custom title
%(prog)s tree.nw output.pdf --title "Phylogenetic Tree of Species"
# Semicircular layout
%(prog)s tree.nw output.pdf --mode c --arc-start -90 --arc-span 180
"""
)
parser.add_argument("input", help="Input tree file (Newick format)")
parser.add_argument("output", help="Output image file (png, pdf, or svg)")
# Tree format
parser.add_argument("--format", type=int, default=0,
help="Newick format number (default: 0)")
# Display options
display = parser.add_argument_group("Display options")
display.add_argument("--no-names", dest="show_names", action="store_false",
help="Don't show leaf names")
display.add_argument("--show-lengths", action="store_true",
help="Show branch lengths")
display.add_argument("--show-support", action="store_true",
help="Show support values")
display.add_argument("--show-scale", action="store_true",
help="Show scale bar")
# Layout options
layout = parser.add_argument_group("Layout options")
layout.add_argument("--mode", choices=["r", "c"], default="r",
help="Tree mode: r=rectangular, c=circular (default: r)")
layout.add_argument("--rotation", type=int, default=0,
help="Tree rotation in degrees (default: 0)")
layout.add_argument("--arc-start", type=int, default=0,
help="Circular tree start angle (default: 0)")
layout.add_argument("--arc-span", type=int, default=360,
help="Circular tree arc span (default: 360)")
# Styling options
styling = parser.add_argument_group("Styling options")
styling.add_argument("--leaf-color", default="blue",
help="Leaf node color (default: blue)")
styling.add_argument("--leaf-size", type=int, default=6,
help="Leaf node size (default: 6)")
styling.add_argument("--internal-color", default="gray",
help="Internal node color (default: gray)")
styling.add_argument("--internal-size", type=int, default=4,
help="Internal node size (default: 4)")
styling.add_argument("--color-by-support", action="store_true",
help="Color internal nodes by support value")
# Size and spacing
size = parser.add_argument_group("Size and spacing")
size.add_argument("--width", type=int, help="Output width")
size.add_argument("--height", type=int, help="Output height")
size.add_argument("--units", choices=["px", "mm", "in"],
help="Size units (px, mm, in)")
size.add_argument("--dpi", type=int, help="DPI for raster output")
size.add_argument("--scale-factor", type=int,
help="Branch length scale factor (pixels per unit)")
size.add_argument("--vertical-margin", type=int, default=10,
help="Vertical margin between branches (default: 10)")
# Other options
parser.add_argument("--title", help="Tree title")
args = parser.parse_args()
# Validate output format
output_path = Path(args.output)
valid_extensions = {".png", ".pdf", ".svg"}
if output_path.suffix.lower() not in valid_extensions:
print(f"Error: Output must be PNG, PDF, or SVG file")
sys.exit(1)
# Visualize
visualize_tree(args.input, args.output, args)
if __name__ == "__main__":
main()