61 lines
1.7 KiB
Python
61 lines
1.7 KiB
Python
 
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#!/usr/bin/env python3
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"""
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使用 matplotlib + Bio.Phylo 绘制进化树 (无头模式)
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"""
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import sys
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import os
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os.environ['QT_QPA_PLATFORM'] = 'offscreen' # 无头模式
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os.environ['MPLBACKEND'] = 'Agg' # 使用Agg后端
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from pathlib import Path
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import matplotlib
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matplotlib.use('Agg') # 无头后端
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import matplotlib.pyplot as plt
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from Bio import Phylo
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def plot_tree(treefile, output_dir):
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"""绘制进化树并输出PDF和PNG"""
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treefile = Path(treefile)
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output_dir = Path(output_dir)
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output_dir.mkdir(parents=True, exist_ok=True)
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# 读取树 (Newick格式)
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tree = Phylo.read(str(treefile), "newick")
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# 输出文件名
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base_name = treefile.stem.replace('.iqtree', '').replace('.treefile', '')
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pdf_file = output_dir / f"{base_name}.pdf"
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png_file = output_dir / f"{base_name}.png"
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# 创建图形
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fig, ax = plt.subplots(figsize=(14, 10))
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# 绘制进化树
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Phylo.draw(tree, axes=ax, do_show=False,
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branch_labels=lambda c: c.confidence if c.confidence else None)
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# 设置标题
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ax.set_title("Interspecies Phylogenetic Tree", fontsize=14, fontweight='bold')
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# 保存PDF
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plt.savefig(str(pdf_file), format='pdf', bbox_inches='tight', dpi=300)
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print(f"PDF: {pdf_file}")
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# 保存PNG
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plt.savefig(str(png_file), format='png', bbox_inches='tight', dpi=300)
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print(f"PNG: {png_file}")
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plt.close()
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print("完成")
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return True
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if __name__ == "__main__":
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if len(sys.argv) < 2:
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print("用法: python plot_tree.py <treefile> [output_dir]")
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sys.exit(1)
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treefile = sys.argv[1]
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output_dir = sys.argv[2] if len(sys.argv) >= 3 else Path(treefile).parent
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plot_tree(treefile, output_dir)
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