Toytree: A minimalist tree visualization and manipulation library for Python
Toytree: A minimalist tree visualization and manipulation library for Python
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DOI：
10.1111/2041-210x.13313
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发表时间：
2019-11-04
影响因子：
6.6
通讯作者：
Eaton, Deren A. R.
中科院分区：
文献类型：
--
作者：
Eaton, Deren A. R.
Toytree 是一个轻量级 Python 库，用于以编程方式可视化和操作基于树的数据结构。它实现了极简主义设计美学和现代绘图架构，适合 IPython/Jupyter 中的交互式编码。树图是使用 toyplot 库后端以 HTML 形式生成的，并在具有交互功能的 Jupyter 笔记本中本地显示。树图可以与 toyplot 库中的其他绘图功能（例如散点图、直方图）相结合，在共享坐标网格上创建复合图形，并且可以导出为其他格式，包括 PNG、PDF 和 SVG。为了解析和存储树数据，toytree 使用 ete3 TreeNode 对象的修改后的分支，其中包括用于操作、注释和比较树的函数。 Toytree 将这些函数与绘图布局集成在一起，以允许以正确的顺序从树中提取节点值，以设置用于绘图的节点样式。此外，toytree 还提供了解析其他树格式、生成随机树、推断共识树以及从多个树中绘制网格或云以可视化不一致的功能。 toytree 的目标是提供一个简单的 Python，相当于 R 中常用的树操作和绘图库，并以此促进 Python 中系统发育和其他基于树的方法的进一步发展。 Toytree 在 GPLv3 许可证下发布。源代码可在 GitHub 上获取，文档可在 上获取。
Toytree is a lightweight Python library for programmatically visualizing and manipulating tree-based data structures. It implements a minimalist design aesthetic and modern plotting architecture suited for interactive coding in IPython/Jupyter. Tree drawings are generated in HTML using the toyplot library backend, and display natively in Jupyter notebooks with interactivity features. Tree drawings can be combined with other plotting functions from the toyplot library (e.g. scatterplots, histograms) to create composite figures on a shared coordinate grid, and can be exported to additional formats including PNG, PDF and SVG. To parse and store tree data, toytree uses a modified fork of the ete3 TreeNode object, which includes functions for manipulating, annotating and comparing trees. Toytree integrates these functions with a plotting layout to allow node values to be extracted from trees in the correct order to style nodes for plotting. In addition, toytree provides functions for parsing additional tree formats, generating random trees, inferring consensus trees and drawing grids or clouds from multiple trees to visualize discordance. The goal of toytree is to provide a simple Python equivalent to commonly used tree manipulation and plotting libraries in R, and in doing so, to promote further development of phylogenetic and other tree-based methods in Python. Toytree is released under the GPLv3 license. Source code is available on GitHub and documentation is available at .