Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees.
ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree.
The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.
A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images.
The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).

本文介绍一款名为ggtree的R包，可实现进化树（phylogenetic tree）的可编程可视化与注释功能。
相较于其他同类软件，ggtree支持的进化树文件格式更为丰富，涵盖newick、nexus、NHX、phylip及jplace格式；同时可可视化其他R包中定义的phylo、multiphylo、phylo4、phylo4d、obkdata与phyloseq树对象。
该包可从beast、epa、hyphy、paml、phylodog、pplacer、r8s、raxml及revbayes等软件的分析结果中，提取树、分支、节点专属数据及其他相关信息，并支持利用这些数据对进化树进行注释。
本包支持基于数值或分类节点属性对进化树进行着色与注释，可通过旋转、折叠、缩放支系（clade）等操作编辑进化树，高亮用户选定的支系或操作分类单元（operational taxonomic unit, OTU），还可通过缩放选定区域以探索大型进化树。
可基于节点属性调整树的宽度，绘制二维进化树；还可通过关联数值矩阵（热图，heat map）、多序列比对（multiple sequence alignment）、子图或剪影图像对进化树进行注释。
ggtree包采用Artistic-2.0开源许可证发布，其源代码与文档可通过Bioconductor平台（http://www.bioconductor.org/packages/ggtree）免费获取。