GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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DOI：
10.1111/2041-210x.12628
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发表时间：
2017-01-01
影响因子：
6.6
通讯作者：
Lam, Tommy Tsan-Yuk
中科院分区：
文献类型：
--
作者：
Yu, Guangchuang;Smith, David K.;Lam, Tommy Tsan-Yuk
我们提出了一个r包，ggtree，它提供了系统发育树的可编程可视化和注释。Ggtree可以读取比其他软件更多的树文件格式，包括Newick、Nexus、NHx、Phylip和jplace格式，并支持在其他r包中定义的Phylo、MultiPhylo、Phylo4、Phylo4d、obkdata和Phyloseq树对象的可视化。它还可以从Beast、EPA、HYPHY、PAML、PHOLODOG、PPLAER、R8S、raXML和Revbayes软件的分析输出中提取树/分支/节点特定的数据和其他数据，并允许使用这些数据来注释树。该包允许通过数字/分类节点属性对树进行着色和注释，通过旋转、折叠和缩小分支来操纵树，突出显示用户选择的分支或操作分类单元，以及通过放大到选定的部分来探索大树。可以通过基于节点的属性缩放树宽度来绘制二维树。树可以用相关联的数字矩阵(作为热图)、多序列比对、子图或轮廓图像来注释。Ggtree包是在ARTIC-2.0许可下发布的。源代码和文档可通过BioConductor(Ggtree)免费获取。
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 (ggtree).