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- <center><span class="zaln"><a href="https://guangchuangyu.github.io/2017/11/bmc-journal-protects-paper-of-plagiarism/" class="zb">Plea to against BMC</a></span></center> |
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- <center><span class="zaln"><a href="https://guangchuangyu.github.io/blog_images/pay_qrcode.png" class="zb">赞赏</a></span></center> |
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- <div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&m=0&c=ff0000&cr1=ffffff&sx=0" async="async"></script></div> |
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- <h1>ggtree: visualization and annotation of phylogenetic trees </h1> |
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- <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p> |
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| 348 |
-<p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p> |
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| 349 |
-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.4-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.5-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-24849/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1222/month-blue.svg?style=flat" alt="month" /></a></p> |
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| 350 |
-<p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p> |
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| 351 |
-<div id="authors" class="section level2"> |
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| 352 |
-<h2><i class="fa fa-user"></i> Authors</h2> |
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-<p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p> |
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-</div> |
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-<div id="citation" class="section level2"> |
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| 356 |
-<h2><i class="fa fa-book"></i> Citation</h2> |
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| 357 |
-<p>Please cite the following article when using <code>ggtree</code>:</p> |
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| 358 |
-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-326-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-85-blue.svg?style=flat" alt="citation" /></a></p> |
|
| 359 |
-<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p> |
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-<h2><i class="fa fa-pencil"></i> Featured Articles</h2> |
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-<div class="figure"> |
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-<img src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /> |
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| 365 |
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-<p><i class="fa fa-hand-o-right"></i> Find out more on <i class="fa fa-pencil"></i> <a href="https://guangchuangyu.github.io/ggtree/featuredArticles/">Featured Articles</a>.</p> |
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-</div> |
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-<div id="installation" class="section level2"> |
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| 370 |
-<h2><i class="fa fa-download"></i> Installation</h2> |
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| 371 |
-<p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor page</a>:</p> |
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| 372 |
-<pre class="r"><code>## try http:// if https:// URLs are not supported |
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| 373 |
-source("https://bioconductor.org/biocLite.R") |
|
| 374 |
-## biocLite("BiocUpgrade") ## you may need this |
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| 375 |
-biocLite("ggtree")</code></pre> |
|
| 376 |
-<p>If you have problems when installing some of the dependent packages, please refer to the <a href="https://github.com/GuangchuangYu/ggtree/wiki/ggtree-installation">ggtree-installation</a> wiki page.</p> |
|
| 377 |
-</div> |
|
| 378 |
-<div id="overview" class="section level2"> |
|
| 379 |
-<h2><i class="fa fa-cogs"></i> Overview</h2> |
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| 380 |
-<div id="getting-tree-into-r" class="section level4"> |
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| 381 |
-<h4><i class="fa fa-angle-double-right"></i> Getting tree into R</h4> |
|
| 382 |
-<ul> |
|
| 383 |
-<li>tree parsers: bring evolution evidences to be used/analyzed in <code>R</code></li> |
|
| 384 |
-<li><code>merge_tree</code>: allows evolution evidences to be merged and compared</li> |
|
| 385 |
-<li><code>fortify</code> methods: convert tree objects into tidy data frame</li> |
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| 386 |
-</ul> |
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| 387 |
-</div> |
|
| 388 |
-<div id="tree-visualization-annotation" class="section level4"> |
|
| 389 |
-<h4><i class="fa fa-angle-double-right"></i> Tree visualization & annotation</h4> |
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| 390 |
-<ul> |
|
| 391 |
-<li>parsing tree as a collection of nodes allows grammar of graphics to be supported</li> |
|
| 392 |
-<li><code>geom_tree</code>: extends <code>ggplot2</code> to support tree structure</li> |
|
| 393 |
-<li>several layers and functions for tree annotation</li> |
|
| 394 |
-<li>supports annotating phylogenetic trees with user’s own data</li> |
|
| 395 |
-</ul> |
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| 396 |
-</div> |
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| 397 |
-<div id="tree-manipulation" class="section level4"> |
|
| 398 |
-<h4><i class="fa fa-angle-double-right"></i> Tree manipulation</h4> |
|
| 399 |
-<ul> |
|
| 400 |
-<li>helper functions for tree manipulation, make it possible to explore the tree visually</li> |
|
| 401 |
-</ul> |
|
| 402 |
-<p><i class="fa fa-hand-o-right"></i> Find out details and examples on <i class="fa fa-book"></i> <a href="https://guangchuangyu.github.io/ggtree/documentation/">Documentation</a>.</p> |
|
| 403 |
-</div> |
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| 404 |
-</div> |
|
| 405 |
-<div id="projects-that-depend-on-ggtree" class="section level2"> |
|
| 406 |
-<h2><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2> |
|
| 407 |
-<div id="cran-packages" class="section level4"> |
|
| 408 |
-<h4><i class="fa fa-angle-double-right"></i> CRAN packages</h4> |
|
| 409 |
-<ul> |
|
| 410 |
-<li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle Phylogenetic Distance Matrices and Other Utilities</li> |
|
| 411 |
-</ul> |
|
| 412 |
-</div> |
|
| 413 |
-<div id="bioconductor-packages" class="section level4"> |
|
| 414 |
-<h4><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4> |
|
| 415 |
-<ul> |
|
| 416 |
-<li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of lincRNAs and protein-coding genes</li> |
|
| 417 |
-<li><a href="https://www.bioconductor.org/packages/LymphoSeq">LymphoSeq</a>: Analyze high-throughput sequencing of T and B cell receptors</li> |
|
| 418 |
-<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li> |
|
| 419 |
-</ul> |
|
| 420 |
-</div> |
|
| 421 |
-<div id="other-applications" class="section level4"> |
|
| 422 |
-<h4><i class="fa fa-angle-double-right"></i> Other applications</h4> |
|
| 423 |
-<ul> |
|
| 424 |
-<li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>: Collection of scripts for metagenomics analysis</li> |
|
| 425 |
-<li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>: Utilities for Creating and Validating Degenerate primers</li> |
|
| 426 |
-<li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies created along a genome for patterns</li> |
|
| 427 |
-</ul> |
|
| 428 |
-</div> |
|
| 429 |
-</div> |
|
| 430 |
-<div id="feedback" class="section level2"> |
|
| 431 |
-<h2><i class="fa fa-comments"></i> Feedback</h2> |
|
| 432 |
-<ul class="fa-ul"> |
|
| 433 |
-<li> |
|
| 434 |
-<i class="fa-li fa fa-hand-o-right"></i> Please make sure you have followed <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/"><strong>the important guide</strong></a> before posting any issue/question |
|
| 435 |
-</li> |
|
| 436 |
-<li> |
|
| 437 |
-<i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/ggtree/issues">github issue</a> |
|
| 438 |
-</li> |
|
| 439 |
-<li> |
|
| 440 |
-<i class="fa-li fa fa-question"></i> For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a> |
|
| 441 |
-</li> |
|
| 442 |
-<li> |
|
| 443 |
-<i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org">Bioconductor support site</a> and <a href="https://www.biostars.org">Biostars</a> |
|
| 444 |
-</li> |
|
| 445 |
-<li> |
|
| 446 |
-<i class="fa-li fa fa-commenting"></i> Join the group chat on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a> and <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a> |
|
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