@@ -2,7 +2,7 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.7.11

+Version: 1.9.0

 Authors@R: c(

 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),

@@ -43,4 +43,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues

 Packaged: 2014-12-03 08:16:14 UTC; root

 biocViews: Alignment, Annotation, Clustering, DataImport,

     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization

-RoxygenNote: 5.0.1

+RoxygenNote: 6.0.1

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.8.0

+------------------------

+ o BioC 3.5 release <2017-04-26, Wed>

+

 CHANGES IN VERSION 1.7.11

 ------------------------

  o remove layout.method parameter <2017-04-20, Thu>

@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.11-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-14439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.8.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.11-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-14583/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--04--22-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--04--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)

@@ -27,13 +27,13 @@ Please cite the following article when using `ggtree`:

 **G Yu**, 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. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.

-[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-348-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-347-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

 ------------------------------------------------------------------------

 ### Citation

-[![citation](https://img.shields.io/badge/cited%20by-16-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-green.svg?style=flat)](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004)

+[![citation](https://img.shields.io/badge/cited%20by-16-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection--green.svg?style=flat)](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004)

        +-+---------+---------+---------+---------+---------+---+

     15 +                                                   *   +

@@ -53,7 +53,7 @@ Please cite the following article when using `ggtree`:

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-14439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-14583/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

          ++-------------------+------------------+-------------------+------------------+--------------+

     3000 +                                                                                        *    +

@@ -221,7 +221,7 @@

 <p><a href="https://github.com/GuangchuangYu/featured_img">Let us know</a> if you have

 published using <code>ggtree</code> and your publication will be featured here.</p>

 <p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a>

-<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&amp;customersID=RID&amp;IsProductCode=Yes&amp;product=WOS&amp;Init=Yes&amp;Func=Frame&amp;DestFail=http%3A%2F%2Fwww.webofknowledge.com&amp;action=retrieve&amp;SrcApp=RID&amp;SrcAuth=RID&amp;SID=S1i9ewwKpMcqaWLpgjp&amp;UT=WOS%3A000393305300004"><img alt="" src="https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-blue.svg?style=flat" /></a></p>

+<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&amp;customersID=RID&amp;IsProductCode=Yes&amp;product=WOS&amp;Init=Yes&amp;Func=Frame&amp;DestFail=http%3A%2F%2Fwww.webofknowledge.com&amp;action=retrieve&amp;SrcApp=RID&amp;SrcAuth=RID&amp;SID=S1i9ewwKpMcqaWLpgjp&amp;UT=WOS%3A000393305300004"><img alt="" src="https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection--blue.svg?style=flat" /></a></p>

 <p><link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>

 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>

 <script src='https://guangchuangyu.github.io/resume/css/raphael-min.js' type='text/javascript'></script>

@@ -235,12 +235,12 @@ published using <code>ggtree</code> and your publication will be featured here.<

     height: 300px;

   }<br />

   </style>

-<div id="chartf981ec743" class="rChart morris"></p>

+<div id="chartffa45753c39" class="rChart morris"></p>

 </div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chartf981ec743",

+ "element": "chartffa45753c39",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -259,7 +259,7 @@ published using <code>ggtree</code> and your publication will be featured here.<

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chartf981ec743",

+"id": "chartffa45753c39",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -232,9 +232,9 @@

 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>

 <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>

-<p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.6.11-blue.svg?style=flat" /></a>

+<p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.8.0-blue.svg?style=flat" /></a>

 <a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.7.11-blue.svg?style=flat" /></a>

-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-14439/total-blue.svg?style=flat" /></a>

+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-14583/total-blue.svg?style=flat" /></a>

 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1385/month-blue.svg?style=flat" /></a></p>

 <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>

@@ -256,9 +256,9 @@ University of Hong Kong.</p>

 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>

 <p>Please cite the following article when using <code>ggtree</code>:</p>

 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>

-<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-348-blue.svg?style=flat" /></a>

+<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-347-blue.svg?style=flat" /></a>

 <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a>

-<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&amp;customersID=RID&amp;IsProductCode=Yes&amp;product=WOS&amp;Init=Yes&amp;Func=Frame&amp;DestFail=http%3A%2F%2Fwww.webofknowledge.com&amp;action=retrieve&amp;SrcApp=RID&amp;SrcAuth=RID&amp;SID=S1i9ewwKpMcqaWLpgjp&amp;UT=WOS%3A000393305300004"><img alt="" src="https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-blue.svg?style=flat" /></a></p>

+<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&amp;customersID=RID&amp;IsProductCode=Yes&amp;product=WOS&amp;Init=Yes&amp;Func=Frame&amp;DestFail=http%3A%2F%2Fwww.webofknowledge.com&amp;action=retrieve&amp;SrcApp=RID&amp;SrcAuth=RID&amp;SID=S1i9ewwKpMcqaWLpgjp&amp;UT=WOS%3A000393305300004"><img alt="" src="https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection--blue.svg?style=flat" /></a></p>

 <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

@@ -217,7 +217,7 @@

         }, 

         {

             "location": "/featuredArticles/", 

-            "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chartf981ec743\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\":             15,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chartf981ec743\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.", 

+            "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chartffa45753c39\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\":             15,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chartffa45753c39\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.", 

             "title": "Featured Articles"

         }, 

         {

@@ -4,7 +4,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -12,7 +12,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -20,7 +20,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -28,7 +28,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -36,7 +36,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/gallery/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -45,55 +45,55 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>

-     <lastmod>2017-04-22</lastmod>

+     <lastmod>2017-04-27</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -18,4 +18,3 @@ convert Date to decimal format, eg "2014-05-05" to "2014.34"

 \author{

 Guangchuang Yu

 }

-

@@ -17,4 +17,3 @@ list of all child node id's from starting node.

 \description{

 Get all children of node from df tree using breath-first.

 }

-

@@ -18,4 +18,3 @@ named list of subtrees with the root id of subtree and list of node id's making

 Get all subtrees of specified node. This includes all ancestors and relatives of node and

 return named list of subtrees.

 }

-

@@ -20,4 +20,3 @@ Find Most Recent Common Ancestor among a vector of tips

 \author{

 Guangchuang Yu

 }

-

@@ -31,4 +31,3 @@ print(tree)

 \author{

 ygc

 }

-

@@ -30,4 +30,3 @@ p \%<+\% dd + geom_text(aes(color=place, label=label), hjust=-0.5)

 \author{

 Yu Guangchuang

 }

-

@@ -20,4 +20,3 @@ update data with tree info (y coordination and panel)

 \author{

 Guangchuang Yu

 }

-

@@ -29,4 +29,3 @@ add colorbar legend

 \author{

 Guangchuang Yu

 }

-

@@ -31,4 +31,3 @@ annotation taxa with images

 \author{

 Guangchuang Yu

 }

-

@@ -20,4 +20,3 @@ merge phylo and output of boot.phylo to 'apeBootstrap' object

 \author{

 Guangchuang Yu

 }

-

@@ -18,4 +18,3 @@ list with tree data.frame with updated layout using daylight algorithm and max_c

 Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the

 specified node.

 }

-

@@ -30,4 +30,3 @@ is.binary.tree(tr2)

 \author{

 Guangchuang Yu \url{http://ygc.name}

 }

-

@@ -27,4 +27,3 @@ convert phylo to data.frame

 \author{

 Yu Guangchuang

 }

-

@@ -22,4 +22,3 @@ collapse binary tree to polytomy by applying 'fun' to 'feature'

 \author{

 Guangchuang

 }

-

@@ -17,10 +17,9 @@ tree view

 \description{

 collapse a clade

 }

-\author{

-Guangchuang Yu

-}

 \seealso{

 expand

 }

-

+\author{

+Guangchuang Yu

+}

@@ -18,4 +18,3 @@ convert decimal format to Date, eg "2014.34" to "2014-05-05"

 \author{

 Guangchuang Yu

 }

-

@@ -21,4 +21,3 @@ capture name of variable

 x <- 1

 eval(.(x)[[1]])

 }

-

@@ -24,4 +24,3 @@ download phylopic

 \author{

 Guangchuang Yu

 }

-

@@ -17,10 +17,9 @@ tree view

 \description{

 expand collased clade

 }

-\author{

-Guangchuang Yu

-}

 \seealso{

 collapse

 }

-

+\author{

+Guangchuang Yu

+}

@@ -28,4 +28,3 @@ plot tree associated data in an additional panel

 \author{

 Guangchuang Yu

 }

-

@@ -22,4 +22,3 @@ flip position of two selected branches

 \author{

 Guangchuang Yu

 }

-

@@ -33,4 +33,3 @@ fortify a phylo to data.frame

 \author{

 Yu Guangchuang

 }

-

@@ -24,4 +24,3 @@ add horizontal align lines

 \author{

 Yu Guangchuang

 }

-

@@ -30,11 +30,10 @@ highlights the two direct descendant clades of an internal node

 Particularly useful when studying neighboring clades. Note that balances that

 correspond to multichotomies will not be displayed.

 }

-\author{

-Justin Silverman

-}

 \references{

 J. Silverman, et al. \emph{A phylogenetic transform enhances

   analysis of compositional microbiota data}. (in preparation)

 }

-

+\author{

+Justin Silverman

+}

@@ -48,4 +48,3 @@ annotate a clade with bar and text label

 \author{

 Guangchuang Yu

 }

-

@@ -27,4 +27,3 @@ layer of hilight clade with rectangle

 \author{

 Guangchuang Yu

 }

-

@@ -45,10 +45,9 @@ label layer

 \description{

 geom_label2 support aes(subset) via setup_data

 }

-\author{

-Guangchuang Yu

-}

 \seealso{

 \link[ggplot2]{geom_label}

 }

-

+\author{

+Guangchuang Yu

+}

@@ -31,4 +31,3 @@ add node point

 \author{

 Guangchuang Yu

 }

-

@@ -28,10 +28,9 @@ point layer

 \description{

 geom_point2 support aes(subset) via setup_data

 }

-\author{

-Guangchuang Yu

-}

 \seealso{

 \link[ggplot2]{geom_point}

 }

-

+\author{

+Guangchuang Yu

+}

@@ -20,4 +20,3 @@ bar of range (HPD, range etc) to present uncertainty of evolutionary inference

 \author{

 Guangchuang Yu

 }

-

@@ -31,4 +31,3 @@ add root point

 \author{

 Guangchuang Yu

 }

-

@@ -33,10 +33,9 @@ add segment layer

 \description{

 geom_segment2 support aes(subset) via setup_data

 }

-\author{

-Guangchuang Yu

-}

 \seealso{

 \link[ggplot2]{geom_segment}

 }

-

+\author{

+Guangchuang Yu

+}

@@ -51,4 +51,3 @@ annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic

 \author{

 Guangchuang Yu

 }

-

@@ -26,4 +26,3 @@ link between taxa

 \author{

 Guangchuang Yu

 }

-

@@ -40,10 +40,9 @@ text layer

 \description{

 geom_text2 support aes(subset) via setup_data

 }

-\author{

-Guangchuang Yu

-}

 \seealso{

 \link[ggplot2]{geom_text}

 }

-

+\author{

+Guangchuang Yu

+}

@@ -38,4 +38,3 @@ ggtree(tr) + geom_tiplab()

 \author{

 Yu Guangchuang

 }

-

@@ -19,10 +19,9 @@ tip label layer

 \description{

 add tip label for circular layout

 }

-\author{

-Guangchuang Yu

-}

 \references{

 \url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}

 }

-

+\author{

+Guangchuang Yu

+}

@@ -31,4 +31,3 @@ add tip point

 \author{

 Guangchuang Yu

 }

-

@@ -27,4 +27,3 @@ add tree layer

 \author{

 Yu Guangchuang

 }

-

@@ -20,4 +20,3 @@ add tree layer

 \author{

 Yu Guangchuang

 }

-

@@ -33,4 +33,3 @@ add tree scale

 \author{

 Guangchuang Yu

 }

-

@@ -20,4 +20,3 @@ extract offspring tips

 \author{

 ygc

 }

-

@@ -22,4 +22,3 @@ path from start node to end node

 \author{

 Guangchuang Yu

 }

-

@@ -24,4 +24,3 @@ download phylopic and convert to grob object

 \author{

 Guangchuang Yu

 }

-

@@ -17,4 +17,3 @@ list of child node ids of parent

 \description{

 Get list of child node id numbers of parent node

 }

-

@@ -19,4 +19,3 @@ angle in range [-1, 1], i.e. degrees/180, radians/pi

 \description{

 Get the angle between the two nodes specified.

 }

-

@@ -15,4 +15,3 @@ list of node id's in breadth-first order.

 \description{

 Get the nodes of tree from root in breadth-first order.

 }

-

@@ -17,4 +17,3 @@ integer node id of parent

 \description{

 Get parent node id of child node.

 }

-

@@ -17,4 +17,3 @@ list of all child node id's from starting node.

 \description{

 Get all children of node from tree, including start_node.

 }

-

@@ -18,4 +18,3 @@ named list of subtrees with the root id of subtree and list of node id's making

 Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree)

 return named list of subtrees with list name as starting node id.

 }

-

@@ -20,4 +20,3 @@ named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 =

 Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and

 left (anti-clockwise angle from +ve x-axis to subtree)

 }

-

@@ -22,4 +22,3 @@ get position of balance (xmin, xmax, ymin, ymax)

 \author{

 Justin Silverman

 }

-

@@ -20,4 +20,3 @@ get position of clade (xmin, xmax, ymin, ymax)

 \author{

 Guangchuang Yu

 }

-

@@ -21,4 +21,3 @@ for labeling column names of heatmap produced by `gheatmap` function

 \author{

 Guangchuang Yu

 }

-

@@ -20,4 +20,3 @@ get taxa name of a selected node (or tree if node=NULL) sorted by their position

 \author{

 Guangchuang Yu

 }

-

@@ -11,4 +11,3 @@ StatBalance

 StatHilight

 }

 \keyword{datasets}

-

@@ -3,8 +3,9 @@

 \docType{package}

 \name{ggtree}

 \alias{ggtree}

-\alias{ggtree-package}

 \alias{package-ggtree}

+\alias{ggtree-package}

+\alias{ggtree}

 \title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics

 \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}

 \usage{

@@ -57,4 +58,3 @@ ggtree(tr)

 \author{

 Yu Guangchuang

 }

-

@@ -49,4 +49,3 @@ append a heatmap of a matrix to right side of phylogenetic tree

 \author{

 Guangchuang Yu

 }

-

@@ -18,4 +18,3 @@

 \description{

 groupClade method for ggtree object

 }

-

@@ -20,4 +20,3 @@

 \description{

 groupOTU method for ggtree object

 }

-

@@ -3,12 +3,13 @@

 \docType{methods}

 \name{gzoom}

 \alias{gzoom}

+\alias{gzoom}

+\alias{gzoom,ggtree-method}

 \alias{gzoom,beast-method}

 \alias{gzoom,codeml-method}

-\alias{gzoom,ggtree-method}

+\alias{gzoom,treedata-method}

 \alias{gzoom,paml_rst-method}

 \alias{gzoom,phylo-method}

-\alias{gzoom,treedata-method}

 \title{gzoom method}

 \usage{

 gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

@@ -50,4 +51,3 @@ figure

 \description{

 zoom selected subtree

 }

-

@@ -29,4 +29,3 @@ gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))

 \author{

 ygc

 }

-

@@ -20,4 +20,3 @@ identify node by interactive click

 \author{

 Guangchuang Yu

 }

-

@@ -35,4 +35,3 @@ add insets in a tree

 \author{

 Guangchuang Yu

 }

-

@@ -31,4 +31,3 @@ nodes = remove tip nodes.

 ```

 }

-

@@ -20,4 +20,3 @@ tree as data.frame with equal angle layout.

 \references{

 "Inferring Phylogenies" by Joseph Felsenstein.

 }

-

@@ -28,4 +28,3 @@ multiple sequence alignment with phylogenetic tree

 \author{

 Guangchuang Yu

 }

-

@@ -29,4 +29,3 @@ plot multiple ggplot objects in one page

 \author{

 Guangchuang Yu

 }

-

@@ -26,4 +26,3 @@ generate a list of bar charts for results of ancestral state reconstruction

 \author{

 Guangchuang Yu

 }

-

@@ -20,4 +20,3 @@ convert tip or node label(s) to internal node number

 \author{

 Guangchuang Yu

 }

-

@@ -24,4 +24,3 @@ generate a list of pie charts for results of ancestral stat reconstruction

 \author{

 Guangchuang Yu

 }

-

@@ -20,4 +20,3 @@ open tree with specific angle

 \author{

 Guangchuang Yu

 }

-

@@ -35,4 +35,3 @@ add phylopic layer

 \author{

 Guangchuang Yu

 }

-

@@ -17,4 +17,3 @@ pipe

 \seealso{

 \link[magrittr]{pipe}

 }

-

@@ -20,4 +20,3 @@ print information of a list of beast trees

 \author{

 Guangchuang Yu

 }

-

@@ -26,4 +26,3 @@ tree object

 \description{

 reroot a tree

 }

-

@@ -20,4 +20,3 @@ rescale branch length of tree object

 \author{

 Guangchuang Yu

 }

-

@@ -18,4 +18,3 @@ reverse timescle x-axis

 \author{

 guangchuang yu

 }

-

@@ -20,4 +20,3 @@ remove singleton

 \author{

 Guangchuang Yu \url{http://ygc.name}

 }

-

@@ -20,4 +20,3 @@ rotate 180 degree of a selected branch

 \author{

 Guangchuang Yu

 }

-

@@ -21,4 +21,3 @@ updated tree data.frame with points rotated by angle

 \description{

 Rotate the points in a tree data.frame around a pivot node by the angle specified.

 }

-

@@ -20,4 +20,3 @@ rotate circular tree

 \author{

 Guangchuang Yu

 }

-

@@ -26,4 +26,3 @@ scale clade

 \author{

 Guangchuang Yu

 }

-

@@ -4,9 +4,9 @@

 \name{scale_color}

 \alias{scale_color}

 \alias{scale_color,beast-method}

+\alias{scale_color,treedata-method}

 \alias{scale_color,paml_rst-method}

 \alias{scale_color,phylo-method}

-\alias{scale_color,treedata-method}

 \title{scale_color method}

 \usage{

 scale_color(object, by, ...)

@@ -33,4 +33,3 @@ color vector