1. ggtree
  2. Commit e6b7fb25e5ce52254bb716d0dd982ade083a7783
Browse code

fixed link in homepage

guangchuang yu authored on 28/12/2016 03:30:22
Showing 8 changed files
README.md
History View file @ e6b7fb25
... ... 
@@ -2,9 +2,9 @@
2 2 
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
3 3 
 ===========================================================================================================================
4 4
5 
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.5-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) [![total](https://img.shields.io/badge/downloads-18883/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
5 
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.5-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) [![total](https://img.shields.io/badge/downloads-19096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
6 6
7 
-[![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-2016--12--21-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)
7 
+[![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-2016--12--28-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)
8 8
9 9 
 [![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) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
10 10
... ... 
@@ -51,7 +51,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
51 51
52 52 
 ### Download stats
53 53
54 
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-18883/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
54 
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-19096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
55 55
56 56 
          +----------------------+----------------------+----------------------+----------------------+-+
57 57 
          |                                                                                        *    |
docs/featuredArticles/index.html
History View file @ e6b7fb25
... ... 
@@ -223,11 +223,11 @@
223 223 
   }
224 224 
   </style>
225 225
226 
-<div id = 'chart4fa28c95e5e' class = 'rChart morris'></div>
226 
+<div id = 'chart28d0552c293f' class = 'rChart morris'></div>
227 227
228 228 
 <script type='text/javascript'>
229 229 
     var chartParams = {
230 
- "element": "chart4fa28c95e5e",
230 
+ "element": "chart28d0552c293f",
231 231 
 "width":            800,
232 232 
 "height":            400,
233 233 
 "xkey": "year",
... ... 
@@ -241,7 +241,7 @@
241 241 
 "pubid": "HtEfBTGE9r8C"
242 242 
 }
243 243 
 ],
244 
-"id": "chart4fa28c95e5e",
244 
+"id": "chart28d0552c293f",
245 245 
 "labels": "cites"
246 246 
 },
247 247 
       chartType = "Bar"
docs/index.html
History View file @ e6b7fb25
... ... 
@@ -236,8 +236,8 @@
236 236 
 <p><img src="https://raw.githubusercontent.com/GuangchuangYu/ggtree/master/logo.png" align="right" /></p>
237 237 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
238 238 
 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.5-blue.svg?style=flat" /></a>
239 
-<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.4-blue.svg?style=flat" /></a>
240 
-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-18505/total-blue.svg?style=flat" /></a>
239 
+<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.5-blue.svg?style=flat" /></a>
240 
+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-19096/total-blue.svg?style=flat" /></a>
241 241 
 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat" /></a></p>
242 242 
 <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.
243 243 
 <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>
... ... 
@@ -247,7 +247,7 @@
247 247 
 <p>Please cite the following article when using <code>ggtree</code>:</p>
248 248 
 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="doi" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>
249 249 
 <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-1-blue.svg?style=flat" /></a>
250 
-<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-281-blue.svg?style=flat" /></a></p>
250 
+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-282-blue.svg?style=flat" /></a></p>
251 251 
 <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>. <em>accepted</em>.</p>
252 252 
 <h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
253 253 
 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
... ... 
@@ -294,10 +294,10 @@ biocLite(&quot;ggtree&quot;)
294 294 
 </ul>
295 295 
 <h2 id="feedback"><i class="fa fa-comments"></i> Feedback</h2>
296 296 
 <ul class="fa-ul">
297 
-    <li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you [follow the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) before posting any issue/question</li>
298 
-    <li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> [github issue](https://github.com/GuangchuangYu/ggtree/issues)</li>
299 
-    <li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> [google group](https://groups.google.com/forum/#!forum/bioc-ggtree)</li>
300 
-    <li><i class="fa-li fa fa-support"></i> We are also following every post tagged with **ggtree** on [Bioconductor support site](https://support.bioconductor.org/) and [Biostars](https://www.biostars.org/)</li>
297 
+    <li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/">follow the guide</a> before posting any issue/question</li>
298 
+    <li><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></li>
299 
+    <li><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></li>
300 
+    <li><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></li>
301 301 
     <li><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></li>
302 302 
 </ul></div>
303 303 
         </div>
docs/mkdocs/search_index.json
History View file @ e6b7fb25
... ... 
@@ -2,7 +2,7 @@
2 2 
     "docs": [
3 3 
         {
4 4 
             "location": "/",
5 
-            "text": "The \nggtree\n package extending the \nggplot2\n package. It based on grammar of graphics and takes all the good parts of \nggplot2\n.  \nggtree\n is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.\n\nggtree\n is released within the \nBioconductor\n project and the source code is hosted on \n GitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \nMethods in Ecology and Evolution\n. \naccepted\n.\n\n\n Featured Articles\n\n\n\n\n Find out more on \n \nFeatured Articles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor page\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages, please refer to the \nggtree-installation\n wiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore the tree visually\n\n\n\n\n Find out details and examples on \n \nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n: Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n: Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you [follow the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n [github issue](https://github.com/GuangchuangYu/ggtree/issues)\n\n    \n  For user questions, please post to \n [google group](https://groups.google.com/forum/#!forum/bioc-ggtree)\n\n    \n We are also following every post tagged with **ggtree** on [Bioconductor support site](https://support.bioconductor.org/) and [Biostars](https://www.biostars.org/)\n\n    \n Join the group chat on \n and",
5 
+            "text": "The \nggtree\n package extending the \nggplot2\n package. It based on grammar of graphics and takes all the good parts of \nggplot2\n.  \nggtree\n is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.\n\nggtree\n is released within the \nBioconductor\n project and the source code is hosted on \n GitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \nMethods in Ecology and Evolution\n. \naccepted\n.\n\n\n Featured Articles\n\n\n\n\n Find out more on \n \nFeatured Articles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor page\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages, please refer to the \nggtree-installation\n wiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore the tree visually\n\n\n\n\n Find out details and examples on \n \nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n: Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n: Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you \nfollow the guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and",
6 6 
             "title": "Home"
7 7 
         },
8 8 
         {
... ... 
@@ -62,7 +62,7 @@
62 62 
         },
63 63 
         {
64 64 
             "location": "/#feedback",
65 
-            "text": "Please make sure you [follow the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) before posting any issue/question \n      For bugs or feature requests, please post to   [github issue](https://github.com/GuangchuangYu/ggtree/issues) \n       For user questions, please post to   [google group](https://groups.google.com/forum/#!forum/bioc-ggtree) \n      We are also following every post tagged with **ggtree** on [Bioconductor support site](https://support.bioconductor.org/) and [Biostars](https://www.biostars.org/) \n      Join the group chat on   and",
65 
+            "text": "Please make sure you  follow the guide  before posting any issue/question \n      For bugs or feature requests, please post to    github issue \n       For user questions, please post to    google group \n      We are also following every post tagged with  ggtree  on  Bioconductor support site  and  Biostars \n      Join the group chat on   and",
66 66 
             "title": " Feedback"
67 67 
         },
68 68 
         {
... ... 
@@ -207,7 +207,7 @@
207 207 
         },
208 208 
         {
209 209 
             "location": "/featuredArticles/",
210 
-            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\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  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart4fa28c95e5e\",\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\"id\": \"chart4fa28c95e5e\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976",
210 
+            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\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  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart28d0552c293f\",\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\"id\": \"chart28d0552c293f\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976",
211 211 
             "title": "Featured Articles"
212 212 
         },
213 213 
         {
docs/sitemap.xml
History View file @ e6b7fb25
... ... 
@@ -4,7 +4,7 @@
4 4
5 5 
     <url>
6 6 
      <loc>https://guangchuangyu.github.io/ggtree/</loc>
7 
-     <lastmod>2016-12-17</lastmod>
7 
+     <lastmod>2016-12-28</lastmod>
8 8 
      <changefreq>daily</changefreq>
9 9 
     </url>
10 10
... ... 
@@ -12,7 +12,7 @@
12 12
13 13 
     <url>
14 14 
      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
15 
-     <lastmod>2016-12-17</lastmod>
15 
+     <lastmod>2016-12-28</lastmod>
16 16 
      <changefreq>daily</changefreq>
17 17 
     </url>
18 18
... ... 
@@ -20,7 +20,7 @@
20 20
21 21 
     <url>
22 22 
      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>
23 
-     <lastmod>2016-12-17</lastmod>
23 
+     <lastmod>2016-12-28</lastmod>
24 24 
      <changefreq>daily</changefreq>
25 25 
     </url>
26 26
... ... 
@@ -28,7 +28,7 @@
28 28
29 29 
     <url>
30 30 
      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>
31 
-     <lastmod>2016-12-17</lastmod>
31 
+     <lastmod>2016-12-28</lastmod>
32 32 
      <changefreq>daily</changefreq>
33 33 
     </url>
34 34
... ... 
@@ -37,49 +37,49 @@
37 37
38 38 
     <url>
39 39 
      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>
40 
-     <lastmod>2016-12-17</lastmod>
40 
+     <lastmod>2016-12-28</lastmod>
41 41 
      <changefreq>daily</changefreq>
42 42 
     </url>
43 43
44 44 
     <url>
45 45 
      <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>
46 
-     <lastmod>2016-12-17</lastmod>
46 
+     <lastmod>2016-12-28</lastmod>
47 47 
      <changefreq>daily</changefreq>
48 48 
     </url>
49 49
50 50 
     <url>
51 51 
      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
52 
-     <lastmod>2016-12-17</lastmod>
52 
+     <lastmod>2016-12-28</lastmod>
53 53 
      <changefreq>daily</changefreq>
54 54 
     </url>
55 55
56 56 
     <url>
57 57 
      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>
58 
-     <lastmod>2016-12-17</lastmod>
58 
+     <lastmod>2016-12-28</lastmod>
59 59 
      <changefreq>daily</changefreq>
60 60 
     </url>
61 61
62 62 
     <url>
63 63 
      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
64 
-     <lastmod>2016-12-17</lastmod>
64 
+     <lastmod>2016-12-28</lastmod>
65 65 
      <changefreq>daily</changefreq>
66 66 
     </url>
67 67
68 68 
     <url>
69 69 
      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
70 
-     <lastmod>2016-12-17</lastmod>
70 
+     <lastmod>2016-12-28</lastmod>
71 71 
      <changefreq>daily</changefreq>
72 72 
     </url>
73 73
74 74 
     <url>
75 75 
      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>
76 
-     <lastmod>2016-12-17</lastmod>
76 
+     <lastmod>2016-12-28</lastmod>
77 77 
      <changefreq>daily</changefreq>
78 78 
     </url>
79 79
80 80 
     <url>
81 81 
      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
82 
-     <lastmod>2016-12-17</lastmod>
82 
+     <lastmod>2016-12-28</lastmod>
83 83 
      <changefreq>daily</changefreq>
84 84 
     </url>
85 85
mkdocs/docs/featuredArticles.md
History View file @ e6b7fb25
... ... 
@@ -36,10 +36,10 @@
36 36 
   }
37 37 
   </style>
38 38
39 
-<div id = 'chart4fa28c95e5e' class = 'rChart morris'></div>
39 
+<div id = 'chart28d0552c293f' class = 'rChart morris'></div>
40 40 
 <script type='text/javascript'>
41 41 
     var chartParams = {
42 
- "element": "chart4fa28c95e5e",
42 
+ "element": "chart28d0552c293f",
43 43 
 "width":            800,
44 44 
 "height":            400,
45 45 
 "xkey": "year",
... ... 
@@ -53,7 +53,7 @@
53 53 
 "pubid": "HtEfBTGE9r8C"
54 54 
 }
55 55 
 ],
56 
-"id": "chart4fa28c95e5e",
56 
+"id": "chart28d0552c293f",
57 57 
 "labels": "cites"
58 58 
 },
59 59 
       chartType = "Bar"
mkdocs/docs/index.md
History View file @ e6b7fb25
... ... 
@@ -12,13 +12,17 @@
12 12 
 </div>
13 13 
 <script async src="//static.addtoany.com/menu/page.js"></script>
14 14 
 <!-- AddToAny END -->
15 
+
16 
+
17 
+
15 18 
 <img src="https://raw.githubusercontent.com/GuangchuangYu/ggtree/master/logo.png" align="right" />
16 19
20 
+
17 21 
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
18 22
19 23 
 [![releaseVersion](https://img.shields.io/badge/release%20version-1.6.5-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
20 
-[![develVersion](https://img.shields.io/badge/devel%20version-1.7.4-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
21 
-[![total](https://img.shields.io/badge/downloads-18505/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
24 
+[![develVersion](https://img.shields.io/badge/devel%20version-1.7.5-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
25 
+[![total](https://img.shields.io/badge/downloads-19096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
22 26 
 [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
23 27
24 28
... ... 
@@ -36,7 +40,7 @@ Please cite the following article when using `ggtree`:
36 40
37 41 
 [![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
38 42 
 [![citation](https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
39 
-[![Altmetric](https://img.shields.io/badge/Altmetric-281-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
43 
+[![Altmetric](https://img.shields.io/badge/Altmetric-282-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
40 44
41 45 
 __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*__. *accepted*.
42 46
... ... 
@@ -100,9 +104,11 @@ If you have problems when installing some of the dependent packages, please refe
100 104 
 ## <i class="fa fa-comments"></i> Feedback
101 105
102 106 
 <ul class="fa-ul">
103 
-	<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you [follow the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) before posting any issue/question</li>
104 
-	<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> [github issue](https://github.com/GuangchuangYu/ggtree/issues)</li>
105 
-	<li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> [google group](https://groups.google.com/forum/#!forum/bioc-ggtree)</li>
106 
-	<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with **ggtree** on [Bioconductor support site](https://support.bioconductor.org/) and [Biostars](https://www.biostars.org/)</li>
107 
+	<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/">follow the guide</a> before posting any issue/question</li>
108 
+	<li><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></li>
109 
+	<li><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></li>
110 
+	<li><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></li>
107 111 
 	<li><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></li>
108 112 
 </ul>
113 
+
114 
+
mkdocs/src/index.md
History View file @ e6b7fb25
... ... 
@@ -1,6 +1,10 @@
1 1 
 <!-- addtoany:= -->
2 
+
3 
+
4 
+
2 5 
 <img src="https://raw.githubusercontent.com/GuangchuangYu/ggtree/master/logo.png" align="right" />
3 6
7 
+
4 8 
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
5 9
6 10 
 <!-- release:=ggtree -->
... ... 
@@ -86,9 +90,11 @@ If you have problems when installing some of the dependent packages, please refe
86 90 
 ## <i class="fa fa-comments"></i> Feedback
87 91
88 92 
 <ul class="fa-ul">
89 
-	<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you [follow the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) before posting any issue/question</li>
90 
-	<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> [github issue](https://github.com/GuangchuangYu/ggtree/issues)</li>
91 
-	<li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> [google group](https://groups.google.com/forum/#!forum/bioc-ggtree)</li>
92 
-	<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with **ggtree** on [Bioconductor support site](https://support.bioconductor.org/) and [Biostars](https://www.biostars.org/)</li>
93 
+	<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/">follow the guide</a> before posting any issue/question</li>
94 
+	<li><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></li>
95 
+	<li><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></li>
96 
+	<li><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></li>
93 97 
 	<li><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></li>
94 98 
 </ul>
99 
+
100 
+