@@ -195,6 +195,8 @@

             <li><a href="#application"> Application</a></li>

+            <li><a href="#helper-functions"> Helper functions</a></li>

+        

             <li><a href="#funny-stuff"> Funny stuff</a></li>

             <li><a href="#users-feedback"> User's feedback</a></li>

@@ -285,6 +287,10 @@

 <li><a href="https://github.com/GuangchuangYu/plotTree-ggtree">ggtree version of plotTree.R</a></li>

 <li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>

 </ul>

+<h3 id="helper-functions"><i class="fa fa fa-support"></i> Helper functions</h3>

+<ul>

+<li><a href="https://guangchuangyu.github.io/2016/10/set_tree_xlim-set-x-axis-limits-for-only-tree-panel/">set_tree_xlim: set x axis limits for only Tree panel</a></li>

+</ul>

 <h3 id="funny-stuff"><i class="fa fa-angle-double-right"></i> Funny stuff</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>

@@ -223,11 +223,11 @@

   }  

   </style>

-<div id = 'chart251842506e7a' class = 'rChart morris'></div>

+<div id = 'chart191775d6ce31' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart251842506e7a",

+ "element": "chart191775d6ce31",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -241,7 +241,7 @@

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart251842506e7a",

+"id": "chart191775d6ce31",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -244,7 +244,7 @@

 <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="doi" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-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-1-blue.svg?style=flat" /></a>

-<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-250-blue.svg?style=flat" /></a></p>

+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-275-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 Evolution</em></strong>. <em>accepted</em>.</p>

 <h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>

 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>

@@ -67,7 +67,7 @@

         }, 

         {

             "location": "/documentation/", 

-            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data Import\n\n\nTree Visualization\n\n\nTree Annotation\n\n\nTree Manipulation\n\n\nAdvance Tree Annotation\n\n\nggtree utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with ggtree\n\n\nggtree in Bioconductor 3.1\n\n\nBioC 3.1: NEWS of my BioC packages\n\n\nBioC 3.2: NEWS of my BioC packages\n\n\nNews of ggtree\n\n\nBioC 3.3: NEWS of my BioC packages\n\n\nBioC 3.4: NEWS of my BioC packages\n\n\nggtree paper published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in ggtree\n\n\nggtree supports phylip tree format\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree view\n\n\nan example of drawing beast tree using ggtree\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in ggtree\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with insets\n\n\nggtree annotate phylogenetic tree with local images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function\n\n\nidentify method for ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic tree\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome data\n\n\nggtree for outbreak data\n\n\nggtree version of plotTree.R\n\n\nreproducible logo generated by ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny fonts\n\n\ncomic phylogenetic tree with ggtree and comicR\n\n\nuse emoji font in R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of ggtree\n\n\nJoin the group chat on \n and \n\n\n\n\n Find out more on \nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n ggplot2\n\n\nggtree for visualization and annotation of phylogenetic trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade highlighting\n\n\ninteractive rotating clades\n\n\ninteractive clade labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n, \nScience\n 2010)", 

+            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data Import\n\n\nTree Visualization\n\n\nTree Annotation\n\n\nTree Manipulation\n\n\nAdvance Tree Annotation\n\n\nggtree utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with ggtree\n\n\nggtree in Bioconductor 3.1\n\n\nBioC 3.1: NEWS of my BioC packages\n\n\nBioC 3.2: NEWS of my BioC packages\n\n\nNews of ggtree\n\n\nBioC 3.3: NEWS of my BioC packages\n\n\nBioC 3.4: NEWS of my BioC packages\n\n\nggtree paper published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in ggtree\n\n\nggtree supports phylip tree format\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree view\n\n\nan example of drawing beast tree using ggtree\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in ggtree\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with insets\n\n\nggtree annotate phylogenetic tree with local images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function\n\n\nidentify method for ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic tree\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome data\n\n\nggtree for outbreak data\n\n\nggtree version of plotTree.R\n\n\nreproducible logo generated by ggtree\n\n\n\n\n Helper functions\n\n\n\n\nset_tree_xlim: set x axis limits for only Tree panel\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny fonts\n\n\ncomic phylogenetic tree with ggtree and comicR\n\n\nuse emoji font in R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of ggtree\n\n\nJoin the group chat on \n and \n\n\n\n\n Find out more on \nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n ggplot2\n\n\nggtree for visualization and annotation of phylogenetic trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade highlighting\n\n\ninteractive rotating clades\n\n\ninteractive clade labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n, \nScience\n 2010)", 

             "title": "Documentation"

         }, 

         {

@@ -110,6 +110,11 @@

             "text": "ggtree for microbiome data  ggtree for outbreak data  ggtree version of plotTree.R  reproducible logo generated by ggtree", 

             "title": " Application"

         }, 

+        {

+            "location": "/documentation/#helper-functions", 

+            "text": "set_tree_xlim: set x axis limits for only Tree panel", 

+            "title": " Helper functions"

+        }, 

         {

             "location": "/documentation/#funny-stuff", 

             "text": "ggtree with funny fonts  comic phylogenetic tree with ggtree and comicR  use emoji font in R", 

@@ -197,7 +202,7 @@

         }, 

         {

             "location": "/featuredArticles/", 

-            "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\": \"chart251842506e7a\",\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\": \"chart251842506e7a\",\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", 

+            "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\": \"chart191775d6ce31\",\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\": \"chart191775d6ce31\",\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", 

             "title": "Featured Articles"

         }, 

         {

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

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

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

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

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

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

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

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -37,49 +37,49 @@

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

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

-     <lastmod>2016-10-26</lastmod>

+     <lastmod>2016-10-31</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -70,6 +70,10 @@

 + [ggtree version of plotTree.R](https://github.com/GuangchuangYu/plotTree-ggtree)

 + [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)

+### <i class="fa fa fa-support"></i> Helper functions

+

++ [set_tree_xlim: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/set_tree_xlim-set-x-axis-limits-for-only-tree-panel/)

+

 ### <i class="fa fa-angle-double-right"></i> Funny stuff

 + [ggtree with funny fonts](https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts)

@@ -36,10 +36,10 @@

   }  

   </style>

-<div id = 'chart251842506e7a' class = 'rChart morris'></div>

+<div id = 'chart191775d6ce31' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart251842506e7a",

+ "element": "chart191775d6ce31",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -53,7 +53,7 @@

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart251842506e7a",

+"id": "chart191775d6ce31",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:

 [![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)

 [![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)

-[![Altmetric](https://img.shields.io/badge/Altmetric-250-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![Altmetric](https://img.shields.io/badge/Altmetric-275-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)

 __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*.

@@ -57,6 +57,10 @@

 + [ggtree version of plotTree.R](https://github.com/GuangchuangYu/plotTree-ggtree)

 + [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)

+### <i class="fa fa fa-support"></i> Helper functions

+

++ [set_tree_xlim: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/set_tree_xlim-set-x-axis-limits-for-only-tree-panel/)

+

 ### <i class="fa fa-angle-double-right"></i> Funny stuff

 + [ggtree with funny fonts](https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts)