@@ -10,7 +10,7 @@

     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">

     <meta http-equiv="X-UA-Compatible" content="IE=10" />

     <title>Documentation - ggtree</title>

-    <meta name="generator" content="Hugo 0.24.1" />

+    <meta name="generator" content="Hugo 0.30.2" />

     <meta name="description" content="Visualization and annotation of phylogenetic trees.">

@@ -322,15 +322,16 @@

           <li>

-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

-              Contact via email

-            </a>

+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

+                  Contact via email

+              </a>

           </li>

         </ul>

+        <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>

         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" 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&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

       </div>

     </div>

   </div>

@@ -343,7 +344,7 @@

 			<h1>Documentation </h1>

 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

-<div id="vignettes" class="section level2">

+<section id="vignettes" class="level2">

 <h2><i class="fa fa-book"></i> Vignettes</h2>

 <ul>

 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html">ggtree</a></li>

@@ -355,10 +356,10 @@

 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree utilities</a></li>

 <li><a href="https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html">Phylomoji</a></li>

 </ul>

-</div>

-<div id="blog-posts" class="section level2">

+</section>

+<section id="blog-posts" class="level2">

 <h2><i class="fa fa-wordpress"></i> Blog posts</h2>

-<div id="news-and-updates" class="section level3">

+<section id="news-and-updates" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> News and updates</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with ggtree</a></li>

@@ -370,16 +371,16 @@

 <li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC packages</a></li>

 <li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper published</a></li>

 </ul>

-</div>

-<div id="data-manipulation" class="section level3">

+</section>

+<section id="data-manipulation" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Data manipulation</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>

 <li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>

 <li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using treeio</a></li>

 </ul>

-</div>

-<div id="tree-visualization" class="section level3">

+</section>

+<section id="tree-visualization" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Tree visualization</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>

@@ -388,8 +389,8 @@

 <li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>

 <li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>

 </ul>

-</div>

-<div id="tree-annotation" class="section level3">

+</section>

+<section id="tree-annotation" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Tree annotation</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in ggtree</a></li>

@@ -405,14 +406,14 @@

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

 <li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>

 </ul>

-</div>

-<div id="tree-manipulation" class="section level3">

+</section>

+<section id="tree-manipulation" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>

 </ul>

-</div>

-<div id="application" class="section level3">

+</section>

+<section id="application" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Application</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>

@@ -420,37 +421,37 @@

 <li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>

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

 </ul>

-</div>

-<div id="funny-stuff" class="section level3">

+</section>

+<section id="funny-stuff" class="level3">

 <h3><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>

 <li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and comicR</a></li>

 <li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>

 </ul>

-</div>

-</div>

-<div id="slides" class="section level2">

+</section>

+</section>

+<section id="slides" class="level2">

 <h2><i class="fa fa-slideshare"></i> Slides</h2>

 <ul>

 <li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp; ggplot2</a></li>

 <li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>

 </ul>

-</div>

-<div id="video" class="section level2">

+</section>

+<section id="video" class="level2">

 <h2><i class="fa fa-youtube-play"></i> Video</h2>

 <ul>

 <li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>

 <li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>

 <li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>

 </ul>

-</div>

-<div id="workflow" class="section level2">

+</section>

+<section id="workflow" class="level2">

 <h2><i class="fa fa-gift"></i> Workflow</h2>

 <ul>

 <li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>

 </ul>

-</div>

+</section>

 			<aside class="copyright" role="note">

@@ -10,7 +10,7 @@

     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">

     <meta http-equiv="X-UA-Compatible" content="IE=10" />

     <title>FAQ - ggtree</title>

-    <meta name="generator" content="Hugo 0.24.1" />

+    <meta name="generator" content="Hugo 0.30.2" />

     <meta name="description" content="Visualization and annotation of phylogenetic trees.">

@@ -322,15 +322,16 @@

           <li>

-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

-              Contact via email

-            </a>

+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

+                  Contact via email

+              </a>

           </li>

         </ul>

+        <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>

         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>

-<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

+        <div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

       </div>

     </div>

   </div>

@@ -343,20 +344,20 @@

 			<h1>FAQ </h1>

 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

-<div id="installation" class="section level1">

+<section id="installation" class="level1">

 <h1><i class="fa fa-download"></i> Installation</h1>

-<div id="could-not-find-function" class="section level2">

+<section id="could-not-find-function" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Could not find function</h2>

 <p>If you got <a href="https://github.com/GuangchuangYu/ggtree/issues/12">this error</a>, please make sure you are using the latest R and <code>ggtree</code>.</p>

 <p>Packages in Bioconductor, like <code>ggtree</code>, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to <code>devel</code> branch.</p>

 <p>Sometimes I may write blog post to introduce new functions which is not available in <code>release</code> branch, you need to install the <code>devel</code> version of <code>ggtree</code> in order to use these new functions.</p>

 <p>You can download the <code>devel</code> version of <code>ggtree</code> from <a href="http://bioconductor.org/packages/devel/bioc/html/ggtree.html" class="uri">http://bioconductor.org/packages/devel/bioc/html/ggtree.html</a> and install it, or install the github version of <code>ggtree</code>.</p>

 <p>This also applied to other of my packages, including <code>GOSemSim</code>, <code>DOSE</code>, <code>clusterProfiler</code>, <code>ReactomePA</code> and <code>ChIPseeker</code>. If you got the <code>could not find function</code> error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.</p>

-</div>

-</div>

-<div id="text-label" class="section level1">

+</section>

+</section>

+<section id="text-label" class="level1">

 <h1><i class="fa fa-text-height"></i> Text &amp; Label</h1>

-<div id="tip-label-truncated" class="section level2">

+<section id="tip-label-truncated" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Tip label truncated</h2>

 <p>ggplot2 can’t auto adjust xlim based on added text.</p>

 <pre class="r"><code>library(ggtree)

@@ -365,8 +366,8 @@ tree<-read.tree(text="(Organism1.006G249400.1:0.03977,(Organism2.022118m

 ggtree(tree) + geom_tiplab()</code></pre>

 <p>This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.</p>

 <pre class="r"><code>ggtree(tree) + geom_tiplab() + xlim(0, 0.06)</code></pre>

-</div>

-<div id="modify-tip-labels" class="section level2">

+</section>

+<section id="modify-tip-labels" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Modify (tip) labels</h2>

 <p>This could be easily done via the <code>%&lt;+%</code> operator to attach the modified version of the labels and than use <code>geom_tiplab</code> to display the modified version.</p>

 <pre><code>raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)

@@ -376,8 +377,8 @@ lb = get.tree(raxml)$tip.label

 d = data.frame(label=lb, label2 = paste("AA", substring(lb, 1, 5)))

 ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>

 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>

-</div>

-<div id="formatting-tip-labels" class="section level2">

+</section>

+<section id="formatting-tip-labels" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Formatting (tip) labels</h2>

 <p>If you want to format labels, you need to set <code>parse=TRUE</code> in <code>geom_text</code>/<code>geom_tiplab</code> and the <code>label</code> should be string that can be parsed into expression and displayed as described in <code>?plotmath</code>.</p>

 <p>For example, the tiplabels contains two parts, species name and accession number and we want to display species name in <em>italic</em>, we can use command like this:</p>

@@ -394,8 +395,8 @@ d <- data.frame(label = tr$tip.label, genus = genus,

 ggtree(tr) %<+% d + xlim(NA, 5) +

     geom_tiplab(aes(label=paste0(&#39;italic(&#39;, genus, &#39;)~bolditalic(&#39;, species, &#39;)~&#39;, geo)), parse=T)</code></pre>

 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM" class="uri">https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM</a>.</p>

-</div>

-<div id="avoid-overlapping-text-labels" class="section level2">

+</section>

+<section id="avoid-overlapping-text-labels" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Avoid overlapping text labels</h2>

 <p>User can use <a href="https://cran.r-project.org/web/packages/ggrepel/">ggrepel</a> package to repel overlapping text labels.</p>

 <p>For example:</p>

@@ -405,8 +406,8 @@ raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitions

 raxml <- read.raxml(raxml_file)

 ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))</code></pre>

 <p>For details, please refer to <a href="https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html">ggrepel usage examples</a>.</p>

-</div>

-<div id="bootstrap-values-from-newick-format" class="section level2">

+</section>

+<section id="bootstrap-values-from-newick-format" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> bootstrap values from newick format</h2>

 <p>It’s quite command to store <code>bootstrap</code> value as node label in <code>newick</code> format. Visualizing node label is easy using <code>geom_text2(aes(subset = !isTip, label=label))</code>.</p>

 <p>If you want to only display a subset of <code>bootstrap</code> (e.g. bootstrap &gt; 80), you can’t simply using <code>geom_text2(subset= (label &gt; 80), label=label)</code> since <code>label</code> is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use <code>geom_text2(subset=(as.numeric(label) &gt; 80), label=label)</code>, it will also fail since <code>NAs</code> were introduced by coercion. We need to convert <code>NAs</code> to logical <code>FALSE</code>, this can be done by the following code:</p>

@@ -421,19 +422,19 @@ d$label <- as.numeric(d$label)

 d <- d[d$label > 80,]

 q + geom_text(data=d, aes(label=label))</code></pre>

-</div>

-</div>

-<div id="aesthetic-mapping" class="section level1">

+</section>

+</section>

+<section id="aesthetic-mapping" class="level1">

 <h1><i class="fa fa-map-marker"></i> <em>aesthetic</em> mapping</h1>

-<div id="inherit-aes" class="section level2">

+<section id="inherit-aes" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> inherit <em>aes</em></h2>

 <pre class="r"><code>ggtree(rtree(30)) + geom_point()</code></pre>

 <p>For example, we can add symbolic points to nodes with <code>geom_point()</code> directly. The magic here is we don’t need to map <code>x</code> and <code>y</code> position of the points by providing <code>aes(x, y)</code> to <code>geom_point()</code> since it was already mapped by <code>ggtree</code> function and it serves as a global mapping for all layers.</p>

 <p>But what if we provide a <code>dataset</code> in a layer and the <code>dataset</code> doesn’t contain column of <code>x</code> and/or <code>y</code>, the layer function also try to map <code>x</code> and <code>y</code> and also others if you map them in <code>ggtree</code> function. As these variable is not available in your <code>dataset</code>, you will get the following error:</p>

 <pre><code>Error in eval(expr, envir, enclos) : object &#39;x&#39; not found</code></pre>

 <p>This can be fixed by using parameter <code>inherit.aes=FALSE</code> which will disable inheriting mapping from <code>ggtree</code> function.</p>

-</div>

-<div id="use-in-aes" class="section level2">

+</section>

+<section id="use-in-aes" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> use <code>$</code> in aes</h2>

 <p>NEVER DO THIS.</p>

 <p>see the explaination in the <a href="https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes">ggplot2 book 2ed</a>:</p>

@@ -441,15 +442,15 @@ q + geom_text(data=d, aes(label=label))</code></pre>

 <p>Never refer to a variable with <code>$</code> (e.g., <code>diamonds$carat</code>) in <code>aes()</code>. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.</p>

 </blockquote>

 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hViM6vRZF94/MsZT8qRgBwAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>

-</div>

-</div>

-<div id="annotation" class="section level1">

+</section>

+</section>

+<section id="annotation" class="level1">

 <h1><i class="fa fa-tree"></i> Annotation</h1>

-<div id="colouring-edges-by-user-data" class="section level2">

+<section id="colouring-edges-by-user-data" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> colouring edges by user data</h2>

 <p>see my blog post: <a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a> and also my answer on <a href="https://github.com/GuangchuangYu/ggtree/issues/76" class="uri">https://github.com/GuangchuangYu/ggtree/issues/76</a> and <a href="https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8" class="uri">https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8</a>.</p>

-</div>

-</div>

+</section>

+</section>

 			<aside class="copyright" role="note">

@@ -10,7 +10,7 @@

     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">

     <meta http-equiv="X-UA-Compatible" content="IE=10" />

     <title>Featured Articles - ggtree</title>

-    <meta name="generator" content="Hugo 0.24.1" />

+    <meta name="generator" content="Hugo 0.30.2" />

     <meta name="description" content="Visualization and annotation of phylogenetic trees.">

@@ -322,15 +322,16 @@

           <li>

-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

-              Contact via email

-            </a>

+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

+                  Contact via email

+              </a>

           </li>

         </ul>

+        <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>

         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>

-<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

+        <div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

       </div>

     </div>

   </div>

@@ -345,17 +346,17 @@

 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

 <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><img src="../images/citation.png" width="880"/></p>

-<div id="section" class="section level2">

+<section id="section" class="level2">

 <h2><i class="fa fa-calendar"></i> 2017</h2>

 <p><a href="http://science.sciencemag.org/content/358/6364/789.full">Integrated view of <em>Vibrio cholerae</em> in the Americas</a>. *<strong>Science</strong>, 2017, 358(6364):789-793.</p>

 <p><a href="http://dx.doi.org/10.1073/pnas.1617959114">Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging</a>. <strong><em>PNAS</em></strong>, 2017, 114(5):1105-111-.</p>

 <p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376617/">Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus</a>. <strong><em>Frontiers in Microbiology</em></strong>, 2017, 8:543</p>

 <p><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3">Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in <em>Bacteroides coprocola</em></a>. <strong><em>Microbiome</em></strong>, 2017, 5:15</p>

-</div>

-<div id="section-1" class="section level2">

+</section>

+<section id="section-1" class="level2">

 <h2><i class="fa fa-calendar"></i> 2016</h2>

 <p><a href="http://aem.asm.org/content/82/22/6788.short">Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine</a>. <strong><em>Applied and Environmental Microbiology</em></strong>. 2016, 82(22):6788-6798.</p>

-</div>

+</section>

 			<aside class="copyright" role="note">

@@ -10,7 +10,7 @@

     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">

     <meta http-equiv="X-UA-Compatible" content="IE=10" />

     <title>Gallery - ggtree</title>

-    <meta name="generator" content="Hugo 0.24.1" />

+    <meta name="generator" content="Hugo 0.30.2" />

     <meta name="description" content="Visualization and annotation of phylogenetic trees.">

@@ -322,15 +322,16 @@

           <li>

-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

-              Contact via email

-            </a>

+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

+                  Contact via email

+              </a>

           </li>

         </ul>

+        <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>

         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>

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@@ -343,66 +344,36 @@

 			<h1>Gallery </h1>

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-<div class="figure">

-<img src="https://guangchuangyu.github.io/featured_img/ggtree/2017_science.jpg" />

-

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+<p><img src="https://guangchuangyu.github.io/featured_img/ggtree/2017_science.jpg" /></p>

 <p><a href="http://dx.doi.org/10.1126/science.aao2136" class="uri">http://dx.doi.org/10.1126/science.aao2136</a></p>

 <hr />

-<div class="figure">

-<img src="http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs40168-017-0331-1/MediaObjects/40168_2017_331_Fig3_HTML.gif" />

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+<p><img src="http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs40168-017-0331-1/MediaObjects/40168_2017_331_Fig3_HTML.gif" /></p>

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 <hr />

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-<img src="https://guangchuangyu.github.io/featured_img/ggtree/syen12249-fig-0002.png" />

-

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+<p><img src="https://guangchuangyu.github.io/featured_img/ggtree/syen12249-fig-0002.png" /></p>

 <p><a href="https://doi.org/10.1111/syen.12249" class="uri">https://doi.org/10.1111/syen.12249</a></p>

 <hr />

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-<img src="http://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12915-017-0402-6/MediaObjects/12915_2017_402_Fig2_HTML.gif" />

-

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+<p><img src="http://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12915-017-0402-6/MediaObjects/12915_2017_402_Fig2_HTML.gif" /></p>

 <p><a href="https://doi.org/10.1186/s12915-017-0402-6" class="uri">https://doi.org/10.1186/s12915-017-0402-6</a></p>

 <hr />

-<div class="figure">

-<img src="https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg" />

-

-</div>

+<p><img src="https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg" /></p>

 <p><a href="http://dx.doi.org/10.3389/fmicb.2017.00543" class="uri">http://dx.doi.org/10.3389/fmicb.2017.00543</a></p>

 <hr />

-<div class="figure">

-<img src="http://www.frontiersin.org/files/Articles/220056/fmicb-08-00456-HTML-r1/image_m/fmicb-08-00456-g002.jpg" />

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+<p><img src="http://www.frontiersin.org/files/Articles/220056/fmicb-08-00456-HTML-r1/image_m/fmicb-08-00456-g002.jpg" /></p>

 <p><a href="https://doi.org/10.3389/fmicb.2017.00456" class="uri">https://doi.org/10.3389/fmicb.2017.00456</a></p>

 <hr />

-<div class="figure">

-<img src="https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif" />

-

-</div>

+<p><img src="https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif" /></p>

 <p><a href="http://dx.doi.org/10.1186/s40168-017-0232-3" class="uri">http://dx.doi.org/10.1186/s40168-017-0232-3</a></p>

 <hr />

 <p><img src="https://guangchuangyu.github.io/featured_img/ggtree/C2mxyBuUcAEt391.jpg" /> <a href="http://dx.doi.org/10.1111/2041-210X.12628" class="uri">http://dx.doi.org/10.1111/2041-210X.12628</a></p>

 <hr />

-<div class="figure">

-<img src="https://guangchuangyu.github.io/featured_img/ggtree/2017-01-21-115646_969x444_scrot.png" />

-

-</div>

+<p><img src="https://guangchuangyu.github.io/featured_img/ggtree/2017-01-21-115646_969x444_scrot.png" /></p>

 <p><a href="http://dx.doi.org/10.1128/AEM.02307-16" class="uri">http://dx.doi.org/10.1128/AEM.02307-16</a></p>

 <hr />

-<div class="figure">

-<img src="https://guangchuangyu.github.io/featured_img/ggtree/2016_fcimb-06-00036-g003.jpg" />

-

-</div>

+<p><img src="https://guangchuangyu.github.io/featured_img/ggtree/2016_fcimb-06-00036-g003.jpg" /></p>

 <p><a href="http://dx.doi.org/10.3389%2Ffcimb.2016.00036">http://dx.doi.org/10.3389%2Ffcimb.2016.00036</a></p>

 <hr />

-<div class="figure">

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

-

-</div>

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

 <p><a href="http://dx.doi.org/10.1016/j.meegid.2015.12.006" class="uri">http://dx.doi.org/10.1016/j.meegid.2015.12.006</a></p>

@@ -19,16 +19,16 @@

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- http://dx.doi.org/10.3389/fmicb.2017.00543

- https://doi.org/10.3389/fmicb.2017.00456

- http://dx.doi.org/10.1186/s40168-017-0232-3

+https://doi.org/10.1186/s40168-017-0331-1

+https://doi.org/10.1111/syen.12249

+https://doi.org/10.1186/s12915-017-0402-6

+http://dx.doi.org/10.3389/fmicb.2017.00543

+https://doi.org/10.3389/fmicb.2017.00456

+http://dx.doi.org/10.1186/s40168-017-0232-3

 http://dx.doi.org/10.1111/2041-210X.12628

- http://dx.doi.org/10.1128/AEM.02307-16

- http://dx.doi.org/10.3389%2Ffcimb.2016.00036

- http://dx.doi.org/10.1016/j.meegid.2015.12.006</description>

+http://dx.doi.org/10.1128/AEM.02307-16

+http://dx.doi.org/10.3389%2Ffcimb.2016.00036

+http://dx.doi.org/10.1016/j.meegid.2015.12.006</description>

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@@ -10,7 +10,7 @@

     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">

     <meta http-equiv="X-UA-Compatible" content="IE=10" />

     <title>ggtree</title>

-    <meta name="generator" content="Hugo 0.24.1" />

+    <meta name="generator" content="Hugo 0.30.2" />

     <meta name="description" content="Visualization and annotation of phylogenetic trees.">

@@ -322,15 +322,16 @@

           <li>

-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

-              Contact via email

-            </a>

+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

+                  Contact via email

+              </a>

           </li>

         </ul>

+        <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>

         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>

-<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

+        <div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

       </div>

     </div>

   </div>

@@ -343,36 +344,26 @@

 				<h1>ggtree: visualization and annotation of phylogenetic trees </h1>

-				<div id="plea-to-against-bmc" class="section level2">

-<h2>Plea to against BMC</h2>

-<blockquote class="twitter-tweet"><p lang="en" dir="ltr">BMC journal protects paper of plagiarism <a href="https://t.co/FfSv7dPFXV">https://t.co/FfSv7dPFXV</a> <a href="https://twitter.com/RetractionWatch?ref_src=twsrc%5Etfw">@RetractionWatch</a> <a href="https://twitter.com/C0PE?ref_src=twsrc%5Etfw">@C0PE</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/928836702998638592?ref_src=twsrc%5Etfw">November 10, 2017</a></blockquote>

-<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

-

-<hr />

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

-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21118/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-1156/month-blue.svg?style=flat" alt="month" /></a></p>

+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.1-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21262/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-1156/month-blue.svg?style=flat" alt="month" /></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> 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>

-</div>

-<div id="authors" class="section level2">

+<section id="authors" class="level2">

 <h2><i class="fa fa-user"></i> Authors</h2>

 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>

-</div>

-<div id="citation" class="section level2">

+</section>

+<section id="citation" class="level2">

 <h2><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 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-336-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-47-blue.svg?style=flat" alt="citation" /></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>. 2017, 8(1):28-36.</p>

-</div>

-<div id="featured-articles" class="section level2">

+</section>

+<section id="featured-articles" class="level2">

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

-<div class="figure">

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

-

-</div>

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

 <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>

-</div>

-<div id="installation" class="section level2">

+</section>

+<section id="installation" class="level2">

 <h2><i class="fa fa-download"></i> Installation</h2>

 <p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor page</a>:</p>

 <pre class="r"><code>## try http:// if https:// URLs are not supported

@@ -380,18 +371,18 @@ source("https://bioconductor.org/biocLite.R")

 ## biocLite("BiocUpgrade") ## you may need this

 biocLite(&quot;ggtree&quot;)</code></pre>

 <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>

-</div>

-<div id="overview" class="section level2">

+</section>

+<section id="overview" class="level2">

 <h2><i class="fa fa-cogs"></i> Overview</h2>

-<div id="getting-tree-into-r" class="section level4">

+<section id="getting-tree-into-r" class="level4">

 <h4><i class="fa fa-angle-double-right"></i> Getting tree into R</h4>

 <ul>

 <li>tree parsers: bring evolution evidences to be used/analyzed in <code>R</code></li>

 <li><code>merge_tree</code>: allows evolution evidences to be merged and compared</li>

 <li><code>fortify</code> methods: convert tree objects into tidy data frame</li>

 </ul>

-</div>

-<div id="tree-visualization-annotation" class="section level4">

+</section>

+<section id="tree-visualization-annotation" class="level4">

 <h4><i class="fa fa-angle-double-right"></i> Tree visualization &amp; annotation</h4>

 <ul>

 <li>parsing tree as a collection of nodes allows grammar of graphics to be supported</li>

@@ -399,41 +390,41 @@ biocLite(&quot;ggtree&quot;)</code></pre>

 <li>several layers and functions for tree annotation</li>

 <li>supports annotating phylogenetic trees with user’s own data</li>

 </ul>

-</div>

-<div id="tree-manipulation" class="section level4">

+</section>

+<section id="tree-manipulation" class="level4">

 <h4><i class="fa fa-angle-double-right"></i> Tree manipulation</h4>

 <ul>

 <li>helper functions for tree manipulation, make it possible to explore the tree visually</li>

 </ul>

 <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>

-</div>

-</div>

-<div id="projects-that-depend-on-ggtree" class="section level2">

+</section>

+</section>

+<section id="projects-that-depend-on-ggtree" class="level2">

 <h2><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2>

-<div id="cran-packages" class="section level4">

+<section id="cran-packages" class="level4">

 <h4><i class="fa fa-angle-double-right"></i> CRAN packages</h4>

 <ul>

 <li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle Phylogenetic Distance Matrices and Other Utilities</li>

 </ul>

-</div>

-<div id="bioconductor-packages" class="section level4">

+</section>

+<section id="bioconductor-packages" class="level4">

 <h4><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>

 <ul>

 <li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of lincRNAs and protein-coding genes</li>

 <li><a href="https://www.bioconductor.org/packages/LymphoSeq">LymphoSeq</a>: Analyze high-throughput sequencing of T and B cell receptors</li>

 <li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li>

 </ul>

-</div>

-<div id="other-applications" class="section level4">

+</section>

+<section id="other-applications" class="level4">

 <h4><i class="fa fa-angle-double-right"></i> Other applications</h4>

 <ul>

 <li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>: Collection of scripts for metagenomics analysis</li>

 <li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>: Utilities for Creating and Validating Degenerate primers</li>

 <li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies created along a genome for patterns</li>

 </ul>

-</div>

-</div>

-<div id="feedback" class="section level2">

+</section>

+</section>

+<section id="feedback" class="level2">

 <h2><i class="fa fa-comments"></i> Feedback</h2>

 <ul class="fa-ul">

 <li>

@@ -452,7 +443,7 @@ biocLite(&quot;ggtree&quot;)</code></pre>

 <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>

 </ul>

-</div>

+</section>

@@ -18,9 +18,8 @@

       <pubDate>Thu, 06 Jul 2017 12:08:13 +0100</pubDate>

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

-      <description>Plea to against BMC BMC journal protects paper of plagiarism https://t.co/FfSv7dPFXV @RetractionWatch @C0PE

-— Guangchuang Yu (@guangchuangyu) November 10, 2017     

-The ggtree package extending the ggplot2 package. It based on grammar of graphics and takes all the good parts of ggplot2. ggtree is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. ggtree is released within the Bioconductor project and the source code is hosted on  GitHub.</description>

+      <description>The ggtree package extending the ggplot2 package. It based on grammar of graphics and takes all the good parts of ggplot2. ggtree is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. ggtree is released within the Bioconductor project and the source code is hosted on  GitHub.

+ Authors Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</description>

     </item>

     <item>

@@ -63,16 +62,16 @@ Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotid

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

       <description>http://dx.doi.org/10.1126/science.aao2136

- https://doi.org/10.1186/s40168-017-0331-1

- https://doi.org/10.1111/syen.12249

- https://doi.org/10.1186/s12915-017-0402-6

- http://dx.doi.org/10.3389/fmicb.2017.00543

- https://doi.org/10.3389/fmicb.2017.00456

- http://dx.doi.org/10.1186/s40168-017-0232-3

+https://doi.org/10.1186/s40168-017-0331-1

+https://doi.org/10.1111/syen.12249

+https://doi.org/10.1186/s12915-017-0402-6

+http://dx.doi.org/10.3389/fmicb.2017.00543

+https://doi.org/10.3389/fmicb.2017.00456

+http://dx.doi.org/10.1186/s40168-017-0232-3

 http://dx.doi.org/10.1111/2041-210X.12628

- http://dx.doi.org/10.1128/AEM.02307-16

- http://dx.doi.org/10.3389%2Ffcimb.2016.00036

- http://dx.doi.org/10.1016/j.meegid.2015.12.006</description>

+http://dx.doi.org/10.1128/AEM.02307-16

+http://dx.doi.org/10.3389%2Ffcimb.2016.00036

+http://dx.doi.org/10.1016/j.meegid.2015.12.006</description>

     </item>

     <item>

@@ -10,7 +10,7 @@

     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">

     <meta http-equiv="X-UA-Compatible" content="IE=10" />

     <title>Tweets - ggtree</title>

-    <meta name="generator" content="Hugo 0.24.1" />

+    <meta name="generator" content="Hugo 0.30.2" />

     <meta name="description" content="Visualization and annotation of phylogenetic trees.">

@@ -322,15 +322,16 @@

           <li>

-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

-              Contact via email

-            </a>

+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">

+                  Contact via email

+              </a>

           </li>

         </ul>

+        <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>

         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>

-<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

+        <div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>

       </div>

     </div>

   </div>

@@ -7,7 +7,7 @@ weight: 10

 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

-<div id="vignettes" class="section level2">

+<section id="vignettes" class="level2">

 <h2><i class="fa fa-book"></i> Vignettes</h2>

 <ul>

 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html">ggtree</a></li>

@@ -19,10 +19,10 @@ weight: 10

 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree utilities</a></li>

 <li><a href="https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html">Phylomoji</a></li>

 </ul>

-</div>

-<div id="blog-posts" class="section level2">

+</section>

+<section id="blog-posts" class="level2">

 <h2><i class="fa fa-wordpress"></i> Blog posts</h2>

-<div id="news-and-updates" class="section level3">

+<section id="news-and-updates" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> News and updates</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with ggtree</a></li>

@@ -34,16 +34,16 @@ weight: 10

 <li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC packages</a></li>

 <li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper published</a></li>

 </ul>

-</div>

-<div id="data-manipulation" class="section level3">

+</section>

+<section id="data-manipulation" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Data manipulation</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>

 <li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>

 <li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using treeio</a></li>

 </ul>

-</div>

-<div id="tree-visualization" class="section level3">

+</section>

+<section id="tree-visualization" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Tree visualization</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>

@@ -52,8 +52,8 @@ weight: 10

 <li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>

 <li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>

 </ul>

-</div>

-<div id="tree-annotation" class="section level3">

+</section>

+<section id="tree-annotation" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Tree annotation</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in ggtree</a></li>

@@ -69,14 +69,14 @@ weight: 10

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

 <li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>

 </ul>

-</div>

-<div id="tree-manipulation" class="section level3">

+</section>

+<section id="tree-manipulation" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>

 </ul>

-</div>

-<div id="application" class="section level3">

+</section>

+<section id="application" class="level3">

 <h3><i class="fa fa-angle-double-right"></i> Application</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>

@@ -84,34 +84,34 @@ weight: 10

 <li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>

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

 </ul>

-</div>

-<div id="funny-stuff" class="section level3">

+</section>

+<section id="funny-stuff" class="level3">

 <h3><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>

 <li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and comicR</a></li>

 <li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>

 </ul>

-</div>

-</div>

-<div id="slides" class="section level2">

+</section>

+</section>

+<section id="slides" class="level2">

 <h2><i class="fa fa-slideshare"></i> Slides</h2>

 <ul>

 <li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp; ggplot2</a></li>

 <li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>

 </ul>

-</div>

-<div id="video" class="section level2">

+</section>

+<section id="video" class="level2">

 <h2><i class="fa fa-youtube-play"></i> Video</h2>

 <ul>

 <li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>

 <li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>

 <li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>

 </ul>

-</div>

-<div id="workflow" class="section level2">

+</section>

+<section id="workflow" class="level2">

 <h2><i class="fa fa-gift"></i> Workflow</h2>

 <ul>

 <li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>

 </ul>

-</div>

+</section>

@@ -7,20 +7,20 @@ weight: 20

 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

-<div id="installation" class="section level1">

+<section id="installation" class="level1">

 <h1><i class="fa fa-download"></i> Installation</h1>

-<div id="could-not-find-function" class="section level2">

+<section id="could-not-find-function" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Could not find function</h2>

 <p>If you got <a href="https://github.com/GuangchuangYu/ggtree/issues/12">this error</a>, please make sure you are using the latest R and <code>ggtree</code>.</p>

 <p>Packages in Bioconductor, like <code>ggtree</code>, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to <code>devel</code> branch.</p>

 <p>Sometimes I may write blog post to introduce new functions which is not available in <code>release</code> branch, you need to install the <code>devel</code> version of <code>ggtree</code> in order to use these new functions.</p>

 <p>You can download the <code>devel</code> version of <code>ggtree</code> from <a href="http://bioconductor.org/packages/devel/bioc/html/ggtree.html" class="uri">http://bioconductor.org/packages/devel/bioc/html/ggtree.html</a> and install it, or install the github version of <code>ggtree</code>.</p>

 <p>This also applied to other of my packages, including <code>GOSemSim</code>, <code>DOSE</code>, <code>clusterProfiler</code>, <code>ReactomePA</code> and <code>ChIPseeker</code>. If you got the <code>could not find function</code> error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.</p>

-</div>

-</div>

-<div id="text-label" class="section level1">

+</section>

+</section>

+<section id="text-label" class="level1">

 <h1><i class="fa fa-text-height"></i> Text &amp; Label</h1>

-<div id="tip-label-truncated" class="section level2">

+<section id="tip-label-truncated" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Tip label truncated</h2>

 <p>ggplot2 can’t auto adjust xlim based on added text.</p>

 <pre class="r"><code>library(ggtree)

@@ -29,8 +29,8 @@ tree<-read.tree(text="(Organism1.006G249400.1:0.03977,(Organism2.022118m

 ggtree(tree) + geom_tiplab()</code></pre>

 <p>This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.</p>

 <pre class="r"><code>ggtree(tree) + geom_tiplab() + xlim(0, 0.06)</code></pre>

-</div>

-<div id="modify-tip-labels" class="section level2">

+</section>

+<section id="modify-tip-labels" class="level2">

 <h2><i class="fa fa-angle-double-right"></i> Modify (tip) labels</h2>

 <p>This could be easily done via the <code>%&lt;+%</code> operator to attach the modified version of the labels and than use <code>geom_tiplab</code> to display the modified version.</p>

 <pre><code>raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)

@@ -40,8 +40,8 @@ lb = get.tree(raxml)$tip.label

 d = data.frame(label=lb, label2 = paste("AA", substring(lb, 1, 5)))

 ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>

 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>

-</div>

-<div id="formatting-tip-labels" class="section level2">

+</section>

+<section id="formatting-tip-labels" class="level2">