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<h1>Documentation </h1>
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
<div id="vignettes" class="section 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>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html">Tree Data Import</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html">Tree Visualization</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html">Tree Annotation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html">Tree Manipulation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html">Advance Tree Annotation</a></li>
<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">
<h2><i class="fa fa-wordpress"></i> Blog posts</h2>
<div id="news-and-updates" class="section 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>
<li><a href="https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1">ggtree in Bioconductor 3.1</a></li>
<li><a href="https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages">BioC 3.1: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages">BioC 3.2: NEWS of my BioC packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/12/news-of-ggtree">News of ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/">BioC 3.3: NEWS of my BioC packages</a></li>
<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">
<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">
<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>
<li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>
<li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a></li>
<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>
<li><a href="https://aschuerch.github.io/posts/2017-04-24-blog-post-1">Drawing a tree with colored tips in R (ggtree)</a></li>
</ul>
</div>
<div id="tree-annotation" class="section 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>
<li><a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a></li>
<li><a href="https://guangchuangyu.github.io/2015/08/subview">subview</a></li>
<li><a href="https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets">Annotate a phylogenetic tree with insets</a></li>
<li><a href="https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images">ggtree annotate phylogenetic tree with local images</a></li>
<li><a href="https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function">embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function</a></li>
<li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/">facet_plot: a general solution to associate data with phylogenetic tree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/">align genomic features with phylogenetic tree</a></li>
<li><a href="https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree">ggjoy facet with ggtree</a></li>
<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>
<li><a href="https://rgriff23.github.io/2017/05/11/primate-phylogeny-ggtree.html">Enhanced annotation of a primate phylogeny with ggtree</a></li>
</ul>
</div>
<div id="tree-manipulation" class="section 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>
<li><a href="https://jean.manguy.eu/post/subtrees-as-triangles-with-ggtree/">Subtrees as triangles with ggtree</a></li>
</ul>
</div>
<div id="application" class="section 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>
<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/">ggtree for outbreak data</a></li>
<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">
<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">
<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 & 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">
<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>
<li><a href="https://youtu.be/tqspAXM0UQE">R语言包ggtree 进化树绘图</a></li>
</ul>
</div>
<div id="workflow" class="section 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>
<div id="workshop" class="section level2">
<h2><i class="fa fa-users"></i> Workshop</h2>
<ul>
<li><a href="https://4va.github.io/biodatasci/r-ggtree.html">Visualizing and Annotating Phylogenetic Trees with R+ggtree</a></li>
</ul>
</div>
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