--- date: 2017-07-24T00:11:02+01:00 title: Documentation weight: 10 --- <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> ## <i class="fa fa-book"></i> Vignettes + [ggtree](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html) + [Tree Data Import](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html) + [Tree Visualization](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html) + [Tree Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html) + [Tree Manipulation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html) + [Advance Tree Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html) + [ggtree utilities](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html) + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html) ## <i class="fa fa-wordpress"></i> Blog posts ### <i class="fa fa-angle-double-right"></i> News and updates + [viewing and annotating phylogenetic tree with ggtree](https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree) + [ggtree in Bioconductor 3.1](https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1) + [BioC 3.1: NEWS of my BioC packages](https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages) + [BioC 3.2: NEWS of my BioC packages](https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages) + [News of ggtree](https://guangchuangyu.github.io/2015/12/news-of-ggtree) + [BioC 3.3: NEWS of my BioC packages](https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/) + [BioC 3.4: NEWS of my BioC packages](https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages) + [ggtree paper published](https://guangchuangyu.github.io/2016/08/ggtree-paper-published) ### <i class="fa fa-angle-double-right"></i> Data manipulation + [subsetting data in ggtree](https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree) + [ggtree supports phylip tree format](https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format) + [convert graphic object to tree object using treeio](http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/) ### <i class="fa fa-angle-double-right"></i> Tree visualization + [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/) + [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree) + [Phylogenetic trees in R using ggtree](http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/) + [Growing a ggtree](https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration) + [Growing a ggtree - part 2, adding tip shapes](https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2) + [Drawing a tree with colored tips in R (ggtree)](https://aschuerch.github.io/posts/2017-04-24-blog-post-1) ### <i class="fa fa-angle-double-right"></i> Tree annotation + [label edge number in ggtree](https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree) + [Edge coloring with user data](http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/) + [subview](https://guangchuangyu.github.io/2015/08/subview) + [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets) + [ggtree annotate phylogenetic tree with local images](https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images) + [embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function](https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function) + [identify method for ggtree](https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree) + [facet_plot: a general solution to associate data with phylogenetic tree](https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/) + [align genomic features with phylogenetic tree](https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/) + [ggjoy facet with ggtree](https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree) + [xlim_tree: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/) + [add layer to specific panel of facet_plot output](https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/) + [Enhanced annotation of a primate phylogeny with ggtree](https://rgriff23.github.io/2017/05/11/primate-phylogeny-ggtree.html) ### <i class="fa fa-angle-double-right"></i> Tree manipulation + [flip and rotate branches in ggtree](https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree) + [Subtrees as triangles with ggtree](https://jean.manguy.eu/post/subtrees-as-triangles-with-ggtree/) ### <i class="fa fa-angle-double-right"></i> Application + [ggtree for microbiome data](https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/) + [ggtree for outbreak data](https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/) + [ggtree version of plotTree](http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/) + [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree) ### <i class="fa fa-angle-double-right"></i> Funny stuff + [ggtree with funny fonts](https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts) + [comic phylogenetic tree with ggtree and comicR](https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr) + [use emoji font in R](https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r) ## <i class="fa fa-slideshare"></i> Slides + [Generating publication quality figures using R & ggplot2](https://guangchuangyu.github.io/presentation/2014-ggplot2/) + [ggtree for visualization and annotation of phylogenetic trees](https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/) ## <i class="fa fa-youtube-play"></i> Video + [interactive clade highlighting](https://www.youtube.com/watch?v=KcF8Ec38mzI) + [interactive rotating clades](https://www.youtube.com/watch?v=lKNn4QlPO0E) + [interactive clade labeling](https://www.youtube.com/watch?v=SmcceRD_jxg) + [R语言包ggtree 进化树绘图](https://youtu.be/tqspAXM0UQE) ## <i class="fa fa-gift"></i> Workflow + [recreate a tree from a publication (__Bloom__ *et al*, __*Science*__ 2010)](https://rpubs.com/gutijosh9430/124817) ## <i class="fa fa-users"></i> Workshop + [Visualizing and Annotating Phylogenetic Trees with R+ggtree](https://4va.github.io/biodatasci/r-ggtree.html)