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<title>ggtree</title>
<link>https://guangchuangyu.github.io/ggtree/</link>
<description>Recent content on ggtree</description>
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<copyright>Released under the Artistic-2.0 license</copyright>
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<title>ggtree: visualization and annotation of phylogenetic trees</title>
<link>https://guangchuangyu.github.io/ggtree/</link>
<pubDate>Thu, 06 Jul 2017 12:08:13 +0100</pubDate>
<guid>https://guangchuangyu.github.io/ggtree/</guid>
<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>
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<item>
<title>Documentation</title>
<link>https://guangchuangyu.github.io/ggtree/documentation/</link>
<pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
<guid>https://guangchuangyu.github.io/ggtree/documentation/</guid>
<description> Vignettes ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji Blog posts News and updates viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published Data manipulation subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio Tree visualization ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree The Molecular Ecologist Growing a ggtree Growing a ggtree - part 2, adding tip shapes Tree annotation label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output Tree manipulation flip and rotate branches in ggtree Application ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree Funny stuff ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R Slides Generating publication quality figures using R &amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees Video interactive clade highlighting interactive rotating clades interactive clade labeling Workflow recreate a tree from a publication (Bloom et al, Science 2010) </description>
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<item>
<title>FAQ</title>
<link>https://guangchuangyu.github.io/ggtree/faq/</link>
<pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
<guid>https://guangchuangyu.github.io/ggtree/faq/</guid>
<description>Installation Could not find function If you got this error, please make sure you are using the latest R and ggtree.
Packages in Bioconductor, like ggtree, 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 devel branch.
Sometimes I may write blog post to introduce new functions which is not available in release branch, you need to install the devel version of ggtree in order to use these new functions.</description>
</item>
<item>
<title>Featured Articles</title>
<link>https://guangchuangyu.github.io/ggtree/featured-articles/</link>
<pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
<guid>https://guangchuangyu.github.io/ggtree/featured-articles/</guid>
<description>Let us know if you have published using ggtree and your publication will be featured here.
2017 Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017
Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus. Frontiers in Microbiology, 2017, 8:543
Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola. Microbiome, 2017, 5:15</description>
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<item>
<title>Gallery</title>
<link>https://guangchuangyu.github.io/ggtree/gallery/</link>
<pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
<guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>
<description>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>
</item>
<item>
<title>Tweets</title>
<link>https://guangchuangyu.github.io/ggtree/tweets/</link>
<pubDate>Tue, 25 Jul 2017 00:11:02 +0100</pubDate>
<guid>https://guangchuangyu.github.io/ggtree/tweets/</guid>
<description>Leave me a message on
Possible to combine #ggjoy with #ggtree ? My gg-fu is weak. #rstats #DataViz #JoyPlot https://t.co/4FICfER6Oa
&mdash; Libby Megna (@LibbyMegna) July 29, 2017 Second post with an update on how to add tip shapes and colours to ggtree https://t.co/ezWF4TVQst
&mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 Yes and no. No manual assignment =&gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀</description>
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