<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>ggtree</title>
<link>https://guangchuangyu.github.io/ggtree/</link>
<description>Recent content on ggtree</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<copyright>Released under the Artistic-2.0 license</copyright>
<lastBuildDate>Thu, 06 Jul 2017 12:08:13 +0100</lastBuildDate>
<atom:link href="https://guangchuangyu.github.io/ggtree/index.xml" rel="self" type="application/rss+xml" />
<item>
<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>
</item>
<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 Growing a ggtree Growing a ggtree - part 2, adding tip shapes Drawing a tree with colored tips in R (ggtree) 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 Enhanced annotation of a primate phylogeny with ggtree Tree manipulation flip and rotate branches in ggtree Subtrees as triangles with 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 R语言包ggtree 进化树绘图 Workflow recreate a tree from a publication (Bloom et al, Science 2010) Workshop Visualizing and Annotating Phylogenetic Trees with R+ggtree </description>
</item>
<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 Integrated view of Vibrio cholerae in the Americas. *Science, 2017, 358(6364):789-793.
Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017, 114(5):1105-111-.
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.</description>
</item>
<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>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
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
Subtrees as triangles with ggtree https://t.co/NNdur8PS2Y #rstats https://t.co/7PZbN9daHy
&mdash; Jean 👨💻 (@JeanManguy) December 15, 2017 Drawing a tree with colored tips in R (ggtree)
https://t.co/s9FYUbynCd @guangchuangyu
&mdash; Guanyang Zhang 张冠阳 (@GYZhang2) December 13, 2017 ggtree使ってみた。”注目する枝組み合わせの分布”みたいなものを可視化したいんだけどまだちょっと見にくい。 pic.twitter.com/w5xs7cd0jQ
&mdash; Kenji Fukushima (@kfuku0502) December 13, 2017 ggtreeにはhttps://t.co/8T3WU8h9pWからシルエット画像を取ってくる用の関数まで用意されているのか…。HGTの描画も楽そうだし、これはもう系統樹描画に関してはETEを投げ捨ててggtreeに鞍替えするべきか。https://t.co/gynekuwjCe
&mdash; Kenji Fukushima (@kfuku0502) December 11, 2017 I&#39;ve had good experiences with ggtree https://t.co/eRLhDoc4Hm
&mdash; Philipp Bayer (@PhilippBayer) December 7, 2017 Also, thanks to @guangchuangyu for the R package ggtree - these visualizations are made possible by the reliability that sweet #rstats package!</description>
</item>
</channel>
</rss>
