1. ggtree
  2. Commit f1b9814be0c7c3d6be1a1280257a29234b63c180
Browse code

phylomoji vignette

guangchuang yu authored on 30/04/2017 02:58:51
Showing 11 changed files
README.md
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![](https://img.shields.io/badge/release%20version-1.8.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.0-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-14583/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/release%20version-1.8.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.0-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-14716/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--04--28-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--04--30-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
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@@ -53,7 +53,7 @@ Please cite the following article when using `ggtree`:
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-14583/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-14716/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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          ++-------------------+------------------+-------------------+------------------+--------------+
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     3000 +                                                                                        *    +
docs/documentation/index.html
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     Annotation</a></li>
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 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree
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     utilities</a></li>
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+<li><a href="https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html">Phylomoji</a></li>
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 </ul>
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 <h2 id="blog-posts"><i class="fa fa-wordpress"></i> Blog posts</h2>
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 <h3 id="news-and-updates"><i class="fa fa-angle-double-right"></i> News and updates</h3>
docs/featuredArticles/index.html
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@@ -234,12 +234,12 @@ published using <code>ggtree</code> and your publication will be featured here.<
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     height: 300px;
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   }<br />
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   </style>
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 </div>
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 <script type='text/javascript'>
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 "xkey": "year",
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 "pubid": "HtEfBTGE9r8C"
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 }
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 ],
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       chartType = "Bar"
docs/index.html
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
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 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.8.0-blue.svg?style=flat" /></a>
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 <a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.0-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-14583/total-blue.svg?style=flat" /></a>
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 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1385/month-blue.svg?style=flat" /></a></p>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on
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 grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>
docs/mkdocs/search_index.json
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         },
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         {
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             "location": "/documentation/",
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-            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data\n    Import\n\n\nTree\n    Visualization\n\n\nTree\n    Annotation\n\n\nTree\n    Manipulation\n\n\nAdvance Tree\n    Annotation\n\n\nggtree\n    utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with\n    ggtree\n\n\nggtree in Bioconductor\n    3.1\n\n\nBioC 3.1: NEWS of my BioC\n    packages\n\n\nBioC 3.2: NEWS of my BioC\n    packages\n\n\nNews of\n    ggtree\n\n\nBioC 3.3: NEWS of my BioC\n    packages\n\n\nBioC 3.4: NEWS of my BioC\n    packages\n\n\nggtree paper\n    published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in\n    ggtree\n\n\nggtree supports phylip tree\n    format\n\n\nconvert graphic object to tree object using\n    treeio\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree\n    view\n\n\nan example of drawing beast tree using\n    ggtree\n\n\nPhylogenetic trees in R using\n    ggtree\n\n    \n The Molecular Ecologist\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in\n    ggtree\n\n\nEdge coloring with user\n    data\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with\n    insets\n\n\nggtree annotate phylogenetic tree with local\n    images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic\n    tree with images using inset\n    function\n\n\nidentify method for\n    ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic\n    tree\n\n\nalign genomic features with phylogenetic\n    tree\n\n\nxlim_tree: set x axis limits for only Tree\n    panel\n\n\nadd layer to specific panel of facet_plot\n    output\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in\n    ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome\n    data\n\n\nggtree for outbreak\n    data\n\n\nggtree version of\n    plotTree\n\n\nreproducible logo generated by\n    ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny\n    fonts\n\n\ncomic phylogenetic tree with ggtree and\n    comicR\n\n\nuse emoji font in\n    R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of\n    ggtree\n\n\nJoin the group chat on\n    \n\n    and\n    \n\n\n\n\n Find out more on\n\nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n\n    ggplot2\n\n\nggtree for visualization and annotation of phylogenetic\n    trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade\n    highlighting\n\n\ninteractive rotating\n    clades\n\n\ninteractive clade\n    labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n,\n    \nScience\n 2010)",
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+            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data\n    Import\n\n\nTree\n    Visualization\n\n\nTree\n    Annotation\n\n\nTree\n    Manipulation\n\n\nAdvance Tree\n    Annotation\n\n\nggtree\n    utilities\n\n\nPhylomoji\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with\n    ggtree\n\n\nggtree in Bioconductor\n    3.1\n\n\nBioC 3.1: NEWS of my BioC\n    packages\n\n\nBioC 3.2: NEWS of my BioC\n    packages\n\n\nNews of\n    ggtree\n\n\nBioC 3.3: NEWS of my BioC\n    packages\n\n\nBioC 3.4: NEWS of my BioC\n    packages\n\n\nggtree paper\n    published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in\n    ggtree\n\n\nggtree supports phylip tree\n    format\n\n\nconvert graphic object to tree object using\n    treeio\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree\n    view\n\n\nan example of drawing beast tree using\n    ggtree\n\n\nPhylogenetic trees in R using\n    ggtree\n\n    \n The Molecular Ecologist\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in\n    ggtree\n\n\nEdge coloring with user\n    data\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with\n    insets\n\n\nggtree annotate phylogenetic tree with local\n    images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic\n    tree with images using inset\n    function\n\n\nidentify method for\n    ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic\n    tree\n\n\nalign genomic features with phylogenetic\n    tree\n\n\nxlim_tree: set x axis limits for only Tree\n    panel\n\n\nadd layer to specific panel of facet_plot\n    output\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in\n    ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome\n    data\n\n\nggtree for outbreak\n    data\n\n\nggtree version of\n    plotTree\n\n\nreproducible logo generated by\n    ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny\n    fonts\n\n\ncomic phylogenetic tree with ggtree and\n    comicR\n\n\nuse emoji font in\n    R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of\n    ggtree\n\n\nJoin the group chat on\n    \n\n    and\n    \n\n\n\n\n Find out more on\n\nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n\n    ggplot2\n\n\nggtree for visualization and annotation of phylogenetic\n    trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade\n    highlighting\n\n\ninteractive rotating\n    clades\n\n\ninteractive clade\n    labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n,\n    \nScience\n 2010)",
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-            "text": "ggtree  Tree Data\n    Import  Tree\n    Visualization  Tree\n    Annotation  Tree\n    Manipulation  Advance Tree\n    Annotation  ggtree\n    utilities",
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-            "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chartba8442a5d90\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\":             15,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chartba8442a5d90\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.",
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      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
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-     <lastmod>2017-04-28</lastmod>
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+     <lastmod>2017-04-30</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>
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-     <lastmod>2017-04-28</lastmod>
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+     <lastmod>2017-04-30</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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mkdocs/docs/documentation.md
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@@ -37,6 +37,7 @@ output:
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     Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html)
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 -   [ggtree
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     utilities](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html)
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+-   [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)
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 <i class="fa fa-wordpress"></i> Blog posts
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 ------------------------------------------
mkdocs/docs/featuredArticles.md
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@@ -39,13 +39,13 @@ published using `ggtree` and your publication will be featured here.
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     height: 300px;
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   }
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   </style>
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-<div id="chartba8442a5d90" class="rChart morris">
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+<div id="chart5a529be8ff3" class="rChart morris">
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 </div>
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 <script type='text/javascript'>
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     var chartParams = {
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- "element": "chartba8442a5d90",
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+ "element": "chart5a529be8ff3",
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
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@@ -64,7 +64,7 @@ published using `ggtree` and your publication will be featured here.
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 "pubid": "HtEfBTGE9r8C"
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 }
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 ],
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-"id": "chartba8442a5d90",
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+"id": "chart5a529be8ff3",
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 "labels": "cites"
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 },
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       chartType = "Bar"
mkdocs/docs/index.md
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@@ -29,7 +29,7 @@ ggtree: visualization and annotation of phylogenetic trees
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 [![](https://img.shields.io/badge/release%20version-1.8.0-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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 [![](https://img.shields.io/badge/devel%20version-1.9.0-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
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-[![](https://img.shields.io/badge/download-14583/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-14716/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 The `ggtree` package extending the *ggplot2* package. It based on
mkdocs/src/documentation.rmd
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@@ -20,6 +20,7 @@ html_preview: false
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 + [Tree Manipulation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html)
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 + [Advance Tree Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html)
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 + [ggtree utilities](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html)
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++ [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)
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 ## <i class="fa fa-wordpress"></i> Blog posts
vignettes/ggtree.Rmd
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@@ -6,7 +6,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\
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 date: "`r Sys.Date()`"
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 bibliography: ggtree.bib
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 csl: nature.csl
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-output:
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+output:
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   prettydoc::html_pretty:
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     toc: true
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     theme: cayman
... ... 
@@ -52,7 +52,7 @@ This project arose from our needs to annotate nucleotide substitutions in the ph
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 Previously, phylogenetic trees were much smaller. Annotation of phylogenetic trees was not as necessary as nowadays much more data is becomming available. We want to associate our experimental data, for instance antigenic change, with the evolution relationship. Visualizing these associations in a phylogenetic tree can help us to identify evolution patterns. We believe we need a next generation tree viewer that should be programmable and extensible. It can view a phylogenetic tree easily as we did with classical software and support adding annotation data in a layer above the tree. This is the objective of developing the `ggtree`. Common tasks of annotating a phylogenetic tree should be easy and complicated tasks can be possible to achieve by adding multiple layers of annotation.
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-The `ggtree` is designed by extending the `ggplot2`[@wickham_ggplot2_2009] package. It is based on the grammar of graphics and takes all the good parts of `ggplot2`. There are other R packages that implement tree viewer using `ggplot2`, including `OutbreakTools`, `phyloseq`[@mcmurdie_phyloseq_2013] and [ggphylo](https://github.com/gjuggler/ggphylo); they mostly create complex tree view functions for their specific needs. Internally, these packages interpret a phylogenetic as a collection of `lines`, which makes it hard to annotate diverse user input that are related to node (taxa). The `ggtree` is different to them by interpreting a tree as a collection of `taxa` and allowing general flexibilities of annotating phylogenetic tree with diverse types of user inputs.
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+The `ggtree` is designed by extending the `ggplot2`[@wickham_ggplot2_2009] package. It is based on the grammar of graphics and takes all the good parts of `ggplot2`. There are other R packages that implement tree viewer using `ggplot2`, including `OutbreakTools`, `phyloseq`[@mcmurdie_phyloseq_2013] and [ggphylo](https://github.com/gjuggler/ggphylo); they mostly create complex tree view functions for their specific needs. Internally, these packages interpret a phylogenetic as a collection of `lines`, which makes it hard to annotate diverse user input that are related to node (taxa). The `ggtree` is different to them by interpreting a tree as a collection of `taxa` and allowing general flexibilities of annotating phylogenetic tree with diverse types of user inputs.
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 # Getting data into `R`
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@@ -84,7 +84,7 @@ Most of the phylogenetic trees are scaled by evolutionary distance (substitution
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 The `ggtree` package provides several layers to annotate a phylogenetic tree, including:
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 + `geom_cladelabel` for labelling selected clades
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-+ `geom_hilight` for highlighting selected clades
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++ `geom_hilight` for highlighting selected clades
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 + `geom_range` to indicate uncertainty of branch lengths
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 + `geom_strip` for adding strip/bar to label associated taxa (with optional label)
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 + `geom_taxalink` for connecting related taxa
... ... 
@@ -107,7 +107,7 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype
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 + [Tree Annotation](treeAnnotation.html)
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 + [Advance Tree Annotation](advanceTreeAnnotation.html)
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 + [ggtree utilities](ggtreeUtilities.html)
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-
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++ [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)
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 More documents can be found in <https://guangchuangyu.github.io/ggtree>.
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@@ -115,7 +115,7 @@ More documents can be found in <https://guangchuangyu.github.io/ggtree>.
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  - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).
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  - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree) or post to [Bioconductor support site](https://support.bioconductor.org/) or [Biostars](https://www.biostars.org/). We are following every post tagged with **ggtree**.
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-
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+
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 # Session info
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