1. ggtree
  2. Commit 599e2410d35bfd791db16d778d590c69da38c1b9
Browse code

update docs

guangchuang yu authored on 17/12/2016 05:56:02
Showing 10 changed files
README.md
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@@ -4,7 +4,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.6.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.4-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) [![total](https://img.shields.io/badge/downloads-18505/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
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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-2016--12--14-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-2016--12--17-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) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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@@ -18,7 +18,7 @@ Please cite the following article when using `ggtree`:
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 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted*
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-282-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-281-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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docs/documentation/index.html
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/">ggtree for outbreak data</a></li>
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-<li><a href="https://github.com/GuangchuangYu/plotTree-ggtree">ggtree version of plotTree.R</a></li>
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+<li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>
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 </ul>
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 <h3 id="funny-stuff"><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
docs/featuredArticles/index.html
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docs/index.html
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.5-blue.svg?style=flat" /></a>
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 <a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.4-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-18329/total-blue.svg?style=flat" /></a>
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 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1852/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 grammar of graphics and takes all the good parts of <em>ggplot2</em>.  <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
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 <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
docs/mkdocs/search_index.json
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@@ -67,7 +67,7 @@
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             "location": "/documentation/",
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-            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data Import\n\n\nTree Visualization\n\n\nTree Annotation\n\n\nTree Manipulation\n\n\nAdvance Tree Annotation\n\n\nggtree utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with ggtree\n\n\nggtree in Bioconductor 3.1\n\n\nBioC 3.1: NEWS of my BioC packages\n\n\nBioC 3.2: NEWS of my BioC packages\n\n\nNews of ggtree\n\n\nBioC 3.3: NEWS of my BioC packages\n\n\nBioC 3.4: NEWS of my BioC packages\n\n\nggtree paper published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in ggtree\n\n\nggtree supports phylip tree format\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree view\n\n\nan example of drawing beast tree using ggtree\n\n\nxlim_tree: set x axis limits for only Tree panel\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in ggtree\n\n\nEdge coloring with user data\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with insets\n\n\nggtree annotate phylogenetic tree with local images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function\n\n\nidentify method for ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic tree\n\n\nalign genomic features with phylogenetic tree\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome data\n\n\nggtree for outbreak data\n\n\nggtree version of plotTree.R\n\n\nreproducible logo generated by ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny fonts\n\n\ncomic phylogenetic tree with ggtree and comicR\n\n\nuse emoji font in R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of ggtree\n\n\nJoin the group chat on \n and \n\n\n\n\n Find out more on \nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n ggplot2\n\n\nggtree for visualization and annotation of phylogenetic trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade highlighting\n\n\ninteractive rotating clades\n\n\ninteractive clade labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n, \nScience\n 2010)",
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+            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data Import\n\n\nTree Visualization\n\n\nTree Annotation\n\n\nTree Manipulation\n\n\nAdvance Tree Annotation\n\n\nggtree utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with ggtree\n\n\nggtree in Bioconductor 3.1\n\n\nBioC 3.1: NEWS of my BioC packages\n\n\nBioC 3.2: NEWS of my BioC packages\n\n\nNews of ggtree\n\n\nBioC 3.3: NEWS of my BioC packages\n\n\nBioC 3.4: NEWS of my BioC packages\n\n\nggtree paper published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in ggtree\n\n\nggtree supports phylip tree format\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree view\n\n\nan example of drawing beast tree using ggtree\n\n\nxlim_tree: set x axis limits for only Tree panel\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in ggtree\n\n\nEdge coloring with user data\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with insets\n\n\nggtree annotate phylogenetic tree with local images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function\n\n\nidentify method for ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic tree\n\n\nalign genomic features with phylogenetic tree\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome data\n\n\nggtree for outbreak data\n\n\nggtree version of plotTree\n\n\nreproducible logo generated by ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny fonts\n\n\ncomic phylogenetic tree with ggtree and comicR\n\n\nuse emoji font in R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of ggtree\n\n\nJoin the group chat on \n and \n\n\n\n\n Find out more on \nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n ggplot2\n\n\nggtree for visualization and annotation of phylogenetic trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade highlighting\n\n\ninteractive rotating clades\n\n\ninteractive clade labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n, \nScience\n 2010)",
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-            "text": "Let us know\n if you have published 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  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart5cd55f3ed02\",\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\"id\": \"chart5cd55f3ed02\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976",
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     </url>
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mkdocs/docs/documentation.md
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@@ -71,7 +71,7 @@
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 + [ggtree for microbiome data](https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/)
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 + [ggtree for outbreak data](https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/)
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-+ [ggtree version of plotTree.R](https://github.com/GuangchuangYu/plotTree-ggtree)
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++ [ggtree version of plotTree](http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/)
75 75 
 + [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)
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mkdocs/docs/featuredArticles.md
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@@ -36,10 +36,10 @@
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   }
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   </style>
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-<div id = 'chart5cd55f3ed02' class = 'rChart morris'></div>
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+<div id = 'chart4fa28c95e5e' class = 'rChart morris'></div>
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 <script type='text/javascript'>
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     var chartParams = {
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- "element": "chart5cd55f3ed02",
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+ "element": "chart4fa28c95e5e",
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
... ... 
@@ -53,7 +53,7 @@
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 "pubid": "HtEfBTGE9r8C"
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 }
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 ],
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-"id": "chart5cd55f3ed02",
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+"id": "chart4fa28c95e5e",
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 "labels": "cites"
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 },
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       chartType = "Bar"
mkdocs/docs/index.md
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@@ -18,7 +18,7 @@
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19 19 
 [![releaseVersion](https://img.shields.io/badge/release%20version-1.6.5-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
20 20 
 [![develVersion](https://img.shields.io/badge/devel%20version-1.7.4-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
21 
-[![total](https://img.shields.io/badge/downloads-18329/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
21 
+[![total](https://img.shields.io/badge/downloads-18505/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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mkdocs/src/documentation.md
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@@ -58,7 +58,7 @@
58 58
59 59 
 + [ggtree for microbiome data](https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/)
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 + [ggtree for outbreak data](https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/)
61 
-+ [ggtree version of plotTree.R](https://github.com/GuangchuangYu/plotTree-ggtree)
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++ [ggtree version of plotTree](http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/)
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 + [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)
63 63
64 64