guangchuang yu authored on 08/03/2017 08:42:56
Showing7 changed files

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@@ -47,9 +47,7 @@ mkdocs: mdfiles
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 	mkdocs build;\
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 	cd ../docs;\
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 	rm -rf fonts;\
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-	rm -rf css/font-awesome*;\
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-	Rscript -e 'library(ypages); add_biobabble("index.html")'
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-
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+	rm -rf css/font-awesome*
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 mdfiles:
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 	cd mkdocs;\
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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 id="chart561c721f7a23" class="rChart morris"></p>
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+<div id="chart6a3238092255" class="rChart morris"></p>
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 </div>
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 <script type='text/javascript'>
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     var chartParams = {
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- "element": "chart561c721f7a23",
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+ "element": "chart6a3238092255",
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
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@@ -258,7 +258,7 @@ published using <code>ggtree</code> 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": "chart561c721f7a23",
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+"id": "chart6a3238092255",
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 "labels": "cites" 
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 },
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       chartType = "Bar"
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@@ -205,8 +205,6 @@
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             <li><a href="#projects-that-depend-on-ggtree"> Projects that depend on ggtree</a></li>
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             <li><a href="#feedback"> Feedback</a></li>
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-<img src="https://guangchuangyu.github.io/blog_images/biobabble.jpg" align="center" width="200"/>
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-<br>关注Y叔微信公众号biobabble
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     </ul>
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@@ -232,7 +230,8 @@
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 <!-- AddToAny END -->
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 <p><img src="https://raw.githubusercontent.com/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" /></p>
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-<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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+<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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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="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.10-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-1.7.9-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-12364/total-blue.svg?style=flat" /></a>
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@@ -248,6 +247,12 @@ GitHub</a>.</p>
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 <h2 id="authors"><i class="fa fa-user"></i> Authors</h2>
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 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The
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 University of Hong Kong.</p>
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+<p><a href="https://twitter.com/guangchuangyu"><i class="fa fa-twitter fa-3x"></i></a>
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+<a href="https://guangchuangyu.github.io/blog_images/biobabble.jpg"><i class="fa fa-wechat fa-3x"></i></a>
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+<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Guangchuang+Yu[Author+-+Full]"><i class="ai ai-pubmed ai-3x"></i></a>
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+<a href="https://scholar.google.com.hk/citations?user=DO5oG40AAAAJ&hl=en"><i class="ai ai-google-scholar ai-3x"></i></a>
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+<a href="https://orcid.org/0000-0002-6485-8781"><i class="ai ai-orcid ai-3x"></i></a>
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+<a href="https://impactstory.org/u/0000-0002-6485-8781"><i class="ai ai-impactstory ai-3x"></i></a></p>
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 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>
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 <p>Please cite the following article when using <code>ggtree</code>:</p>
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 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="doi" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>
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@@ -371,4 +376,4 @@ wiki page.</p>
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             </div>
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         </div>
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     </body>
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\ No newline at end of file
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@@ -2,7 +2,7 @@
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     "docs": [
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         {
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             "location": "/", 
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-            "text": "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data\n\n\n\n\n\n\n\n\n\n\n \n\n\n\n\n \n\n\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nThe \nggtree\n package extending the \nggplot2\n package. It based on\ngrammar of graphics and takes all the good parts of \nggplot2\n. \nggtree\n\nis designed for not only viewing phylogenetic tree but also displaying\nannotation data on the tree. \nggtree\n is released within the\n\nBioconductor\n project and\nthe source code is hosted on\n\n\nGitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The\nUniversity of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data. \nMethods in Ecology and\nEvolution\n. 2017, 8(1):28-36.\n\n\n Featured Articles\n\n\n\n\n Find out more on\n\n \nFeatured\nArticles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor\npage\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages,\nplease refer to the\n\nggtree-installation\n\nwiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to\n    be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore\n    the tree visually\n\n\n\n\n Find out details and examples on\n\n\n\nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n CRAN packages\n\n\n\n\nharrietr\n: Wrangle\n    Phylogenetic Distance Matrices and Other Utilities\n\n\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of\n    lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic\n    partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n:\n    Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n:\n    Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies\n    created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you have followed \nthe important guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and", 
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+            "text": "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data\n\n\n\n\n\n\n\n\n\n\n \n\n\n\n\n \n\n\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nThe \nggtree\n package extending the \nggplot2\n package. It based on\ngrammar of graphics and takes all the good parts of \nggplot2\n. \nggtree\n\nis designed for not only viewing phylogenetic tree but also displaying\nannotation data on the tree. \nggtree\n is released within the\n\nBioconductor\n project and\nthe source code is hosted on\n\n\nGitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The\nUniversity of Hong Kong.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data. \nMethods in Ecology and\nEvolution\n. 2017, 8(1):28-36.\n\n\n Featured Articles\n\n\n\n\n Find out more on\n\n \nFeatured\nArticles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor\npage\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages,\nplease refer to the\n\nggtree-installation\n\nwiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to\n    be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore\n    the tree visually\n\n\n\n\n Find out details and examples on\n\n\n\nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n CRAN packages\n\n\n\n\nharrietr\n: Wrangle\n    Phylogenetic Distance Matrices and Other Utilities\n\n\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of\n    lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic\n    partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n:\n    Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n:\n    Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies\n    created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you have followed \nthe important guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and", 
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             "title": "Home"
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         }, 
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         {
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         }, 
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         {
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             "location": "/featuredArticles/", 
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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\": \"chart561c721f7a23\",\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\":              7,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart561c721f7a23\",\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\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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+            "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\": \"chart6a3238092255\",\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\":              7,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart6a3238092255\",\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\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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             "title": "Featured Articles"
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         }, 
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.6.10-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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 [![develVersion](https://img.shields.io/badge/devel%20version-1.7.9-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
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 Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The
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 University of Hong Kong.
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+<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Guangchuang+Yu[Author+-+Full]"><i class="ai ai-pubmed ai-3x"></i></a>
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+<a href="https://scholar.google.com.hk/citations?user=DO5oG40AAAAJ&hl=en"><i class="ai ai-google-scholar ai-3x"></i></a>
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+<a href="https://orcid.org/0000-0002-6485-8781"><i class="ai ai-orcid ai-3x"></i></a>
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 <i class="fa fa-book"></i> Citation
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 -----------------------------------
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 `r badge_bioc_release("ggtree", "blue")`
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 Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.
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 ## <i class="fa fa-book"></i> Citation
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 Please cite the following article when using `ggtree`: