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Packaged: 2014-12-03 08:16:14 UTC; root |
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biocViews: Alignment, Annotation, Clustering, DataImport, |
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MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization |
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-RoxygenNote: 6.0.1 |
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@@ -69,7 +69,7 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali |
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### Citation |
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`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")` |
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-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "green")` |
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```{r echo=F, comment=NA} |
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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://bioconductor.org/packages/ggtree) [](https://github.com/guangchuangyu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
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+[](https://bioconductor.org/packages/ggtree) [](https://github.com/guangchuangyu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
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-[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
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+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
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[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [](https://travis-ci.org/GuangchuangYu/ggtree) [](https://ci.appveyor.com/project/GuangchuangYu/ggtree) |
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### Citation |
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-[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004) |
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+[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
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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://github.com/GuangchuangYu/featured_img">Let us know</a> if you have |
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published using <code>ggtree</code> and your publication will be featured here.</p> |
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-<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a> |
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-<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004"><img alt="" src="https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection--blue.svg?style=flat" /></a></p> |
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+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a></p> |
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<p><link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css> |
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<script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script> |
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<script src='https://guangchuangyu.github.io/resume/css/raphael-min.js' type='text/javascript'></script> |
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height: 300px; |
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}<br /> |
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</style> |
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"pubid": "HtEfBTGE9r8C" |
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} |
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], |
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}, |
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chartType = "Bar" |
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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="" src="https://img.shields.io/badge/release%20version-1.8.0-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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@@ -257,8 +257,7 @@ University of Hong Kong.</p> |
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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="" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> |
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<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-347-blue.svg?style=flat" /></a> |
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-<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004"><img alt="" src="https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection--blue.svg?style=flat" /></a></p> |
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<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R |
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package for visualization and annotation of phylogenetic trees with |
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their covariates and other associated data. <strong><em>Methods in Ecology and |
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"docs": [ |
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{ |
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"location": "/", |
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- "text": "ggtree: visualization and annotation of phylogenetic trees\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\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\nLymphoSeq\n:\n Analyze high-throughput sequencing of T and B cell receptors\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", |
|
5 |
+ "text": "ggtree: visualization and annotation of phylogenetic trees\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\nLymphoSeq\n:\n Analyze high-throughput sequencing of T and B cell receptors\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": "/#citation", |
20 |
- "text": "Please cite the following article when using ggtree : G Yu , DK Smith, H Zhu, Y Guan, TTY Lam * . ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data. Methods in Ecology and\nEvolution . 2017, 8(1):28-36.", |
|
20 |
+ "text": "Please cite the following article when using ggtree : G Yu , DK Smith, H Zhu, Y Guan, TTY Lam * . ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data. Methods in Ecology and\nEvolution . 2017, 8(1):28-36.", |
|
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"title": " Citation" |
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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\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\": \"chartffa45753c39\",\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\": \"chartffa45753c39\",\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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+ "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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{ |
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@@ -28,7 +28,7 @@ |
28 | 28 |
|
29 | 29 |
<url> |
30 | 30 |
<loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc> |
31 |
- <lastmod>2017-04-27</lastmod> |
|
31 |
+ <lastmod>2017-04-28</lastmod> |
|
32 | 32 |
<changefreq>daily</changefreq> |
33 | 33 |
</url> |
34 | 34 |
|
... | ... |
@@ -36,7 +36,7 @@ |
36 | 36 |
|
37 | 37 |
<url> |
38 | 38 |
<loc>https://guangchuangyu.github.io/ggtree/gallery/</loc> |
39 |
- <lastmod>2017-04-27</lastmod> |
|
39 |
+ <lastmod>2017-04-28</lastmod> |
|
40 | 40 |
<changefreq>daily</changefreq> |
41 | 41 |
</url> |
42 | 42 |
|
... | ... |
@@ -45,55 +45,55 @@ |
45 | 45 |
|
46 | 46 |
<url> |
47 | 47 |
<loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc> |
48 |
- <lastmod>2017-04-27</lastmod> |
|
48 |
+ <lastmod>2017-04-28</lastmod> |
|
49 | 49 |
<changefreq>daily</changefreq> |
50 | 50 |
</url> |
51 | 51 |
|
52 | 52 |
<url> |
53 | 53 |
<loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc> |
54 |
- <lastmod>2017-04-27</lastmod> |
|
54 |
+ <lastmod>2017-04-28</lastmod> |
|
55 | 55 |
<changefreq>daily</changefreq> |
56 | 56 |
</url> |
57 | 57 |
|
58 | 58 |
<url> |
59 | 59 |
<loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc> |
60 |
- <lastmod>2017-04-27</lastmod> |
|
60 |
+ <lastmod>2017-04-28</lastmod> |
|
61 | 61 |
<changefreq>daily</changefreq> |
62 | 62 |
</url> |
63 | 63 |
|
64 | 64 |
<url> |
65 | 65 |
<loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc> |
66 |
- <lastmod>2017-04-27</lastmod> |
|
66 |
+ <lastmod>2017-04-28</lastmod> |
|
67 | 67 |
<changefreq>daily</changefreq> |
68 | 68 |
</url> |
69 | 69 |
|
70 | 70 |
<url> |
71 | 71 |
<loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc> |
72 |
- <lastmod>2017-04-27</lastmod> |
|
72 |
+ <lastmod>2017-04-28</lastmod> |
|
73 | 73 |
<changefreq>daily</changefreq> |
74 | 74 |
</url> |
75 | 75 |
|
76 | 76 |
<url> |
77 | 77 |
<loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc> |
78 |
- <lastmod>2017-04-27</lastmod> |
|
78 |
+ <lastmod>2017-04-28</lastmod> |
|
79 | 79 |
<changefreq>daily</changefreq> |
80 | 80 |
</url> |
81 | 81 |
|
82 | 82 |
<url> |
83 | 83 |
<loc>https://guangchuangyu.github.io/ggtree/meshes/</loc> |
84 |
- <lastmod>2017-04-27</lastmod> |
|
84 |
+ <lastmod>2017-04-28</lastmod> |
|
85 | 85 |
<changefreq>daily</changefreq> |
86 | 86 |
</url> |
87 | 87 |
|
88 | 88 |
<url> |
89 | 89 |
<loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc> |
90 |
- <lastmod>2017-04-27</lastmod> |
|
90 |
+ <lastmod>2017-04-28</lastmod> |
|
91 | 91 |
<changefreq>daily</changefreq> |
92 | 92 |
</url> |
93 | 93 |
|
94 | 94 |
<url> |
95 | 95 |
<loc>https://guangchuangyu.github.io/ggtree/treeio/</loc> |
96 |
- <lastmod>2017-04-27</lastmod> |
|
96 |
+ <lastmod>2017-04-28</lastmod> |
|
97 | 97 |
<changefreq>daily</changefreq> |
98 | 98 |
</url> |
99 | 99 |
|
... | ... |
@@ -30,10 +30,11 @@ highlights the two direct descendant clades of an internal node |
30 | 30 |
Particularly useful when studying neighboring clades. Note that balances that |
31 | 31 |
correspond to multichotomies will not be displayed. |
32 | 32 |
} |
33 |
+\author{ |
|
34 |
+Justin Silverman |
|
35 |
+} |
|
33 | 36 |
\references{ |
34 | 37 |
J. Silverman, et al. \emph{A phylogenetic transform enhances |
35 | 38 |
analysis of compositional microbiota data}. (in preparation) |
36 | 39 |
} |
37 |
-\author{ |
|
38 |
-Justin Silverman |
|
39 |
-} |
|
40 |
+ |
... | ... |
@@ -19,9 +19,10 @@ tip label layer |
19 | 19 |
\description{ |
20 | 20 |
add tip label for circular layout |
21 | 21 |
} |
22 |
-\references{ |
|
23 |
-\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0} |
|
24 |
-} |
|
25 | 22 |
\author{ |
26 | 23 |
Guangchuang Yu |
27 | 24 |
} |
25 |
+\references{ |
|
26 |
+\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0} |
|
27 |
+} |
|
28 |
+ |
... | ... |
@@ -18,3 +18,4 @@ named list of subtrees with the root id of subtree and list of node id's making |
18 | 18 |
Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree) |
19 | 19 |
return named list of subtrees with list name as starting node id. |
20 | 20 |
} |
21 |
+ |
... | ... |
@@ -3,9 +3,8 @@ |
3 | 3 |
\docType{package} |
4 | 4 |
\name{ggtree} |
5 | 5 |
\alias{ggtree} |
6 |
-\alias{package-ggtree} |
|
7 | 6 |
\alias{ggtree-package} |
8 |
-\alias{ggtree} |
|
7 |
+\alias{package-ggtree} |
|
9 | 8 |
\title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics |
10 | 9 |
\code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.} |
11 | 10 |
\usage{ |
... | ... |
@@ -58,3 +57,4 @@ ggtree(tr) |
58 | 57 |
\author{ |
59 | 58 |
Yu Guangchuang |
60 | 59 |
} |
60 |
+ |
... | ... |
@@ -3,13 +3,12 @@ |
3 | 3 |
\docType{methods} |
4 | 4 |
\name{gzoom} |
5 | 5 |
\alias{gzoom} |
6 |
-\alias{gzoom} |
|
7 |
-\alias{gzoom,ggtree-method} |
|
8 | 6 |
\alias{gzoom,beast-method} |
9 | 7 |
\alias{gzoom,codeml-method} |
10 |
-\alias{gzoom,treedata-method} |
|
8 |
+\alias{gzoom,ggtree-method} |
|
11 | 9 |
\alias{gzoom,paml_rst-method} |
12 | 10 |
\alias{gzoom,phylo-method} |
11 |
+\alias{gzoom,treedata-method} |
|
13 | 12 |
\title{gzoom method} |
14 | 13 |
\usage{ |
15 | 14 |
gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...) |
... | ... |
@@ -51,3 +50,4 @@ figure |
51 | 50 |
\description{ |
52 | 51 |
zoom selected subtree |
53 | 52 |
} |
53 |
+ |
... | ... |
@@ -4,9 +4,9 @@ |
4 | 4 |
\name{scale_color} |
5 | 5 |
\alias{scale_color} |
6 | 6 |
\alias{scale_color,beast-method} |
7 |
-\alias{scale_color,treedata-method} |
|
8 | 7 |
\alias{scale_color,paml_rst-method} |
9 | 8 |
\alias{scale_color,phylo-method} |
9 |
+\alias{scale_color,treedata-method} |
|
10 | 10 |
\title{scale_color method} |
11 | 11 |
\usage{ |
12 | 12 |
scale_color(object, by, ...) |
... | ... |
@@ -33,3 +33,4 @@ color vector |
33 | 33 |
\description{ |
34 | 34 |
scale color by a numerical tree attribute |
35 | 35 |
} |
36 |
+ |
... | ... |
@@ -25,7 +25,6 @@ output: |
25 | 25 |
published using `ggtree` and your publication will be featured here. |
26 | 26 |
|
27 | 27 |
[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
28 |
-[](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004) |
|
29 | 28 |
|
30 | 29 |
<link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css> |
31 | 30 |
<script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script> |
... | ... |
@@ -40,13 +39,13 @@ published using `ggtree` and your publication will be featured here. |
40 | 39 |
height: 300px; |
41 | 40 |
} |
42 | 41 |
</style> |
43 |
-<div id="chartffa45753c39" class="rChart morris"> |
|
42 |
+<div id="chartba8442a5d90" class="rChart morris"> |
|
44 | 43 |
|
45 | 44 |
</div> |
46 | 45 |
|
47 | 46 |
<script type='text/javascript'> |
48 | 47 |
var chartParams = { |
49 |
- "element": "chartffa45753c39", |
|
48 |
+ "element": "chartba8442a5d90", |
|
50 | 49 |
"width": 800, |
51 | 50 |
"height": 400, |
52 | 51 |
"xkey": "year", |
... | ... |
@@ -65,7 +64,7 @@ published using `ggtree` and your publication will be featured here. |
65 | 64 |
"pubid": "HtEfBTGE9r8C" |
66 | 65 |
} |
67 | 66 |
], |
68 |
-"id": "chartffa45753c39", |
|
67 |
+"id": "chartba8442a5d90", |
|
69 | 68 |
"labels": "cites" |
70 | 69 |
}, |
71 | 70 |
chartType = "Bar" |
... | ... |
@@ -28,7 +28,7 @@ ggtree: visualization and annotation of phylogenetic trees |
28 | 28 |
<link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"> |
29 | 29 |
|
30 | 30 |
[](https://bioconductor.org/packages/ggtree) |
31 |
-[](https://github.com/guangchuangyu/ggtree) |
|
31 |
+[](https://github.com/guangchuangyu/ggtree) |
|
32 | 32 |
[](https://bioconductor.org/packages/stats/bioc/ggtree) |
33 | 33 |
[](https://bioconductor.org/packages/stats/bioc/ggtree) |
34 | 34 |
|
... | ... |
@@ -62,7 +62,6 @@ Please cite the following article when using `ggtree`: |
62 | 62 |
[](http://dx.doi.org/10.1111/2041-210X.12628) |
63 | 63 |
[](https://www.altmetric.com/details/10533079) |
64 | 64 |
[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
65 |
-[](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004) |
|
66 | 65 |
|
67 | 66 |
**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R |
68 | 67 |
package for visualization and annotation of phylogenetic trees with |
... | ... |
@@ -16,7 +16,7 @@ html_preview: false |
16 | 16 |
|
17 | 17 |
|
18 | 18 |
`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "blue")` |
19 |
-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "blue")` |
|
19 |
+ |
|
20 | 20 |
|
21 | 21 |
`r article_citation_trend("HtEfBTGE9r8C")` |
22 | 22 |
|
... | ... |
@@ -51,7 +51,7 @@ Please cite the following article when using `ggtree`: |
51 | 51 |
`r badge_doi("10.1111/2041-210X.12628", "blue")` |
52 | 52 |
`r badge_altmetric("10533079", "blue")` |
53 | 53 |
`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "blue")` |
54 |
-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "blue")` |
|
54 |
+ |
|
55 | 55 |
|
56 | 56 |
|
57 | 57 |
__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*__. 2017, 8(1):28-36. |