Browse code

treeio link

guangchuang yu authored on 03/01/2017 09:43:41
Showing22 changed files

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@@ -8,3 +8,5 @@ __init__.py
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 __pycache__
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 __init__.pyc
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+mkdocs/mysoftware
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+mkdocs/mysoftware
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new file mode 100644
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+[submodule "mkdocs/mysoftware"]
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+	path = mkdocs/mysoftware
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+	url = git@github.com:GuangchuangYu/mysoftware.git
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@@ -50,6 +50,8 @@ mkdocs: mdfiles
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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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+mysoftware:
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+	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware
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 mdfiles:
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 	cd mkdocs;\
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@@ -258,6 +258,7 @@
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>
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+<li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using treeio</a></li>
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 </ul>
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 <h3 id="tree-visualization"><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
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 <ul>
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   }  
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   </style>
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-<div id = 'chart3626c560073' class = 'rChart morris'></div>
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+<div id = 'chart39c868440081' class = 'rChart morris'></div>
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 <script type='text/javascript'>
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     var chartParams = {
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- "element": "chart3626c560073",
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+ "element": "chart39c868440081",
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
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 "pubid": "HtEfBTGE9r8C" 
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 } 
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 ],
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-"id": "chart3626c560073",
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+"id": "chart39c868440081",
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 "labels": "cites" 
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 },
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       chartType = "Bar"
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@@ -235,9 +235,9 @@
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 <p><img src="https://raw.githubusercontent.com/GuangchuangYu/ggtree/master/logo.png" 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><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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+<p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.6-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-1.7.5-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-19096/total-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-19152/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>
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@@ -247,7 +247,7 @@
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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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 <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat" /></a>
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-<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-283-blue.svg?style=flat" /></a></p>
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+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-284-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 package for visualization and annotation of phylogenetic trees with their covariates and other associated data. <strong><em>Methods in Ecology and Evolution</em></strong>. <em>accepted</em>.</p>
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 <h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
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 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
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@@ -67,7 +67,7 @@
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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 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\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\nxlim_tree: set x axis limits for only Tree panel\n\n\nadd layer to specific panel of facet_plot output\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": "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\nconvert graphic object to tree object using treeio\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\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\nxlim_tree: set x axis limits for only Tree panel\n\n\nadd layer to specific panel of facet_plot output\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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             "title": "Documentation"
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         }, 
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         {
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         }, 
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         {
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             "location": "/documentation/#data-manipulation", 
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-            "text": "subsetting data in ggtree  ggtree supports phylip tree format", 
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+            "text": "subsetting data in ggtree  ggtree supports phylip tree format  convert graphic object to tree object using treeio", 
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             "title": " Data manipulation"
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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 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\": \"chart3626c560073\",\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\": \"chart3626c560073\",\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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+            "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\": \"chart39c868440081\",\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\": \"chart39c868440081\",\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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             "title": "Featured Articles"
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         }, 
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         {
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/</loc>
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      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
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      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>
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      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>
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      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
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      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
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      <changefreq>daily</changefreq>
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      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
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      <changefreq>daily</changefreq>
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      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
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 + [subsetting data in ggtree](https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree)
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 + [ggtree supports phylip tree format](https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format)
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++ [convert graphic object to tree object using treeio](http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/)
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 ### <i class="fa fa-angle-double-right"></i> Tree visualization
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   }  
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   </style>
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 <script type='text/javascript'>
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     var chartParams = {
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 "width":            800,
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 "xkey": "year",
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 "pubid": "HtEfBTGE9r8C" 
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 } 
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 ],
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 "labels": "cites" 
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 },
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       chartType = "Bar"
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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-1.6.5-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.6-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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 [![develVersion](https://img.shields.io/badge/devel%20version-1.7.5-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
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-[![total](https://img.shields.io/badge/downloads-19096/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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@@ -40,7 +40,7 @@ Please cite the following article when using `ggtree`:
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 [![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
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 [![citation](https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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-[![Altmetric](https://img.shields.io/badge/Altmetric-283-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![Altmetric](https://img.shields.io/badge/Altmetric-284-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
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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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 + [subsetting data in ggtree](https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree)
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 + [ggtree supports phylip tree format](https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format)
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++ [convert graphic object to tree object using treeio](http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/)
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 ### <i class="fa fa-angle-double-right"></i> Tree visualization
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