Browse code

update site

guangchuang yu authored on 20/07/2017 10:04:35
Showing9 changed files

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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="chart90c7785d73f" class="rChart morris"></p>
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+<div id="chart41ca67213e2b" 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": "chart90c7785d73f",
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+ "element": "chart41ca67213e2b",
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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": "chart90c7785d73f",
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+"id": "chart41ca67213e2b",
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 "labels": "cites" 
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 },
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       chartType = "Bar"
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@@ -228,6 +228,11 @@
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 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg" /></p>
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 <hr />
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 <ul>
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+<li><a href="https://doi.org/10.3389/fmicb.2017.00456">https://doi.org/10.3389/fmicb.2017.00456</a></li>
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+</ul>
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+<p><img alt="" src="http://www.frontiersin.org/files/Articles/220056/fmicb-08-00456-HTML-r1/image_m/fmicb-08-00456-g002.jpg" /></p>
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+<hr />
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+<ul>
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 <li><a href="http://dx.doi.org/10.1186/s40168-017-0232-3">http://dx.doi.org/10.1186/s40168-017-0232-3</a></li>
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 </ul>
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 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif" /></p>
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@@ -234,7 +234,7 @@
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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-1.8.1-blue.svg?style=flat" /></a>
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 <a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.2-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-17163/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-17269/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-885/month-blue.svg?style=flat" /></a></p>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on
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 grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>
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@@ -217,7 +217,7 @@
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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\": \"chart90c7785d73f\",\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\":             25,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart90c7785d73f\",\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\": \"chart41ca67213e2b\",\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\":             25,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart41ca67213e2b\",\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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             "title": "Featured Articles"
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         }, 
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         {
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@@ -232,12 +232,12 @@
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         }, 
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         {
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             "location": "/gallery/", 
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-            "text": "Journal Articles\n\n\n\n\nhttp://dx.doi.org/10.3389/fmicb.2017.00543\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1186/s40168-017-0232-3\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1111/2041-210X.12628\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1128/AEM.02307-16\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\n\n\n Tweets\n\n\n\n\n\nAdaptive radiation of\n\n\\#Darwin\n's\nfinches showing\n\n\\#genotypic\n\nand\n\n\\#morphometric\n\nevolution. Good excuse to practice with\n\n\\#ggtree\n\n\n@guangchuangyu\n\n\npic.twitter.com/JJZ3Yje58s\n\n\n\n\u2014 Will Harvey (@_wharvey)\n\nFebruary\n15, 2017\n\n\n\n\n\n\n\n\nam quite liking\n\n\\#ggtree\n\n\n\\#rstats\n\n\n\\#ggplot\n\n\npic.twitter.com/hvywS2z4ps\n\n\n\n\u2014 Nicholas E Ilott (@IlottNick)\n\nOctober\n19, 2016\n\n\n\n\n\n\n\n\nCapital G, a reproducible logo produced by\n\n\\#ggtree\n\n\n\\#dataviz\n\n\n\\#rstats\n\n\n\\#ggplot2\n\n\npic.twitter.com/lJDcgfxAEh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nOctober\n13, 2016\n\n\n\n\n\n\n\n\nassociate tree with different type of data by\n\n\\#ggtree\n\n\nhttps://t.co/6w755VWytZ\n\n\npic.twitter.com/K8WViEi13E\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nSeptember\n7, 2016\n\n\n\n\n\n\n\n\nhow about using emoji to label host species in phylogenetic tree?\n\n\\#rstats\n\n\n\\#visualization\n\n\n\\#ggtree\n\n\n\\#emojifont\n\n\npic.twitter.com/MRKQvNNAUh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMarch\n11, 2016\n\n\n\n\n\n\n\n\n\n\\#phylomoji\n\nwith \n\\#ggtree\n\n\npic.twitter.com/yMUtm1jYF9\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nNovember\n19, 2015\n\n\n\n\n\n\n\n\nmultiple sequence alignment with\n\n\\#phylogenetic\n\ntree via\n\n\\#rstats\n pkg\n\n\\#ggtree\n.\n\npic.twitter.com/6CY57dLdeb\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n22, 2015\n\n\n\n\n\n\n\n\n\n\\#comictree\n\nvia \n\\#ggtree\n\nand \n\\#comicR\n\nin \n\\#rstats\n\n\npic.twitter.com/zwCuOQ49bq\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n15, 2015", 
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+            "text": "Journal Articles\n\n\n\n\nhttp://dx.doi.org/10.3389/fmicb.2017.00543\n\n\n\n\n\n\n\n\n\n\nhttps://doi.org/10.3389/fmicb.2017.00456\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1186/s40168-017-0232-3\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1111/2041-210X.12628\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1128/AEM.02307-16\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\n\n\n Tweets\n\n\n\n\n\nAdaptive radiation of\n\n\\#Darwin\n's\nfinches showing\n\n\\#genotypic\n\nand\n\n\\#morphometric\n\nevolution. Good excuse to practice with\n\n\\#ggtree\n\n\n@guangchuangyu\n\n\npic.twitter.com/JJZ3Yje58s\n\n\n\n\u2014 Will Harvey (@_wharvey)\n\nFebruary\n15, 2017\n\n\n\n\n\n\n\n\nam quite liking\n\n\\#ggtree\n\n\n\\#rstats\n\n\n\\#ggplot\n\n\npic.twitter.com/hvywS2z4ps\n\n\n\n\u2014 Nicholas E Ilott (@IlottNick)\n\nOctober\n19, 2016\n\n\n\n\n\n\n\n\nCapital G, a reproducible logo produced by\n\n\\#ggtree\n\n\n\\#dataviz\n\n\n\\#rstats\n\n\n\\#ggplot2\n\n\npic.twitter.com/lJDcgfxAEh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nOctober\n13, 2016\n\n\n\n\n\n\n\n\nassociate tree with different type of data by\n\n\\#ggtree\n\n\nhttps://t.co/6w755VWytZ\n\n\npic.twitter.com/K8WViEi13E\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nSeptember\n7, 2016\n\n\n\n\n\n\n\n\nhow about using emoji to label host species in phylogenetic tree?\n\n\\#rstats\n\n\n\\#visualization\n\n\n\\#ggtree\n\n\n\\#emojifont\n\n\npic.twitter.com/MRKQvNNAUh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMarch\n11, 2016\n\n\n\n\n\n\n\n\n\n\\#phylomoji\n\nwith \n\\#ggtree\n\n\npic.twitter.com/yMUtm1jYF9\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nNovember\n19, 2015\n\n\n\n\n\n\n\n\nmultiple sequence alignment with\n\n\\#phylogenetic\n\ntree via\n\n\\#rstats\n pkg\n\n\\#ggtree\n.\n\npic.twitter.com/6CY57dLdeb\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n22, 2015\n\n\n\n\n\n\n\n\n\n\\#comictree\n\nvia \n\\#ggtree\n\nand \n\\#comicR\n\nin \n\\#rstats\n\n\npic.twitter.com/zwCuOQ49bq\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n15, 2015", 
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             "title": "Gallery"
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         }, 
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         {
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             "location": "/gallery/#journal-articles", 
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-            "text": "http://dx.doi.org/10.3389/fmicb.2017.00543      http://dx.doi.org/10.1186/s40168-017-0232-3      http://dx.doi.org/10.1111/2041-210X.12628      http://dx.doi.org/10.1128/AEM.02307-16      http://dx.doi.org/10.3389%2Ffcimb.2016.00036      http://dx.doi.org/10.1016/j.meegid.2015.12.006", 
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+            "text": "http://dx.doi.org/10.3389/fmicb.2017.00543      https://doi.org/10.3389/fmicb.2017.00456      http://dx.doi.org/10.1186/s40168-017-0232-3      http://dx.doi.org/10.1111/2041-210X.12628      http://dx.doi.org/10.1128/AEM.02307-16      http://dx.doi.org/10.3389%2Ffcimb.2016.00036      http://dx.doi.org/10.1016/j.meegid.2015.12.006", 
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             "title": " Journal 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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-     <lastmod>2017-07-17</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>
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      <changefreq>daily</changefreq>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/gallery/</loc>
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-     <lastmod>2017-07-17</lastmod>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>
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      <changefreq>daily</changefreq>
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     </url>
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@@ -39,13 +39,13 @@ published using `ggtree` and your publication will be featured here.
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     height: 300px;
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   }  
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   </style>
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-<div id="chart90c7785d73f" class="rChart morris">
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+<div id="chart41ca67213e2b" class="rChart morris">
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 </div>
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 <script type='text/javascript'>
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     var chartParams = {
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
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@@ -64,7 +64,7 @@ published using `ggtree` and your publication will be featured here.
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 "pubid": "HtEfBTGE9r8C" 
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 } 
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 ],
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-"id": "chart90c7785d73f",
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+"id": "chart41ca67213e2b",
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 "labels": "cites" 
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 },
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       chartType = "Bar"
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 ------------------------------------------------------------------------
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+-   <https://doi.org/10.3389/fmicb.2017.00456>
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+
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+![](http://www.frontiersin.org/files/Articles/220056/fmicb-08-00456-HTML-r1/image_m/fmicb-08-00456-g002.jpg)
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+
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+------------------------------------------------------------------------
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+
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 -   <http://dx.doi.org/10.1186/s40168-017-0232-3>
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 ![](https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif)
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@@ -29,7 +29,7 @@ ggtree: visualization and annotation of phylogenetic trees
29 29
 
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 [![](https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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 [![](https://img.shields.io/badge/devel%20version-1.9.2-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
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-[![](https://img.shields.io/badge/download-17163/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-17269/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
34 34
 
35 35
 The `ggtree` package extending the *ggplot2* package. It based on
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 ----
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++ <https://doi.org/10.3389/fmicb.2017.00456>
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+![](http://www.frontiersin.org/files/Articles/220056/fmicb-08-00456-HTML-r1/image_m/fmicb-08-00456-g002.jpg)
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+
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+----
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+
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 + <http://dx.doi.org/10.1186/s40168-017-0232-3>
28 34
 
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 ![](https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif)