1. ggtree
  2. Commit bd105c7be00972f6c698d0057baac076ed17c836
Browse code

new citations

GuangchuangYu authored on 12/02/2017 11:23:54
Showing 11 changed files
README.md
History View file @ bd105c7b
... ... 
@@ -2,9 +2,9 @@
2 2 
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
3 3 
 ===========================================================================================================================
4 4
5 
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.7-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-20046/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1177/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
5 
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.9-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.7-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-21539/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
6 6
7 
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--01--21-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
7 
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--02--12-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
8 8
9 9 
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
10 10
... ... 
@@ -18,7 +18,7 @@ Please cite the following article when using `ggtree`:
18 18
19 19 
 **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.
20 20
21 
-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-2-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-309-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
21 
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-5-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-346-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
22 22
23 23 
 ------------------------------------------------------------------------
24 24
... ... 
@@ -31,50 +31,50 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
31 31
32 32 
 ### Citation
33 33
34 
-[![citation](https://img.shields.io/badge/cited%20by-2-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
34 
+[![citation](https://img.shields.io/badge/cited%20by-5-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
35 35
36 36 
         +-+---------+---------+---------+---------+--------+---+
37 
+      4 +                                                  *   +
37 38 
         |                                                      |
39 
+    3.5 +                                                      +
38 40 
         |                                                      |
39 
-    1.2 +                                                      +
41 
+      3 +                                                      +
40 42 
         |                                                      |
43 
+    2.5 +                                                      +
44 
+      2 +                                                      +
41 45 
         |                                                      |
42 
-      1 + *                                                *   +
46 
+    1.5 +                                                      +
43 47 
         |                                                      |
44 
-        |                                                      |
45 
-        |                                                      |
46 
-    0.8 +                                                      +
47 
-        |                                                      |
48 
-        |                                                      |
49 
-    0.6 +-+---------+---------+---------+---------+--------+---+
48 
+      1 + *                                                    +
49 
+        +-+---------+---------+---------+---------+--------+---+
50 50 
         2016     2016.2    2016.4    2016.6    2016.8    2017
51 51
52 52 
 ### Download stats
53 53
54 
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-20046/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1177/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
54 
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-21539/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
55 55
56 
-         ++---------------------+---------------------+---------------------+---------------------+----+
57 
-         |                                                                                    *        |
56 
+         ++--------------------+--------------------+--------------------+--------------------+--------+
57 
+         |                                                                                        *    |
58 
+         |                                                                                 *           |
58 59 
          |                                                                                             |
59 
-         |                                                                            *                |
60 
-         |                                                                                *            |
61 
-    1500 +                                                                                             +
60 
+         |                                                                         *   *               |
62 61 
          |                                                                                             |
62 
+    1500 +                                                                                             +
63 63 
          |                                                                                             |
64 
-         |                                                                 *                           |
65 
-         |                                                      *                  *              *    |
66 
-         |                                                              *      *                       |
67 
-    1000 +                                                          *                                  +
64 
+         |                                                               *                             |
65 
+         |                                                                                    *        |
66 
+         |                                                    *             *   *                      |
67 
+    1000 +                                                        *  *                                 +
68 68 
          |                                                                                             |
69 
-         |                                        *      *                                             |
70 
-         |                                           *       *                                         |
71 
-         |                                *   *                                                        |
69 
+         |                                      *      *                                               |
70 
+         |                                                 *                                           |
71 
+         |                               *   *      *                                                  |
72 72 
          |                                                                                             |
73 
-     500 +                             *                                                               +
74 
-         |                     *   *                                                                   |
75 
-         |                  *                                                                          |
73 
+     500 +                            *                                                                +
74 
+         |                     *  *                                                                    |
75 
+         |                 *                                                                           |
76 76 
          |              *                                                                              |
77 77 
          |                                                                                             |
78 
-       0 +   *   *  *                                                                                  +
79 
-         ++---------------------+---------------------+---------------------+---------------------+----+
80 
-        2015                 2015.5                 2016                 2016.5                 2017
78 
+       0 +   *  *   *                                                                                  +
79 
+         ++--------------------+--------------------+--------------------+--------------------+--------+
80 
+        2015                2015.5                2016                2016.5                2017
docs/featuredArticles/index.html
History View file @ bd105c7b
... ... 
@@ -220,7 +220,7 @@
220 220
221 221 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
222 222 
 <p><a href="https://github.com/GuangchuangYu/featured_img">Let us know</a> if you have published using <code>ggtree</code> and your publication will be featured here.</p>
223 
-<p><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-2-blue.svg?style=flat" /></a></p>
223 
+<p><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-5-blue.svg?style=flat" /></a></p>
224 224 
 <p><link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>
225 225 
 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>
226 226 
 <script src='https://guangchuangyu.github.io/resume/css/raphael-min.js' type='text/javascript'></script>
... ... 
@@ -235,11 +235,11 @@
235 235 
   }
236 236 
   </style>
237 237
238 
-<div id = 'chart3bd26687fb99' class = 'rChart morris'></div>
238 
+<div id = 'chart3a016a995a42' class = 'rChart morris'></div>
239 239
240 240 
 <script type='text/javascript'>
241 241 
     var chartParams = {
242 
- "element": "chart3bd26687fb99",
242 
+ "element": "chart3a016a995a42",
243 243 
 "width":            800,
244 244 
 "height":            400,
245 245 
 "xkey": "year",
... ... 
@@ -254,11 +254,11 @@
254 254 
 },
255 255 
 {
256 256 
  "year": 2017,
257 
-"cites":              1,
257 
+"cites":              4,
258 258 
 "pubid": "HtEfBTGE9r8C"
259 259 
 }
260 260 
 ],
261 
-"id": "chart3bd26687fb99",
261 
+"id": "chart3a016a995a42",
262 262 
 "labels": "cites"
263 263 
 },
264 264 
       chartType = "Bar"
... ... 
@@ -267,6 +267,7 @@
267 267
268 268 
 <h2 id="2017"><i class="fa fa-calendar"></i> 2017</h2>
269 269 
 <p><a href="http://dx.doi.org/10.1073/pnas.1617959114">Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging</a>. <strong><em>PNAS</em></strong>, 2017</p>
270 
+<p><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3">Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in <em>Bacteroides coprocola</em></a>. <strong><em>Microbiome</em></strong>, 2017, 5:15</p>
270 271 
 <h2 id="2016"><i class="fa fa-calendar"></i> 2016</h2>
271 272 
 <p><a href="http://aem.asm.org/content/82/22/6788.short">Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine</a>. <strong><em>Applied and Environmental Microbiology</em></strong>. 2016,82(22):6788-6798. </p></div>
272 273 
         </div>
docs/gallery/index.html
History View file @ bd105c7b
... ... 
@@ -213,7 +213,11 @@
213 213 
 <!-- AddToAny END -->
214 214
215 215 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
216 
-<p><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-2-blue.svg?style=flat" /></a></p>
216 
+<p><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-5-blue.svg?style=flat" /></a></p>
217 
+<ul>
218 
+<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>
219 
+</ul>
220 
+<p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif" /></p>
217 221 
 <ul>
218 222 
 <li><a href="http://dx.doi.org/10.1111/2041-210X.12628">http://dx.doi.org/10.1111/2041-210X.12628</a></li>
219 223 
 </ul>
docs/index.html
History View file @ bd105c7b
... ... 
@@ -247,10 +247,10 @@
247 247
248 248 
 <p><img src="https://raw.githubusercontent.com/GuangchuangYu/ggtree/master/logo.png" align="right" /></p>
249 249 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
250 
-<p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.7-blue.svg?style=flat" /></a>
250 
+<p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.9-blue.svg?style=flat" /></a>
251 251 
 <a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.7-blue.svg?style=flat" /></a>
252 
-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-20046/total-blue.svg?style=flat" /></a>
253 
-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1177/month-blue.svg?style=flat" /></a></p>
252 
+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-21539/total-blue.svg?style=flat" /></a>
253 
+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat" /></a></p>
254 254 
 <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.
255 255 
 <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>
256 256 
 <h2 id="authors"><i class="fa fa-user"></i> Authors</h2>
... ... 
@@ -258,8 +258,8 @@
258 258 
 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>
259 259 
 <p>Please cite the following article when using <code>ggtree</code>:</p>
260 260 
 <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>
261 
-<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-2-blue.svg?style=flat" /></a>
262 
-<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-309-blue.svg?style=flat" /></a></p>
261 
+<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-5-blue.svg?style=flat" /></a>
262 
+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat" /></a></p>
263 263 
 <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>. 2017, 8(1):28-36.</p>
264 264 
 <h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
265 265 
 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
docs/mkdocs/search_index.json
History View file @ bd105c7b
... ... 
@@ -207,12 +207,12 @@
207 207 
         },
208 208 
         {
209 209 
             "location": "/featuredArticles/",
210 
-            "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\": \"chart3bd26687fb99\",\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\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart3bd26687fb99\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging\n. \nPNAS\n, 2017\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine\n. \nApplied and Environmental Microbiology\n. 2016,82(22):6788-6798.",
210 
+            "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\": \"chart3a016a995a42\",\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\":              4,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart3a016a995a42\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging\n. \nPNAS\n, 2017\n\n\nGut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in \nBacteroides coprocola\n. \nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine\n. \nApplied and Environmental Microbiology\n. 2016,82(22):6788-6798.",
211 211 
             "title": "Featured Articles"
212 212 
         },
213 213 
         {
214 214 
             "location": "/featuredArticles/#2017",
215 
-            "text": "Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging .  PNAS , 2017",
215 
+            "text": "Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging .  PNAS , 2017  Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in  Bacteroides coprocola .  Microbiome , 2017, 5:15",
216 216 
             "title": " 2017"
217 217 
         },
218 218 
         {
... ... 
@@ -222,7 +222,7 @@
222 222 
         },
223 223 
         {
224 224 
             "location": "/gallery/",
225 
-            "text": "http://dx.doi.org/10.1111/2041-210X.12628\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\nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006",
225 
+            "text": "http://dx.doi.org/10.1186/s40168-017-0232-3\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\nhttp://dx.doi.org/10.1128/AEM.02307-16\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\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006",
226 226 
             "title": "Gallery"
227 227 
         },
228 228 
         {
docs/sitemap.xml
History View file @ bd105c7b
... ... 
@@ -4,7 +4,7 @@
4 4
5 5 
     <url>
6 6 
      <loc>https://guangchuangyu.github.io/ggtree/</loc>
7 
-     <lastmod>2017-01-21</lastmod>
7 
+     <lastmod>2017-02-12</lastmod>
8 8 
      <changefreq>daily</changefreq>
9 9 
     </url>
10 10
... ... 
@@ -12,7 +12,7 @@
12 12
13 13 
     <url>
14 14 
      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
15 
-     <lastmod>2017-01-21</lastmod>
15 
+     <lastmod>2017-02-12</lastmod>
16 16 
      <changefreq>daily</changefreq>
17 17 
     </url>
18 18
... ... 
@@ -20,7 +20,7 @@
20 20
21 21 
     <url>
22 22 
      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>
23 
-     <lastmod>2017-01-21</lastmod>
23 
+     <lastmod>2017-02-12</lastmod>
24 24 
      <changefreq>daily</changefreq>
25 25 
     </url>
26 26
... ... 
@@ -28,7 +28,7 @@
28 28
29 29 
     <url>
30 30 
      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>
31 
-     <lastmod>2017-01-21</lastmod>
31 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
39 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
48 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
54 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
60 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
66 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
72 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
78 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
84 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
90 
+     <lastmod>2017-02-12</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>2017-01-21</lastmod>
96 
+     <lastmod>2017-02-12</lastmod>
97 97 
      <changefreq>daily</changefreq>
98 98 
     </url>
99 99
mkdocs/docs/featuredArticles.md
History View file @ bd105c7b
... ... 
@@ -18,7 +18,7 @@
18 18
19 19 
 [Let us know](https://github.com/GuangchuangYu/featured_img) if you have published using `ggtree` and your publication will be featured here.
20 20
21 
-[![citation](https://img.shields.io/badge/cited%20by-2-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
21 
+[![citation](https://img.shields.io/badge/cited%20by-5-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
22 22
23 23 
 <link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>
24 24 
 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>
... ... 
@@ -36,10 +36,10 @@
36 36 
   }
37 37 
   </style>
38 38
39 
-<div id = 'chart3bd26687fb99' class = 'rChart morris'></div>
39 
+<div id = 'chart3a016a995a42' class = 'rChart morris'></div>
40 40 
 <script type='text/javascript'>
41 41 
     var chartParams = {
42 
- "element": "chart3bd26687fb99",
42 
+ "element": "chart3a016a995a42",
43 43 
 "width":            800,
44 44 
 "height":            400,
45 45 
 "xkey": "year",
... ... 
@@ -54,11 +54,11 @@
54 54 
 },
55 55 
 {
56 56 
  "year": 2017,
57 
-"cites":              1,
57 
+"cites":              4,
58 58 
 "pubid": "HtEfBTGE9r8C"
59 59 
 }
60 60 
 ],
61 
-"id": "chart3bd26687fb99",
61 
+"id": "chart3a016a995a42",
62 62 
 "labels": "cites"
63 63 
 },
64 64 
       chartType = "Bar"
... ... 
@@ -70,6 +70,8 @@
70 70
71 71 
 [Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging](http://dx.doi.org/10.1073/pnas.1617959114). ***PNAS***, 2017
72 72
73 
+[Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in *Bacteroides coprocola*](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3). ***Microbiome***, 2017, 5:15
74 
+
73 75
74 76 
 ## <i class="fa fa-calendar"></i> 2016
75 77
mkdocs/docs/gallery.md
History View file @ bd105c7b
... ... 
@@ -15,7 +15,11 @@
15 15
16 16 
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
17 17
18 
-[![citation](https://img.shields.io/badge/cited%20by-2-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
18 
+[![citation](https://img.shields.io/badge/cited%20by-5-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
19 
+
20 
++ <http://dx.doi.org/10.1186/s40168-017-0232-3>
21 
+
22 
+![](https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif)
19 23
20 24 
 + <http://dx.doi.org/10.1111/2041-210X.12628>
21 25
mkdocs/docs/index.md
History View file @ bd105c7b
... ... 
@@ -20,10 +20,10 @@
20 20
21 21 
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
22 22
23 
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.7-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
23 
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.9-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
24 24 
 [![develVersion](https://img.shields.io/badge/devel%20version-1.7.7-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
25 
-[![total](https://img.shields.io/badge/downloads-20046/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
26 
-[![month](https://img.shields.io/badge/downloads-1177/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
25 
+[![total](https://img.shields.io/badge/downloads-21539/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
26 
+[![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
27 27
28 28
29 29 
 The `ggtree` package extending the *ggplot2* package. It based on grammar of graphics and takes all the good parts of *ggplot2*.  *ggtree* is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
... ... 
@@ -39,8 +39,8 @@ Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University o
39 39 
 Please cite the following article when using `ggtree`:
40 40
41 41 
 [![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)
42 
-[![citation](https://img.shields.io/badge/cited%20by-2-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
43 
-[![Altmetric](https://img.shields.io/badge/Altmetric-309-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
42 
+[![citation](https://img.shields.io/badge/cited%20by-5-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
43 
+[![Altmetric](https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
44 44
45 45 
 __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.
46 46
mkdocs/src/featuredArticles.md
History View file @ bd105c7b
... ... 
@@ -14,6 +14,8 @@
14 14
15 15 
 [Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging](http://dx.doi.org/10.1073/pnas.1617959114). ***PNAS***, 2017
16 16
17 
+[Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in *Bacteroides coprocola*](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3). ***Microbiome***, 2017, 5:15
18 
+
17 19
18 20 
 ## <i class="fa fa-calendar"></i> 2016
19 21
mkdocs/src/gallery.md
History View file @ bd105c7b
... ... 
@@ -4,6 +4,10 @@
4 4
5 5 
 <!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
6 6
7 
++ <http://dx.doi.org/10.1186/s40168-017-0232-3>
8 
+
9 
+![](https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif)
10 
+
7 11 
 + <http://dx.doi.org/10.1111/2041-210X.12628>
8 12
9 13 
 ![](https://guangchuangyu.github.io/featured_img/ggtree/C2mxyBuUcAEt391.jpg)