Browse code

biobabble

guangchuang yu authored on 10/11/2016 10:50:49
Showing8 changed files

... ...
@@ -47,7 +47,10 @@ mkdocs: mdfiles
47 47
 	mkdocs build;\
48 48
 	cd ../docs;\
49 49
 	rm -rf fonts;\
50
-	rm -rf css/font-awesome*
50
+	rm -rf css/font-awesome*;\
51
+	cd ../../docs;\
52
+	Rscript -e 'library(ypages); add_biobabble("index.html")'
53
+
51 54
 
52 55
 mdfiles:
53 56
 	cd mkdocs;\
... ...
@@ -58,7 +61,6 @@ mdfiles:
58 61
 	cd docs;\
59 62
 	ln -f -s ../mysoftware/* ./
60 63
 
61
-
62 64
 svnignore:
63 65
 	svn propset svn:ignore -F .svnignore .
64 66
 
... ...
@@ -3,7 +3,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
3 3
 
4 4
 [![releaseVersion](https://img.shields.io/badge/release%20version-1.6.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.3-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-16443/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
5 5
 
6
-[![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-2016--11--09-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)
6
+[![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-2016--11--10-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 7
 
8 8
 [![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)
9 9
 
... ...
@@ -52,11 +52,6 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
52 52
 
53 53
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-16443/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
54 54
 
55
-    ggtree v1.7.3  For help: https://guangchuangyu.github.io/ggtree
56
-
57
-    If you use ggtree in published research, please cite:
58
-    Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628
59
-
60 55
          +------------------------+-----------------------+-----------------------+--------------------+
61 56
          |                                                                                    *        |
62 57
          |                                                                                         *   |
... ...
@@ -223,11 +223,11 @@
223 223
   }  
224 224
   </style>
225 225
 
226
-<div id = 'chartaf51aba2c20' class = 'rChart morris'></div>
226
+<div id = 'chart15f016b25061' class = 'rChart morris'></div>
227 227
 
228 228
 <script type='text/javascript'>
229 229
     var chartParams = {
230
- "element": "chartaf51aba2c20",
230
+ "element": "chart15f016b25061",
231 231
 "width":            800,
232 232
 "height":            400,
233 233
 "xkey": "year",
... ...
@@ -241,7 +241,7 @@
241 241
 "pubid": "HtEfBTGE9r8C" 
242 242
 } 
243 243
 ],
244
-"id": "chartaf51aba2c20",
244
+"id": "chart15f016b25061",
245 245
 "labels": "cites" 
246 246
 },
247 247
       chartType = "Bar"
... ...
@@ -178,7 +178,7 @@
178 178
             <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">
179 179
     <ul class="nav bs-sidenav">
180 180
     
181
-        <li class="main active"><a href="#authors"> Authors </a></li>
181
+        <li class="main active"><a href="#authors"> Authors</a></li>
182 182
         
183 183
     
184 184
         <li class="main "><a href="#citation"> Citation</a></li>
... ...
@@ -207,6 +207,7 @@
207 207
         
208 208
     
209 209
         <li class="main "><a href="#feedback"> Feedback</a></li>
210
+<img src="https://guangchuangyu.github.io/blog_images/biobabble.jpg" align="center" width="250"/>
210 211
         
211 212
     
212 213
     </ul>
... ...
@@ -238,7 +239,7 @@
238 239
 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat" /></a></p>
239 240
 <p>The <code>ggtree</code> package extending the <code>ggplot2</code> package. It based on grammar of graphics and takes all the good parts of <code>ggplot2</code>.  <code>ggtree</code> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
240 241
 <code>ggtree</code> 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>
241
-<h2 id="authors"><i class="fa fa-user"></i> Authors <img src="https://guangchuangyu.github.io/blog_images/biobabble.jpg" align="right" width="150"/></h2>
242
+<h2 id="authors"><i class="fa fa-user"></i> Authors</h2>
242 243
 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
243 244
 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>
244 245
 <p>Please cite the following article when using <code>ggtree</code>:</p>
... ...
@@ -339,4 +340,4 @@ biocLite(&quot;ggtree&quot;)
339 340
             </div>
340 341
         </div>
341 342
     </body>
342
-</html>
343 343
\ No newline at end of file
344
+</html>
... ...
@@ -2,13 +2,13 @@
2 2
     "docs": [
3 3
         {
4 4
             "location": "/", 
5
-            "text": "The \nggtree\n package extending the \nggplot2\n package. It based on grammar of graphics and takes all the good parts of \nggplot2\n.  \nggtree\n is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.\n\nggtree\n is released within the \nBioconductor\n project and the source code is hosted on \n GitHub\n.\n\n\n Authors \n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \nMethods in Ecology and Evolution\n. \naccepted\n.\n\n\n Featured Articles\n\n\n\n\n Find out more on \n \nFeatured Articles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor page\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, please refer to the \nggtree-installation\n wiki 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 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 the tree visually\n\n\n\n\n Find out details and examples on \n \nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n: Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n: Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you \nfollow the 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": "The \nggtree\n package extending the \nggplot2\n package. It based on grammar of graphics and takes all the good parts of \nggplot2\n.  \nggtree\n is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.\n\nggtree\n is released within the \nBioconductor\n project and the source code is hosted on \n GitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \nMethods in Ecology and Evolution\n. \naccepted\n.\n\n\n Featured Articles\n\n\n\n\n Find out more on \n \nFeatured Articles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor page\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, please refer to the \nggtree-installation\n wiki 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 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 the tree visually\n\n\n\n\n Find out details and examples on \n \nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n: Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n: Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you \nfollow the 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", 
6 6
             "title": "Home"
7 7
         }, 
8 8
         {
9 9
             "location": "/#authors", 
10 10
             "text": "Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.", 
11
-            "title": " Authors "
11
+            "title": " Authors"
12 12
         }, 
13 13
         {
14 14
             "location": "/#citation", 
... ...
@@ -197,7 +197,7 @@
197 197
         }, 
198 198
         {
199 199
             "location": "/featuredArticles/", 
200
-            "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\": \"chartaf51aba2c20\",\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\": \"chartaf51aba2c20\",\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", 
200
+            "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\": \"chart15f016b25061\",\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\": \"chart15f016b25061\",\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", 
201 201
             "title": "Featured Articles"
202 202
         }, 
203 203
         {
... ...
@@ -36,10 +36,10 @@
36 36
   }  
37 37
   </style>
38 38
 
39
-<div id = 'chartaf51aba2c20' class = 'rChart morris'></div>
39
+<div id = 'chart15f016b25061' class = 'rChart morris'></div>
40 40
 <script type='text/javascript'>
41 41
     var chartParams = {
42
- "element": "chartaf51aba2c20",
42
+ "element": "chart15f016b25061",
43 43
 "width":            800,
44 44
 "height":            400,
45 45
 "xkey": "year",
... ...
@@ -53,7 +53,7 @@
53 53
 "pubid": "HtEfBTGE9r8C" 
54 54
 } 
55 55
 ],
56
-"id": "chartaf51aba2c20",
56
+"id": "chart15f016b25061",
57 57
 "labels": "cites" 
58 58
 },
59 59
       chartType = "Bar"
... ...
@@ -25,7 +25,7 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
25 25
 `ggtree` is released within the [Bioconductor](https://bioconductor.org/packages/ggtree/) 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>.
26 26
 
27 27
 
28
-## <i class="fa fa-user"></i> Authors <img src="https://guangchuangyu.github.io/blog_images/biobabble.jpg" align="right" width="150"/>
28
+## <i class="fa fa-user"></i> Authors
29 29
 
30 30
 Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.
31 31
 
... ...
@@ -12,7 +12,7 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
12 12
 `ggtree` is released within the [Bioconductor](https://bioconductor.org/packages/ggtree/) 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>.
13 13
 
14 14
 
15
-## <i class="fa fa-user"></i> Authors <img src="https://guangchuangyu.github.io/blog_images/biobabble.jpg" align="right" width="150"/>
15
+## <i class="fa fa-user"></i> Authors
16 16
 
17 17
 Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.
18 18