| ... | ... |
@@ -64,7 +64,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/ |
| 64 | 64 |
|
| 65 | 65 |
```{r echo=F, comment=NA}
|
| 66 | 66 |
d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
|
| 67 |
-txtplot(d$year, d$cites) |
|
| 67 |
+txtplot(d$year, d$cites, xlim=c(2015, 2017)) |
|
| 68 | 68 |
``` |
| 69 | 69 |
|
| 70 | 70 |
### Download stats |
| ... | ... |
@@ -1,9 +1,9 @@ |
| 1 | 1 |
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
| 2 | 2 |
=========================================================================================================================== |
| 3 | 3 |
|
| 4 |
-[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 4 |
+[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 5 | 5 |
|
| 6 |
-[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
| 6 |
+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
| 7 | 7 |
|
| 8 | 8 |
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [](https://travis-ci.org/GuangchuangYu/ggtree) [](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html) |
| 9 | 9 |
|
| ... | ... |
@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`: |
| 17 | 17 |
|
| 18 | 18 |
**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* |
| 19 | 19 |
|
| 20 |
-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [](https://www.altmetric.com/details/10533079) |
|
| 20 |
+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [](https://www.altmetric.com/details/10533079) |
|
| 21 | 21 |
|
| 22 | 22 |
------------------------------------------------------------------------ |
| 23 | 23 |
|
| ... | ... |
@@ -32,7 +32,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/ |
| 32 | 32 |
|
| 33 | 33 |
[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
| 34 | 34 |
|
| 35 |
- +---------+---------------+----------------+-----------+ |
|
| 35 |
+ +-------------+------------+------------+-------------++ |
|
| 36 | 36 |
| | |
| 37 | 37 |
| | |
| 38 | 38 |
1.2 + + |
| ... | ... |
@@ -45,12 +45,12 @@ For details, please visit our project website, <https://guangchuangyu.github.io/ |
| 45 | 45 |
0.8 + + |
| 46 | 46 |
| | |
| 47 | 47 |
| | |
| 48 |
- 0.6 +---------+---------------+----------------+-----------+ |
|
| 49 |
- 1500 2000 2500 |
|
| 48 |
+ 0.6 +-------------+------------+------------+-------------++ |
|
| 49 |
+ 2015 2015.5 2016 2016.5 2017 |
|
| 50 | 50 |
|
| 51 | 51 |
### Download stats |
| 52 | 52 |
|
| 53 |
-[](https://bioconductor.org/packages/stats/bioc/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 53 |
+[](https://bioconductor.org/packages/stats/bioc/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 54 | 54 |
|
| 55 | 55 |
+--------------------------+--------------------------+--------------------------+------------+ |
| 56 | 56 |
| * | |
| ... | ... |
@@ -166,11 +166,11 @@ |
| 166 | 166 |
} |
| 167 | 167 |
</style> |
| 168 | 168 |
|
| 169 |
-<div id = 'chart27d5145094bc' class = 'rChart morris'></div> |
|
| 169 |
+<div id = 'chart330312a992d' class = 'rChart morris'></div> |
|
| 170 | 170 |
|
| 171 | 171 |
<script type='text/javascript'> |
| 172 | 172 |
var chartParams = {
|
| 173 |
- "element": "chart27d5145094bc", |
|
| 173 |
+ "element": "chart330312a992d", |
|
| 174 | 174 |
"width": 800, |
| 175 | 175 |
"height": 400, |
| 176 | 176 |
"xkey": "year", |
| ... | ... |
@@ -184,7 +184,7 @@ |
| 184 | 184 |
"pubid": "HtEfBTGE9r8C" |
| 185 | 185 |
} |
| 186 | 186 |
], |
| 187 |
-"id": "chart27d5145094bc", |
|
| 187 |
+"id": "chart330312a992d", |
|
| 188 | 188 |
"labels": "cites" |
| 189 | 189 |
}, |
| 190 | 190 |
chartType = "Bar" |
| ... | ... |
@@ -146,6 +146,8 @@ |
| 146 | 146 |
|
| 147 | 147 |
<li><a href="#bioconductor-packages"> Bioconductor packages</a></li> |
| 148 | 148 |
|
| 149 |
+ <li><a href="#other-applications"> Other applications</a></li> |
|
| 150 |
+ |
|
| 149 | 151 |
|
| 150 | 152 |
<li class="main "><a href="#feedback"> Feedback</a></li> |
| 151 | 153 |
|
| ... | ... |
@@ -175,9 +177,9 @@ |
| 175 | 177 |
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p> |
| 176 | 178 |
<p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.4.20-blue.svg?style=flat" /></a> |
| 177 | 179 |
<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.5.14-blue.svg?style=flat" /></a> |
| 178 |
-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-13333/total-blue.svg?style=flat" /></a> |
|
| 180 |
+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-13439/total-blue.svg?style=flat" /></a> |
|
| 179 | 181 |
<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1122/month-blue.svg?style=flat" /></a></p> |
| 180 |
-<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. |
|
| 182 |
+<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. |
|
| 181 | 183 |
<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> |
| 182 | 184 |
<h2 id="authors"><i class="fa fa-user"></i> Authors</h2> |
| 183 | 185 |
<p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p> |
| ... | ... |
@@ -185,8 +187,8 @@ |
| 185 | 187 |
<p>Please cite the following article when using <code>ggtree</code>:</p> |
| 186 | 188 |
<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> |
| 187 | 189 |
<a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat" /></a> |
| 188 |
-<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-147-blue.svg?style=flat" /></a></p> |
|
| 189 |
-<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> |
|
| 190 |
+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-166-blue.svg?style=flat" /></a></p> |
|
| 191 |
+<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> |
|
| 190 | 192 |
<h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2> |
| 191 | 193 |
<p><img alt="" src="./featured_img/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p> |
| 192 | 194 |
<p><i class="fa fa-hand-o-right"></i> Find out more on <i class="fa fa-pencil"></i> <a href="https://guangchuangyu.github.io/ggtree/featuredArticles/">Featured Articles</a>.</p> |
| ... | ... |
@@ -223,6 +225,10 @@ biocLite("ggtree") |
| 223 | 225 |
<ul> |
| 224 | 226 |
<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic paritioning based ILR transform for metagenomics data</li> |
| 225 | 227 |
</ul> |
| 228 |
+<h4 id="other-applications"><i class="fa fa-angle-double-right"></i> Other applications</h4> |
|
| 229 |
+<ul> |
|
| 230 |
+<li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>: Collection of scripts for metagenomics analysis</li> |
|
| 231 |
+</ul> |
|
| 226 | 232 |
<h2 id="feedback"><i class="fa fa-comments"></i> Feedback</h2> |
| 227 | 233 |
<p><ul class="fa-ul"> |
| 228 | 234 |
<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/">follow the guide</a> before posting any issue/question</li> |
| ... | ... |
@@ -2,7 +2,7 @@ |
| 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\nphilr\n: Phylogenetic paritioning based ILR transform for metagenomics data\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\nphilr\n: Phylogenetic paritioning 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\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 |
{
|
| ... | ... |
@@ -55,6 +55,11 @@ |
| 55 | 55 |
"text": "philr : Phylogenetic paritioning based ILR transform for metagenomics data", |
| 56 | 56 |
"title": " Bioconductor packages" |
| 57 | 57 |
}, |
| 58 |
+ {
|
|
| 59 |
+ "location": "/#other-applications", |
|
| 60 |
+ "text": "BreadCrumbs : Collection of scripts for metagenomics analysis", |
|
| 61 |
+ "title": " Other applications" |
|
| 62 |
+ }, |
|
| 58 | 63 |
{
|
| 59 | 64 |
"location": "/#feedback", |
| 60 | 65 |
"text": "Please make sure you follow the guide before posting any issue/question \n For bugs or feature requests, please post to github issue \n For user questions, please post to google group \n We are also following every post tagged with ggtree on Bioconductor support site and Biostars \n Join the group chat on and", |
| ... | ... |
@@ -177,7 +182,7 @@ |
| 177 | 182 |
}, |
| 178 | 183 |
{
|
| 179 | 184 |
"location": "/featuredArticles/", |
| 180 |
- "text": "Let us know 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\": \"chart27d5145094bc\",\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\": \"chart27d5145094bc\",\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",
|
|
| 185 |
+ "text": "Let us know 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\": \"chart330312a992d\",\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\": \"chart330312a992d\",\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",
|
|
| 181 | 186 |
"title": "Featured Articles" |
| 182 | 187 |
}, |
| 183 | 188 |
{
|
| ... | ... |
@@ -4,7 +4,7 @@ |
| 4 | 4 |
|
| 5 | 5 |
<url> |
| 6 | 6 |
<loc>https://guangchuangyu.github.io/ggtree/</loc> |
| 7 |
- <lastmod>2016-09-19</lastmod> |
|
| 7 |
+ <lastmod>2016-09-21</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>2016-09-19</lastmod> |
|
| 15 |
+ <lastmod>2016-09-21</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>2016-09-19</lastmod> |
|
| 23 |
+ <lastmod>2016-09-21</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>2016-09-19</lastmod> |
|
| 31 |
+ <lastmod>2016-09-21</lastmod> |
|
| 32 | 32 |
<changefreq>daily</changefreq> |
| 33 | 33 |
</url> |
| 34 | 34 |
|
| ... | ... |
@@ -36,10 +36,10 @@ Let us know if you have published using `ggtree` and your publication will be fe |
| 36 | 36 |
} |
| 37 | 37 |
</style> |
| 38 | 38 |
|
| 39 |
-<div id = 'chart27d5145094bc' class = 'rChart morris'></div> |
|
| 39 |
+<div id = 'chart330312a992d' class = 'rChart morris'></div> |
|
| 40 | 40 |
<script type='text/javascript'> |
| 41 | 41 |
var chartParams = {
|
| 42 |
- "element": "chart27d5145094bc", |
|
| 42 |
+ "element": "chart330312a992d", |
|
| 43 | 43 |
"width": 800, |
| 44 | 44 |
"height": 400, |
| 45 | 45 |
"xkey": "year", |
| ... | ... |
@@ -53,7 +53,7 @@ Let us know if you have published using `ggtree` and your publication will be fe |
| 53 | 53 |
"pubid": "HtEfBTGE9r8C" |
| 54 | 54 |
} |
| 55 | 55 |
], |
| 56 |
-"id": "chart27d5145094bc", |
|
| 56 |
+"id": "chart330312a992d", |
|
| 57 | 57 |
"labels": "cites" |
| 58 | 58 |
}, |
| 59 | 59 |
chartType = "Bar" |
| ... | ... |
@@ -17,11 +17,11 @@ |
| 17 | 17 |
|
| 18 | 18 |
[](https://bioconductor.org/packages/ggtree) |
| 19 | 19 |
[](https://github.com/GuangchuangYu/ggtree) |
| 20 |
-[](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 20 |
+[](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 21 | 21 |
[](https://bioconductor.org/packages/stats/bioc/ggtree) |
| 22 | 22 |
|
| 23 | 23 |
|
| 24 |
-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. |
|
| 24 |
+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. |
|
| 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 |
|
| ... | ... |
@@ -35,9 +35,9 @@ Please cite the following article when using `ggtree`: |
| 35 | 35 |
|
| 36 | 36 |
[](http://dx.doi.org/10.1111/2041-210X.12628) |
| 37 | 37 |
[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
| 38 |
-[](https://www.altmetric.com/details/10533079) |
|
| 38 |
+[](https://www.altmetric.com/details/10533079) |
|
| 39 | 39 |
|
| 40 |
-__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*. |
|
| 40 |
+__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*. |
|
| 41 | 41 |
|
| 42 | 42 |
## <i class="fa fa-pencil"></i> Featured Articles |
| 43 | 43 |
|
| ... | ... |
@@ -88,6 +88,9 @@ If you have problems when installing some of the dependent packages, please refe |
| 88 | 88 |
#### <i class="fa fa-angle-double-right"></i> Bioconductor packages |
| 89 | 89 |
+ [philr](https://www.bioconductor.org/packages/philr): Phylogenetic paritioning based ILR transform for metagenomics data |
| 90 | 90 |
|
| 91 |
+#### <i class="fa fa-angle-double-right"></i> Other applications |
|
| 92 |
++ [BreadCrumbs](https://bitbucket.org/biobakery/breadcrumbs): Collection of scripts for metagenomics analysis |
|
| 93 |
+ |
|
| 91 | 94 |
|
| 92 | 95 |
## <i class="fa fa-comments"></i> Feedback |
| 93 | 96 |
<ul class="fa-ul"> |
| ... | ... |
@@ -8,7 +8,7 @@ |
| 8 | 8 |
<!-- download:=ggtree:=month --> |
| 9 | 9 |
|
| 10 | 10 |
|
| 11 |
-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. |
|
| 11 |
+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. |
|
| 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 |
|
| ... | ... |
@@ -24,7 +24,7 @@ Please cite the following article when using `ggtree`: |
| 24 | 24 |
<!-- citation:=HtEfBTGE9r8C:=7268358477862164627 --> |
| 25 | 25 |
<!-- altmetric:=10533079 --> |
| 26 | 26 |
|
| 27 |
-__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*. |
|
| 27 |
+__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*. |
|
| 28 | 28 |
|
| 29 | 29 |
## <i class="fa fa-pencil"></i> Featured Articles |
| 30 | 30 |
|
| ... | ... |
@@ -75,6 +75,9 @@ If you have problems when installing some of the dependent packages, please refe |
| 75 | 75 |
|
| 76 | 76 |
<!-- package_depend:=ggtree:=BioC --> |
| 77 | 77 |
|
| 78 |
+#### <i class="fa fa-angle-double-right"></i> Other applications |
|
| 79 |
++ [BreadCrumbs](https://bitbucket.org/biobakery/breadcrumbs): Collection of scripts for metagenomics analysis |
|
| 80 |
+ |
|
| 78 | 81 |
|
| 79 | 82 |
## <i class="fa fa-comments"></i> Feedback |
| 80 | 83 |
<ul class="fa-ul"> |
