Browse code

update site

guangchuang yu authored on 14/11/2017 06:05:53
Showing5 changed files

... ...
@@ -344,9 +344,16 @@
344 344
 				<h1>ggtree: visualization and annotation of phylogenetic trees </h1>
345 345
 
346 346
 				<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
347
+<div id="plea-to-against-bmc" class="section level2">
348
+<h2>Plea to against BMC</h2>
349
+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">BMC journal protects paper of plagiarism <a href="https://t.co/FfSv7dPFXV">https://t.co/FfSv7dPFXV</a> <a href="https://twitter.com/RetractionWatch?ref_src=twsrc%5Etfw">@RetractionWatch</a> <a href="https://twitter.com/C0PE?ref_src=twsrc%5Etfw">@C0PE</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/928836702998638592?ref_src=twsrc%5Etfw">November 10, 2017</a></blockquote>
350
+<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
351
+
352
+<hr />
347 353
 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
348
-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-20978/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
354
+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21118/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
349 355
 <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. <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>
356
+</div>
350 357
 <div id="authors" class="section level2">
351 358
 <h2><i class="fa fa-user"></i> Authors</h2>
352 359
 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
... ...
@@ -354,7 +361,7 @@
354 361
 <div id="citation" class="section level2">
355 362
 <h2><i class="fa fa-book"></i> Citation</h2>
356 363
 <p>Please cite the following article when using <code>ggtree</code>:</p>
357
-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-337-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-45-blue.svg?style=flat" alt="citation" /></a></p>
364
+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-336-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-47-blue.svg?style=flat" alt="citation" /></a></p>
358 365
 <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>
359 366
 </div>
360 367
 <div id="featured-articles" class="section level2">
... ...
@@ -18,8 +18,9 @@
18 18
       <pubDate>Thu, 06 Jul 2017 12:08:13 +0100</pubDate>
19 19
       
20 20
       <guid>https://guangchuangyu.github.io/ggtree/</guid>
21
-      <description>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. ggtree is released within the Bioconductor project and the source code is hosted on  GitHub.
22
- Authors Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</description>
21
+      <description>Plea to against BMC BMC journal protects paper of plagiarism https://t.co/FfSv7dPFXV @RetractionWatch @C0PE
22
+&amp;mdash; Guangchuang Yu (@guangchuangyu) November 10, 2017     
23
+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. ggtree is released within the Bioconductor project and the source code is hosted on  GitHub.</description>
23 24
     </item>
24 25
     
25 26
     <item>
... ...
@@ -352,7 +352,7 @@
352 352
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
353 353
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">New Post: Plotting a Sequential Binary Partition on a Tree in R <a href="https://twitter.com/alex_washburne?ref_src=twsrc%5Etfw">@alex_washburne</a> <a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> <a href="https://t.co/6jQKMof5aW">https://t.co/6jQKMof5aW</a></p>&mdash; Justin Silverman (@inschool4life) <a href="https://twitter.com/inschool4life/status/910671384069722112?ref_src=twsrc%5Etfw">September 21, 2017</a></blockquote>
354 354
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
355
-<blockquote class="twitter-tweet"><p lang="sv" dir="ltr">blog: Introduction to ggplot2 and to ggtree πŸ“πŸ“ˆπŸ‘¨β€πŸ”¬πŸ‘©β€πŸ”¬ <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://twitter.com/hashtag/phdchat?src=hash&amp;ref_src=twsrc%5Etfw">#phdchat</a> <a href="https://t.co/ndmRitxpeH">https://t.co/ndmRitxpeH</a></p>&mdash; Jean (@JeanManguy) <a href="https://twitter.com/JeanManguy/status/903786057182957568?ref_src=twsrc%5Etfw">September 2, 2017</a></blockquote>
355
+<blockquote class="twitter-tweet"><p lang="sv" dir="ltr">blog: Introduction to ggplot2 and to ggtree πŸ“πŸ“ˆπŸ‘¨β€πŸ”¬πŸ‘©β€πŸ”¬ <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://twitter.com/hashtag/phdchat?src=hash&amp;ref_src=twsrc%5Etfw">#phdchat</a> <a href="https://t.co/ndmRitxpeH">https://t.co/ndmRitxpeH</a></p>&mdash; Jean πŸ‘¨β€πŸ’» (@JeanManguy) <a href="https://twitter.com/JeanManguy/status/903786057182957568?ref_src=twsrc%5Etfw">September 2, 2017</a></blockquote>
356 356
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
357 357
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">The ggtree package looks like a cool way to visualize hierarchical data<a href="https://t.co/spsqLkqeVG">https://t.co/spsqLkqeVG</a> <a href="https://t.co/GRODlrBahW">pic.twitter.com/GRODlrBahW</a></p>&mdash; Nathan Brouwer (@lobrowR) <a href="https://twitter.com/lobrowR/status/899635001247059969?ref_src=twsrc%5Etfw">August 21, 2017</a></blockquote>
358 358
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
... ...
@@ -382,7 +382,7 @@
382 382
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
383 383
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">OMG SO USEFUL! &quot;Phylogenetic trees in R using ggtree&quot; <a href="https://t.co/Yr8HNdWXV0">https://t.co/Yr8HNdWXV0</a></p>&mdash; Stephen Taerum (@BrahStevovo) <a href="https://twitter.com/BrahStevovo/status/829398997735313408?ref_src=twsrc%5Etfw">February 8, 2017</a></blockquote>
384 384
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
385
-<blockquote class="twitter-tweet"><p lang="en" dir="ltr">I like ggtree to plot phylogenetic trees and annotate them. And I haven&#39;t found any other tools as customizable as ggtree</p>&mdash; Le NΓ©matode (@LeNematode) <a href="https://twitter.com/LeNematode/status/824264788456984576?ref_src=twsrc%5Etfw">January 25, 2017</a></blockquote>
385
+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">I like ggtree to plot phylogenetic trees and annotate them. And I haven&#39;t found any other tools as customizable as ggtree</p>&mdash; Matthias G. (@LeNematode) <a href="https://twitter.com/LeNematode/status/824264788456984576?ref_src=twsrc%5Etfw">January 25, 2017</a></blockquote>
386 386
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
387 387
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">The R <a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> is now published in <a href="https://twitter.com/MethodsEcolEvol?ref_src=twsrc%5Etfw">@MethodsEcolEvol</a> <a href="https://t.co/6fvSRQo2CC">https://t.co/6fvSRQo2CC</a> <a href="https://twitter.com/hashtag/evomics2017?src=hash&amp;ref_src=twsrc%5Etfw">#evomics2017</a> <a href="https://t.co/Dwq1DD84A2">pic.twitter.com/Dwq1DD84A2</a></p>&mdash; Elin Videvall (@ElinVidevall) <a href="https://twitter.com/ElinVidevall/status/822383911258890242?ref_src=twsrc%5Etfw">January 20, 2017</a></blockquote>
388 388
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
... ...
@@ -400,7 +400,7 @@
400 400
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
401 401
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">am quite liking <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://twitter.com/hashtag/ggplot?src=hash&amp;ref_src=twsrc%5Etfw">#ggplot</a> <a href="https://t.co/hvywS2z4ps">pic.twitter.com/hvywS2z4ps</a></p>&mdash; Nicholas E Ilott (@IlottNick) <a href="https://twitter.com/IlottNick/status/788751417746059264?ref_src=twsrc%5Etfw">October 19, 2016</a></blockquote>
402 402
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
403
-<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Treespace visualization of a heuristic best tree search in <a href="https://twitter.com/hashtag/R?src=hash&amp;ref_src=twsrc%5Etfw">#R</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/hnSJpIABql">pic.twitter.com/hnSJpIABql</a></p>&mdash; Alex DamiΓ‘nSerrano β‘‚ (@antropoteuthis) <a href="https://twitter.com/antropoteuthis/status/693123105707986944?ref_src=twsrc%5Etfw">January 29, 2016</a></blockquote>
403
+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Treespace visualization of a heuristic best tree search in <a href="https://twitter.com/hashtag/R?src=hash&amp;ref_src=twsrc%5Etfw">#R</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/hnSJpIABql">pic.twitter.com/hnSJpIABql</a></p>&mdash; Alejandro DamiΓ‘n Serrano β‘‚πŸŒŠπŸ”¬ (@antropoteuthis) <a href="https://twitter.com/antropoteuthis/status/693123105707986944?ref_src=twsrc%5Etfw">January 29, 2016</a></blockquote>
404 404
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
405 405
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr"><a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> Updated to latest <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> and <a href="https://twitter.com/hashtag/ggplot2?src=hash&amp;ref_src=twsrc%5Etfw">#ggplot2</a> and very impressed! Any ideas on using geom_label with tip labels to add box/fill?</p>&mdash; Jo Williams-Newkirk (@ajwnewkirk) <a href="https://twitter.com/ajwnewkirk/status/691762302492790788?ref_src=twsrc%5Etfw">January 25, 2016</a></blockquote>
406 406
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
... ...
@@ -8,9 +8,14 @@ weight: 1
8 8
 
9 9
 
10 10
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
11
+<div id="plea-to-against-bmc" class="section level2">
12
+<h2>Plea to against BMC</h2>
13
+{{% tweet "928836702998638592" %}}
14
+<hr />
11 15
 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
12
-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-20978/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
16
+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21118/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
13 17
 <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. <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>
18
+</div>
14 19
 <div id="authors" class="section level2">
15 20
 <h2><i class="fa fa-user"></i> Authors</h2>
16 21
 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
... ...
@@ -18,7 +23,7 @@ weight: 1
18 23
 <div id="citation" class="section level2">
19 24
 <h2><i class="fa fa-book"></i> Citation</h2>
20 25
 <p>Please cite the following article when using <code>ggtree</code>:</p>
21
-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-337-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-45-blue.svg?style=flat" alt="citation" /></a></p>
26
+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-336-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-47-blue.svg?style=flat" alt="citation" /></a></p>
22 27
 <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>
23 28
 </div>
24 29
 <div id="featured-articles" class="section level2">
... ...
@@ -7,6 +7,15 @@ weight: 1
7 7
 
8 8
 
9 9
 
10
+## Plea to against BMC
11
+
12
+```{r echo=FALSE}
13
+blogdown::shortcode('tweet', '928836702998638592')
14
+```
15
+
16
+----
17
+
18
+
10 19
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
11 20
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css">
12 21