1. ggtree
  2. Commit 09d9e0706c0931faf5e0069a39d78d00b4d6043f
Browse code

update site

guangchuang yu authored on 25/07/2017 05:29:36
Showing 59 changed files
Makefile
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@@ -44,11 +44,14 @@ clean:
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 	cd ..;\
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 	$(RM) -r $(PKGNAME).Rcheck/
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-site:
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+site:
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 	cd site_src;\
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 	Rscript -e 'blogdown::build_site()';\
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 	cd ..
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+preview:
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+	Rscript -e 'setwd("site_src"); blogdown::serve_site()'
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+
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 mkdocs: mdfiles
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 	cd mkdocs;\
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 	mkdocs build;\
README.Rmd
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 library("badger")
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 library("ypages")
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 library("ggplot2")
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+library("yyplot")
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 ```
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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@@ -65,28 +66,22 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 `r badge_doi("10.1111/2041-210X.12628", "green")`
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 `r badge_altmetric("10533079", "green")`
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+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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+
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 ----------------------------------------------------------------------------------------
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 ### Citation
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-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-
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-
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 ```{r echo=F, comment=NA}
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-d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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-## txtplot(d$year, d$cites)
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-## library("ggalt")
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-## p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') +
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-p <- ggplot(d, aes(year, cites)) + geom_segment(aes(xend=year, yend=0)) + geom_point(size=3, color='firebrick') +
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-    theme_minimal() + xlab(NULL) + ylab(NULL) + labs(title="Citation", caption="data from Google Scholar")
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-ggsave(p, file="docs/citation.png", width=8, height=4)
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+p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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+ggsave(p, file="docs/images/citation.png", width=8, height=4)
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 ```
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-<img src="docs/citation.png" width="890"/>
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+<img src="docs/images/citation.png" width="890"/>
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 ### Download stats
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 p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
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     theme_minimal() +xlab(NULL) + ylab(NULL) +
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     labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")
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-ggsave(p, file="docs/dlstats.png", width=8, height=4)
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+ggsave(p, file="docs/images/dlstats.png", width=8, height=4)
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 ```
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-<img src="docs/dlstats.png" width="890"/>
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+<img src="docs/images/dlstats.png" width="890"/>
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 ## Contributors
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README.md
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@@ -27,21 +27,19 @@ Please cite the following article when using `ggtree`:
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 **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.
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-[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-351-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-351-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-28-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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 ------------------------------------------------------------------------
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 ### Citation
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-[![citation](https://img.shields.io/badge/cited%20by-28-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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-
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-<img src="docs/citation.png" width="890"/>
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+<img src="docs/images/citation.png" width="890"/>
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 ### Download stats
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 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-17269/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-<img src="docs/dlstats.png" width="890"/>
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+<img src="docs/images/dlstats.png" width="890"/>
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 Contributors
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 ------------
docs/categories/index.xml
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     <title>Categories on ggtree - Guangchuang Yu</title>
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     <description>Recent content in Categories on ggtree - Guangchuang Yu</description>
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     <generator>Hugo -- gohugo.io</generator>
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     <language>en-us</language>
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     <copyright>Released under the Artistic-2.0 license</copyright>
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docs/citation.png
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docs/documentation/index.html
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
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     <style>
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     <title>Documentations on ggtree - Guangchuang Yu</title>
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     <description>Recent content in Documentations on ggtree - Guangchuang Yu</description>
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     <lastBuildDate>Mon, 24 Jul 2017 00:11:02 +0100</lastBuildDate>
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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       <description>Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R    User’s feedback  tweets of ggtree Join the group chat on  and    Find out more on https://guangchuangyu.</description>
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docs/faq/index.html
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     <copyright>Released under the Artistic-2.0 license</copyright>
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       <description>Installation  Could not find function If you got this error, please make sure you are using the latest R and ggtree.
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 Packages in Bioconductor, like ggtree, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to devel branch.
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 Sometimes I may write blog post to introduce new functions which is not available in release branch, you need to install the devel version of ggtree in order to use these new functions.</description>
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-    <meta property="og:image" content="https://guangchuangyu.github.io/ggtree/images/gc.png">
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+    <meta property="og:image" content="/images/gc.png">
26 26 
     <meta name="apple-mobile-web-app-title" content="ggtree - Guangchuang Yu">
27 27 
     <meta name="apple-mobile-web-app-capable" content="yes">
28 28 
     <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
29 29
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-    <link rel="shortcut icon" type="image/x-icon" href="https://guangchuangyu.github.io/ggtree/images/favicon.ico">
31 
-    <link rel="icon" type="image/x-icon" href="https://guangchuangyu.github.io/ggtree/images/favicon.ico">
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+    <link rel="shortcut icon" type="image/x-icon" href="../images/favicon.ico">
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+    <link rel="icon" type="image/x-icon" href="../images/favicon.ico">
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+        src: url('/fonts/icon.eot');
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+        src: url('/fonts/icon.eot')
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                format('embedded-opentype'),
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-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.woff')
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+             url('/fonts/icon.woff')
40 40 
                format('woff'),
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-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.ttf')
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+             url('/fonts/icon.ttf')
42 42 
                format('truetype'),
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-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.svg')
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+             url('/fonts/icon.svg')
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                format('svg');
45 45 
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/palettes.css">
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/highlight/highlight.css">
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+    <link rel="stylesheet" href="../stylesheets/application.css">
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     </style>
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     <div class="banner">
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-          <img src="https://guangchuangyu.github.io/ggtree/images/gc.png">
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325 325
326 326 
 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
327 327 
 <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>
328 
-<p><img src="../featured-articles/index_files/figure-html/unnamed-chunk-1-1.png" width="844.8" /></p>
329 
-<!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
330 
-<!-- article_citation:=HtEfBTGE9r8C -->
328 
+<p><img src="../images/citation.png" width="880"/></p>
331 329 
 <div id="section" class="section level2">
332 330 
 <h2><i class="fa fa-calendar"></i> 2017</h2>
333 331 
 <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>
... ... 
@@ -356,7 +354,7 @@
356 354 
 <nav class="pagination" aria-label="Footer">
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   <div class="previous">
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-      <a href="https://guangchuangyu.github.io/ggtree/faq/" title="FAQ">
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+      <a href="../faq/" title="FAQ">
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           Previous
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         </span>
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   <div class="next">
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-      <a href="https://guangchuangyu.github.io/ggtree/gallery/" title="Gallery">
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+      <a href="../gallery/" title="Gallery">
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           Next
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+      var base_url = '\/';
419 417 
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     </script>
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-    <script src="https://guangchuangyu.github.io/ggtree/javascripts/application.js"></script>
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+    <script src="../javascripts/application.js"></script>
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     <script>
docs/featured-articles/index.rmd
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@@ -11,28 +11,9 @@ weight: 30
11 11 
 [Let us know](https://github.com/GuangchuangYu/featured_img) if you have published using `ggtree` and your publication will be featured here.
12 12
13 13
14 
+<img src="../images/citation.png" width="880"/>
14 15
15 16
16 
-```{r echo=F, message=F, fig.width=8.8, fig.height=4.5}
17 
-library(scholar)
18 
-library(ggplot2)
19 
-
20 
-id <- "DO5oG40AAAAJ"
21 
-pubid <- "HtEfBTGE9r8C"
22 
-df <- get_article_cite_history(id, pubid)
23 
-df$year <- as.factor(df$year)
24 
-p <- ggplot(df, aes(year, cites)) + geom_col(fill='steelblue', width=.6) + theme_minimal()
25 
-title <- paste('Cited by', sum(df$cites))
26 
-p <- p + xlab(NULL) + ylab(NULL) + ggtitle(title)
27 
-print(p)
28 
-#ggplotly(p, height=440, width=880)
29 
-```
30 
-
31 
-
32 
-<!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
33 
-
34 
-<!-- article_citation:=HtEfBTGE9r8C -->
35 
-
36 17
37 18 
 ## <i class="fa fa-calendar"></i> 2017
38 19
docs/featured-articles/index.xml
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2 2 
 <rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
3 3 
   <channel>
4 4 
     <title>Featured-articles on ggtree - Guangchuang Yu</title>
5 
-    <link>https://guangchuangyu.github.io/ggtree/featured-articles/</link>
5 
+    <link>/featured-articles/</link>
6 6 
     <description>Recent content in Featured-articles on ggtree - Guangchuang Yu</description>
7 7 
     <generator>Hugo -- gohugo.io</generator>
8 8 
     <language>en-us</language>
9 9 
     <copyright>Released under the Artistic-2.0 license</copyright>
10 10 
     <lastBuildDate>Mon, 24 Jul 2017 00:11:02 +0100</lastBuildDate>
11 11
12 
-	<atom:link href="https://guangchuangyu.github.io/ggtree/featured-articles/index.xml" rel="self" type="application/rss+xml" />
12 
+	<atom:link href="/featured-articles/index.xml" rel="self" type="application/rss+xml" />
13 13
14 14
15 15 
     <item>
16 16 
       <title>Featured Articles</title>
17 
-      <link>https://guangchuangyu.github.io/ggtree/featured-articles/</link>
17 
+      <link>/featured-articles/</link>
18 18 
       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
19 19
20 
-      <guid>https://guangchuangyu.github.io/ggtree/featured-articles/</guid>
20 
+      <guid>/featured-articles/</guid>
21 21 
       <description>Let us know if you have published using ggtree and your publication will be featured here.
22 22 
  2017 Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017
23 23 
 Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus. Frontiers in Microbiology, 2017, 8:543
docs/featured-articles/index_files/figure-html/unnamed-chunk-1-1.png
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15 15
16 16 
     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
17 17
18 
-    <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/gallery/">
18 
+    <link rel="canonical" href="../gallery/">
19 19
20 20 
     <meta name="author" content="Guangchuang Yu">
21 21
22 22
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-    <meta property="og:url" content="https://guangchuangyu.github.io/ggtree/gallery/">
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+    <meta property="og:url" content="/gallery/">
24 24 
     <meta property="og:title" content="ggtree - Guangchuang Yu">
25 
-    <meta property="og:image" content="https://guangchuangyu.github.io/ggtree/images/gc.png">
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+    <meta property="og:image" content="/images/gc.png">
26 26 
     <meta name="apple-mobile-web-app-title" content="ggtree - Guangchuang Yu">
27 27 
     <meta name="apple-mobile-web-app-capable" content="yes">
28 28 
     <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
29 29
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-    <link rel="shortcut icon" type="image/x-icon" href="https://guangchuangyu.github.io/ggtree/images/favicon.ico">
31 
-    <link rel="icon" type="image/x-icon" href="https://guangchuangyu.github.io/ggtree/images/favicon.ico">
30 
+    <link rel="shortcut icon" type="image/x-icon" href="../images/favicon.ico">
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+    <link rel="icon" type="image/x-icon" href="../images/favicon.ico">
32 32
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34 34 
       @font-face {
35 35 
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-        src: url('https://guangchuangyu.github.io/ggtree/fonts/icon.eot')
36 
+        src: url('/fonts/icon.eot');
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+        src: url('/fonts/icon.eot')
38 38 
                format('embedded-opentype'),
39 
-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.woff')
39 
+             url('/fonts/icon.woff')
40 40 
                format('woff'),
41 
-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.ttf')
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+             url('/fonts/icon.ttf')
42 42 
                format('truetype'),
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-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.svg')
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+             url('/fonts/icon.svg')
44 44 
                format('svg');
45 45 
         font-weight: normal;
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         font-style: normal;
47 47 
       }
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     </style>
49 49
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/application.css">
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/highlight/highlight.css">
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+    <link rel="stylesheet" href="../stylesheets/application.css">
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+    <link rel="stylesheet" href="../stylesheets/temporary.css">
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+    <link rel="stylesheet" href="../stylesheets/palettes.css">
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+    <link rel="stylesheet" href="../stylesheets/highlight/highlight.css">
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     </style>
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-    <script src="https://guangchuangyu.github.io/ggtree/javascripts/modernizr.js"></script>
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+    <script src="../javascripts/modernizr.js"></script>
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138 138 
     <div class="banner">
139 139
140 140 
         <div class="logo">
141 
-          <img src="https://guangchuangyu.github.io/ggtree/images/gc.png">
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+          <img src="../images/gc.png">
142 142 
         </div>
143 143
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       <div class="name">
... ... 
@@ -460,7 +460,7 @@ multiple sequence alignment with <a href="https://twitter.com/hashtag/phylogenet
460 460 
 <nav class="pagination" aria-label="Footer">
461 461 
   <div class="previous">
462 462
463 
-      <a href="https://guangchuangyu.github.io/ggtree/featured-articles/" title="Featured Articles">
463 
+      <a href="../featured-articles/" title="Featured Articles">
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         <span class="direction">
465 465 
           Previous
466 466 
         </span>
... ... 
@@ -503,12 +503,12 @@ multiple sequence alignment with <a href="https://twitter.com/hashtag/phylogenet
503 503
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     <script>
505 505
506 
-      var base_url = 'https:\/\/guangchuangyu.github.io\/ggtree\/';
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+      var base_url = '\/';
507 507 
       var repo_id  = 'GuangchuangYu\/ggtree';
508 508
509 509 
     </script>
510 510
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-    <script src="https://guangchuangyu.github.io/ggtree/javascripts/application.js"></script>
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+    <script src="../javascripts/application.js"></script>
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docs/gallery/index.xml
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@@ -2,22 +2,22 @@
2 2 
 <rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
3 3 
   <channel>
4 4 
     <title>Galleries on ggtree - Guangchuang Yu</title>
5 
-    <link>https://guangchuangyu.github.io/ggtree/gallery/</link>
5 
+    <link>/gallery/</link>
6 6 
     <description>Recent content in Galleries on ggtree - Guangchuang Yu</description>
7 7 
     <generator>Hugo -- gohugo.io</generator>
8 8 
     <language>en-us</language>
9 9 
     <copyright>Released under the Artistic-2.0 license</copyright>
10 10 
     <lastBuildDate>Mon, 24 Jul 2017 00:11:02 +0100</lastBuildDate>
11 11
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-	<atom:link href="https://guangchuangyu.github.io/ggtree/gallery/index.xml" rel="self" type="application/rss+xml" />
12 
+	<atom:link href="/gallery/index.xml" rel="self" type="application/rss+xml" />
13 13
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     <item>
16 16 
       <title>Gallery</title>
17 
-      <link>https://guangchuangyu.github.io/ggtree/gallery/</link>
17 
+      <link>/gallery/</link>
18 18 
       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
19 19
20 
-      <guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>
20 
+      <guid>/gallery/</guid>
21 21 
       <description>Journal Articles  http://dx.doi.org/10.3389/fmicb.2017.00543    https://doi.org/10.3389/fmicb.2017.00456    http://dx.doi.org/10.1186/s40168-017-0232-3    http://dx.doi.org/10.1111/2041-210X.12628    http://dx.doi.org/10.1128/AEM.02307-16    http://dx.doi.org/10.3389%2Ffcimb.2016.00036    http://dx.doi.org/10.1016/j.meegid.2015.12.006     Tweets Adaptive radiation of #Darwin&#39;s finches showing #genotypic and #morphometric evolution. Good excuse to practice with #ggtree @guangchuangyu pic.twitter.com/JJZ3Yje58s — Will Harvey (@_wharvey) February 15, 2017  am quite liking #ggtree #rstats #ggplot pic.</description>
22 22 
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23 23
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
17 17
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-    <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/">
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     <meta name="author" content="Guangchuang Yu">
21 21
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-    <meta property="og:url" content="https://guangchuangyu.github.io/ggtree/">
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+    <meta property="og:url" content="/">
24 24 
     <meta property="og:title" content="ggtree - Guangchuang Yu">
25 
-    <meta property="og:image" content="https://guangchuangyu.github.io/ggtree/images/gc.png">
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+    <meta property="og:image" content="/images/gc.png">
26 26 
     <meta name="apple-mobile-web-app-title" content="ggtree - Guangchuang Yu">
27 27 
     <meta name="apple-mobile-web-app-capable" content="yes">
28 28 
     <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
29 29
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-    <link rel="shortcut icon" type="image/x-icon" href="https://guangchuangyu.github.io/ggtree/images/favicon.ico">
31 
-    <link rel="icon" type="image/x-icon" href="https://guangchuangyu.github.io/ggtree/images/favicon.ico">
30 
+    <link rel="shortcut icon" type="image/x-icon" href="./images/favicon.ico">
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+    <link rel="icon" type="image/x-icon" href="./images/favicon.ico">
32 32
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     <style>
34 34 
       @font-face {
35 35 
         font-family: 'Icon';
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-        src: url('https://guangchuangyu.github.io/ggtree/fonts/icon.eot');
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-        src: url('https://guangchuangyu.github.io/ggtree/fonts/icon.eot')
36 
+        src: url('/fonts/icon.eot');
37 
+        src: url('/fonts/icon.eot')
38 38 
                format('embedded-opentype'),
39 
-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.woff')
39 
+             url('/fonts/icon.woff')
40 40 
                format('woff'),
41 
-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.ttf')
41 
+             url('/fonts/icon.ttf')
42 42 
                format('truetype'),
43 
-             url('https://guangchuangyu.github.io/ggtree/fonts/icon.svg')
43 
+             url('/fonts/icon.svg')
44 44 
                format('svg');
45 45 
         font-weight: normal;
46 46 
         font-style: normal;
47 47 
       }
48 48 
     </style>
49 49
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/application.css">
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/temporary.css">
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/palettes.css">
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-    <link rel="stylesheet" href="https://guangchuangyu.github.io/ggtree/stylesheets/highlight/highlight.css">
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+    <link rel="stylesheet" href="./stylesheets/application.css">
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+    <link rel="stylesheet" href="./stylesheets/temporary.css">
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+    <link rel="stylesheet" href="./stylesheets/palettes.css">
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+    <link rel="stylesheet" href="./stylesheets/highlight/highlight.css">
54 54
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66 66 
     </style>
67 67
68 68
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-    <script src="https://guangchuangyu.github.io/ggtree/javascripts/modernizr.js"></script>
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+    <script src="./javascripts/modernizr.js"></script>
70 70
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-    <link href="https://guangchuangyu.github.io/ggtree/index.xml" rel="alternate" type="application/rss+xml" title="ggtree - Guangchuang Yu" />
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-    <link href="https://guangchuangyu.github.io/ggtree/index.xml" rel="feed" type="application/rss+xml" title="ggtree - Guangchuang Yu" />
72 
+    <link href="./index.xml" rel="alternate" type="application/rss+xml" title="ggtree - Guangchuang Yu" />
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+    <link href="./index.xml" rel="feed" type="application/rss+xml" title="ggtree - Guangchuang Yu" />
74 74
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@@ -141,7 +141,7 @@
141 141 
     <div class="banner">
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143 143 
         <div class="logo">
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-          <img src="https://guangchuangyu.github.io/ggtree/images/gc.png">
144 
+          <img src="./images/gc.png">
145 145 
         </div>
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       <div class="name">
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@@ -187,12 +187,15 @@
187 187
188 188
189 189
190 
-<a  title="ggtree" href="./">
190 
+<a class="current" title="ggtree" href="./">
191 191
192 192 
 	ggtree
193 193 
 </a>
194 194
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+<ul id="scrollspy">
197 
+</ul>
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+
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 </li>
... ... 
@@ -453,7 +456,7 @@ biocLite(&quot;ggtree&quot;)</code></pre>
453 456
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   <div class="next">
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-      <a href="https://guangchuangyu.github.io/ggtree/documentation/" title="Documentation">
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+      <a href="./documentation/" title="Documentation">
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489 492
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     <script>
491 494
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-      var base_url = 'https:\/\/guangchuangyu.github.io\/ggtree\/';
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+      var base_url = '\/';
493 496 
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494 497
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     </script>
496 499
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 <rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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     <title>ggtree - Guangchuang Yu</title>
5 
-    <link>https://guangchuangyu.github.io/ggtree/</link>
5 
+    <link>/</link>
6 6 
     <description>Recent content on ggtree - Guangchuang Yu</description>
7 7 
     <generator>Hugo -- gohugo.io</generator>
8 8 
     <language>en-us</language>
9 9 
     <copyright>Released under the Artistic-2.0 license</copyright>
10 10 
     <lastBuildDate>Sat, 08 Jul 2017 21:07:13 +0100</lastBuildDate>
11 11
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-	<atom:link href="https://guangchuangyu.github.io/ggtree/index.xml" rel="self" type="application/rss+xml" />
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+	<atom:link href="/index.xml" rel="self" type="application/rss+xml" />
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     <item>
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       <title>ggtree: visualization and annotation of phylogenetic trees</title>
17 
-      <link>https://guangchuangyu.github.io/ggtree/</link>
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+      <link>/</link>
18 18 
       <pubDate>Sat, 08 Jul 2017 21:07:13 +0100</pubDate>
19 19
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-      <guid>https://guangchuangyu.github.io/ggtree/</guid>
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+      <guid>/</guid>
21 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 22 
  Authors Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</description>
23 23 
     </item>
24 24
25 25 
     <item>
26 26 
       <title>Documentation</title>
27 
-      <link>https://guangchuangyu.github.io/ggtree/documentation/</link>
27 
+      <link>/documentation/</link>
28 28 
       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
29 29
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-      <guid>https://guangchuangyu.github.io/ggtree/documentation/</guid>
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+      <guid>/documentation/</guid>
31 31 
       <description>Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R    User’s feedback  tweets of ggtree Join the group chat on  and    Find out more on https://guangchuangyu.</description>
32 32 
     </item>
33 33
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     <item>
35 35 
       <title>FAQ</title>
36 
-      <link>https://guangchuangyu.github.io/ggtree/faq/</link>
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+      <link>/faq/</link>
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
38 38
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-      <guid>https://guangchuangyu.github.io/ggtree/faq/</guid>
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+      <guid>/faq/</guid>
40 40 
       <description>Installation  Could not find function If you got this error, please make sure you are using the latest R and ggtree.
41 41 
 Packages in Bioconductor, like ggtree, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to devel branch.
42 42 
 Sometimes I may write blog post to introduce new functions which is not available in release branch, you need to install the devel version of ggtree in order to use these new functions.</description>
... ... 
@@ -44,10 +44,10 @@ Sometimes I may write blog post to introduce new functions which is not availabl
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     <item>
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       <title>Featured Articles</title>
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-      <link>https://guangchuangyu.github.io/ggtree/featured-articles/</link>
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+      <link>/featured-articles/</link>
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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-      <guid>https://guangchuangyu.github.io/ggtree/featured-articles/</guid>
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+      <guid>/featured-articles/</guid>
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       <description>Let us know if you have published using ggtree and your publication will be featured here.
52 52 
  2017 Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017
53 53 
 Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus. Frontiers in Microbiology, 2017, 8:543
... ... 
@@ -56,10 +56,10 @@ Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotid
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     <item>
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       <title>Gallery</title>
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-      <link>https://guangchuangyu.github.io/ggtree/gallery/</link>
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+      <link>/gallery/</link>
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
61 61
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-      <guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>
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+      <guid>/gallery/</guid>
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       <description>Journal Articles  http://dx.doi.org/10.3389/fmicb.2017.00543    https://doi.org/10.3389/fmicb.2017.00456    http://dx.doi.org/10.1186/s40168-017-0232-3    http://dx.doi.org/10.1111/2041-210X.12628    http://dx.doi.org/10.1128/AEM.02307-16    http://dx.doi.org/10.3389%2Ffcimb.2016.00036    http://dx.doi.org/10.1016/j.meegid.2015.12.006     Tweets Adaptive radiation of #Darwin&#39;s finches showing #genotypic and #morphometric evolution. Good excuse to practice with #ggtree @guangchuangyu pic.twitter.com/JJZ3Yje58s — Will Harvey (@_wharvey) February 15, 2017  am quite liking #ggtree #rstats #ggplot pic.</description>
64 64 
     </item>
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-(function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(require,module,exports){
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-"use strict";
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-});
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-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
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-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
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-function getFilterSet(group) {
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-  var fsVar = group.var("filterset");
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-  /**
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-   * for the given group of widgets. Filter input controls should create one
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-   * an array of keys which should be displayed. Crosstalk will aggregate the
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-   * various key arrays by finding their intersection; only keys that are
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-  function FilterHandle(group, extraInfo) {
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-    this._eventRelay = new _events2.default();
152 
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153 
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155 
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156 
-    // The filterSet that we're tracking, if any. Can change over time.
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-    // The Var we're currently tracking, if any. Can change over time.
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-  /**
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-   */
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-
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-
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-  _createClass(FilterHandle, [{
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-    key: "setGroup",
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-    value: function setGroup(group) {
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-
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-
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-      if (this._filterVar) {
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-        this._filterVar.off("change", this._varOnChangeSub);
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-        this._filterVar = null;
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-        this._filterSet = null;
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-      }
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-      this._group = group;
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-
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-      if (group) {
203 
-        group = (0, _group2.default)(group);
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-        this._filterSet = getFilterSet(group);
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-        this._filterVar = (0, _group2.default)(group).var("filter");
206 
-        var sub = this._filterVar.on("change", function (e) {
207 
-          _this._eventRelay.trigger("change", e, _this);
208 
-        });
209 
-        this._varOnChangeSub = sub;
210 
-      }
211 
-    }
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-
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-    /**
214 
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215 
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217 
-     */
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-
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-  }, {
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-    value: function _mergeExtraInfo(extraInfo) {
222 
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223 
-    }
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-
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-    /**
226 
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227 
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-
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-  }, {
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-    key: "close",
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-    value: function close() {
233 
-      this._emitter.removeAllListeners();
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236 
-    }
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-
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-    /**
239 
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240 
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-     * @param {Object} [extraInfo] - Extra properties to be included on the event
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-     *   object that's passed to listeners (in addition to any options that were
243 
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244 
-     */
245 
-
246 
-  }, {
247 
-    key: "clear",
248 
-    value: function clear(extraInfo) {
249 
-      if (!this._filterSet) return;
250 
-      this._filterSet.clear(this._id);
251 
-      this._onChange(extraInfo);
252 
-    }
253 
-
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-    /**
255 
-     * Set this handle's contribution to the filter set. This array should consist
256 
-     * of the keys of the rows that _should_ be displayed; any keys that are not
257 
-     * present in the array will be considered _filtered out_. Note that multiple
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-     * `FilterHandle` instances in the group may each contribute an array of keys,
259 
-     * and only those keys that appear in _all_ of the arrays make it through the
260 
-     * filter.
261 
-     *
262 
-     * @param {string[]} keys - Empty array, or array of keys. To clear the
263 
-     *   filter, don't pass an empty array; instead, use the
264 
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265 
-     * @param {Object} [extraInfo] - Extra properties to be included on the event
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-     *   object that's passed to listeners (in addition to any options that were
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-     *   passed into the `FilterHandle` constructor).
268 
-     */
269 
-
270 
-  }, {
271 
-    key: "set",
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-    value: function set(keys, extraInfo) {
273 
-      if (!this._filterSet) return;
274 
-      this._filterSet.update(this._id, keys);
275 
-      this._onChange(extraInfo);
276 
-    }
277 
-
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-    /**
279 
-     * @return {string[]|null} - Either: 1) an array of keys that made it through
280 
-     *   all of the `FilterHandle` instances, or, 2) `null`, which means no filter
281 
-     *   is being applied (all data should be displayed).
282 
-     */
283 
-
284 
-  }, {
285 
-    key: "on",
286 
-
287 
-
288 
-    /**
289 
-     * Subscribe to events on this `FilterHandle`.
290 
-     *
291 
-     * @param {string} eventType - Indicates the type of events to listen to.
292 
-     *   Currently, only `"change"` is supported.
293 
-     * @param {FilterHandle~listener} listener - The callback function that
294 
-     *   will be invoked when the event occurs.
295 
-     * @return {string} - A token to pass to {@link FilterHandle#off} to cancel
296 
-     *   this subscription.
297 
-     */
298 
-    value: function on(eventType, listener) {
299 
-      return this._emitter.on(eventType, listener);
300 
-    }
301 
-
302 
-    /**
303 
-     * Cancel event subscriptions created by {@link FilterHandle#on}.
304 
-     *
305 
-     * @param {string} eventType - The type of event to unsubscribe.
306 
-     * @param {string|FilterHandle~listener} listener - Either the callback
307 
-     *   function previously passed into {@link FilterHandle#on}, or the
308 
-     *   string that was returned from {@link FilterHandle#on}.
309 
-     */
310 
-
311 
-  }, {
312 
-    key: "off",
313 
-    value: function off(eventType, listener) {
314 
-      return this._emitter.off(eventType, listener);
315 
-    }
316 
-  }, {
317 
-    key: "_onChange",
318 
-    value: function _onChange(extraInfo) {
319 
-      if (!this._filterSet) return;
320 
-      this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));
321 
-    }
322 
-
323 
-    /**
324 
-     * @callback FilterHandle~listener
325 
-     * @param {Object} event - An object containing details of the event. For
326 
-     *   `"change"` events, this includes the properties `value` (the new
327 
-     *   value of the filter set, or `null` if no filter set is active),
328 
-     *   `oldValue` (the previous value of the filter set), and `sender` (the
329 
-     *   `FilterHandle` instance that made the change).
330 
-     */
331 
-
332 
-    /**
333 
-     * @event FilterHandle#change
334 
-     * @type {object}
335 
-     * @property {object} value - The new value of the filter set, or `null`
336 
-     *   if no filter set is active.
337 
-     * @property {object} oldValue - The previous value of the filter set.
338 
-     * @property {FilterHandle} sender - The `FilterHandle` instance that
339 
-     *   changed the value.
340 
-     */
341 
-
342 
-  }, {
343 
-    key: "filteredKeys",
344 
-    get: function get() {
345 
-      return this._filterSet ? this._filterSet.value : null;
346 
-    }
347 
-  }]);
348 
-
349 
-  return FilterHandle;
350 
-}();
351 
-
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-},{"./events":1,"./filterset":3,"./group":4,"./util":11}],3:[function(require,module,exports){
353 
-"use strict";
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-
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-Object.defineProperty(exports, "__esModule", {
356 
-  value: true
357 
-});
358 
-
359 
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
360 
-
361 
-var _util = require("./util");
362 
-
363 
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
364 
-
365 
-function naturalComparator(a, b) {
366 
-  if (a === b) {
367 
-    return 0;
368 
-  } else if (a < b) {
369 
-    return -1;
370 
-  } else if (a > b) {
371 
-    return 1;
372 
-  }
373 
-}
374 
-
375 
-/**
376 
- * @private
377 
- */
378 
-
379 
-var FilterSet = function () {
380 
-  function FilterSet() {
381 
-    _classCallCheck(this, FilterSet);
382 
-
383 
-    this.reset();
384 
-  }
385 
-
386 
-  _createClass(FilterSet, [{
387 
-    key: "reset",
388 
-    value: function reset() {
389 
-      // Key: handle ID, Value: array of selected keys, or null
390 
-      this._handles = {};
391 
-      // Key: key string, Value: count of handles that include it
392 
-      this._keys = {};
393 
-      this._value = null;
394 
-      this._activeHandles = 0;
395 
-    }
396 
-  }, {
397 
-    key: "update",
398 
-    value: function update(handleId, keys) {
399 
-      if (keys !== null) {
400 
-        keys = keys.slice(0); // clone before sorting
401 
-        keys.sort(naturalComparator);
402 
-      }
403 
-
404 
-      var _diffSortedLists = (0, _util.diffSortedLists)(this._handles[handleId], keys),
405 
-          added = _diffSortedLists.added,
406 
-          removed = _diffSortedLists.removed;
407 
-
408 
-      this._handles[handleId] = keys;
409 
-
410 
-      for (var i = 0; i < added.length; i++) {
411 
-        this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;
412 
-      }
413 
-      for (var _i = 0; _i < removed.length; _i++) {
414 
-        this._keys[removed[_i]]--;
415 
-      }
416 
-
417 
-      this._updateValue(keys);
418 
-    }
419 
-
420 
-    /**
421 
-     * @param {string[]} keys Sorted array of strings that indicate
422 
-     * a superset of possible keys.
423 
-     * @private
424 
-     */
425 
-
426 
-  }, {
427 
-    key: "_updateValue",
428 
-    value: function _updateValue() {
429 
-      var keys = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : this._allKeys;
430 
-
431 
-      var handleCount = Object.keys(this._handles).length;
432 
-      if (handleCount === 0) {
433 
-        this._value = null;
434 
-      } else {
435 
-        this._value = [];
436 
-        for (var i = 0; i < keys.length; i++) {
437 
-          var count = this._keys[keys[i]];
438 
-          if (count === handleCount) {
439 
-            this._value.push(keys[i]);
440 
-          }
441 
-        }