Bioconductor Code: Browse

Browse code

fixed homepage order

GuangchuangYu authored on 24/07/2017 16:13:01
Showing 14 changed files

docs/documentation/index.html index ef7be9ce..86e0e2a7 100644
docs/faq/index.html index acbe04fb..19bcda2b 100644
docs/featuredarticles/index.html index cdb50911..7a0cfa9c 100644
docs/featuredarticles/index.xml index d0aed203..fff532b9 100644
docs/gallery/index.html index af8a7dec..50981da1 100644
site_src/ggtree.png
docs/index.html index 0bf44efa..58ad2f55 100644
docs/index.rmd index ee5ba781..f2d4f997 100644
docs/index.xml index 10742ac1..8590324f 100644
docs/sitemap.xml index 35ea0392..a986a517 100644
site_src/config.toml index 4859bddb..bf64c8f4 100644
site_src/content/featuredArticles/index.html index 0c1c4b71..70daab12 100644
site_src/content/index.html index 98254d7e..3669d21d 100644
site_src/content/index.rmd index ee5ba781..f2d4f997 100644

History View file @ 773e11e3

@@ -184,15 +184,12 @@
                     -<a class="current" title="Documentation" href="../documentation/">
                     +<a  title="ggtree" href="../">
                     -	Documentation
                     +	ggtree
                      </a>
                     -<ul id="scrollspy">
                     -</ul>
+                    -
                      </li>
@@ -205,12 +202,15 @@
                     -<a  title="FAQ" href="../faq/">
                     +<a class="current" title="Documentation" href="../documentation/">
                     -	FAQ
                     +	Documentation
                      </a>
                     +<ul id="scrollspy">
                     +</ul>
+                    +
                      </li>
@@ -223,9 +223,9 @@
                     -<a  title="Featured Articles" href="../featuredArticles/">
                     +<a  title="FAQ" href="../faq/">
                     -	Featured Articles
                     +	FAQ
                      </a>
@@ -241,9 +241,9 @@
                     -<a  title="Gallery" href="../gallery/">
                     +<a  title="Featured Articles" href="../featuredArticles/">
                     -	Gallery
                     +	Featured Articles
                      </a>
@@ -259,9 +259,9 @@
                     -<a  title="ggtree" href="../">
                     +<a  title="Gallery" href="../gallery/">
                     -	ggtree
                     +	Gallery
                      </a>
@@ -455,6 +455,22 @@
                      <nav class="pagination" aria-label="Footer">
                        <div class="previous">
                     +      <a href="https://guangchuangyu.github.io/ggtree/" title="ggtree: visualization and annotation of phylogenetic trees">
                     +        <span class="direction">
                     +          Previous
                     +        </span>
                     +        <div class="page">
                     +          <div class="button button-previous" role="button" aria-label="Previous">
                     +            <i class="icon icon-back"></i>
                     +          </div>
                     +          <div class="stretch">
                     +            <div class="title">
                     +              ggtree: visualization and annotation of phylogenetic trees
                     +            </div>
                     +          </div>
                     +        </div>
                     +      </a>
+                    +
                        </div>
                        <div class="next">

docs/faq/index.html

History View file @ 773e11e3

@@ -184,9 +184,9 @@
                     -<a  title="Documentation" href="../documentation/">
                     +<a  title="ggtree" href="../">
                     -	Documentation
                     +	ggtree
                      </a>
@@ -202,15 +202,12 @@
                     -<a class="current" title="FAQ" href="../faq/">
                     +<a  title="Documentation" href="../documentation/">
                     -	FAQ
                     +	Documentation
                      </a>
                     -<ul id="scrollspy">
                     -</ul>
+                    -
                      </li>
@@ -223,12 +220,15 @@
                     -<a  title="Featured Articles" href="../featuredArticles/">
                     +<a class="current" title="FAQ" href="../faq/">
                     -	Featured Articles
                     +	FAQ
                      </a>
                     +<ul id="scrollspy">
                     +</ul>
+                    +
                      </li>
@@ -241,9 +241,9 @@
                     -<a  title="Gallery" href="../gallery/">
                     +<a  title="Featured Articles" href="../featuredArticles/">
                     -	Gallery
                     +	Featured Articles
                      </a>
@@ -259,9 +259,9 @@
                     -<a  title="ggtree" href="../">
                     +<a  title="Gallery" href="../gallery/">
                     -	ggtree
                     +	Gallery
                      </a>

docs/featuredarticles/index.html

History View file @ 773e11e3

@@ -184,9 +184,9 @@
                     -<a  title="Documentation" href="../documentation/">
                     +<a  title="ggtree" href="../">
                     -	Documentation
                     +	ggtree
                      </a>
@@ -202,9 +202,9 @@
                     -<a  title="FAQ" href="../faq/">
                     +<a  title="Documentation" href="../documentation/">
                     -	FAQ
                     +	Documentation
                      </a>
@@ -220,9 +220,9 @@
                     -<a  title="Featured Articles" href="../featuredArticles/">
                     +<a  title="FAQ" href="../faq/">
                     -	Featured Articles
                     +	FAQ
                      </a>
@@ -238,9 +238,9 @@
                     -<a  title="Gallery" href="../gallery/">
                     +<a  title="Featured Articles" href="../featuredArticles/">
                     -	Gallery
                     +	Featured Articles
                      </a>
@@ -256,9 +256,9 @@
                     -<a  title="ggtree" href="../">
                     +<a  title="Gallery" href="../gallery/">
                     -	ggtree
                     +	Gallery
                      </a>
@@ -342,12 +342,12 @@
                          height: 300px;
+                       }
                        </style>
                     -<div id="chart7d9e7b2133f2" class="rChart morris">
                     +<div id="chart144017eefeff" class="rChart morris">
                      </div>
                      <script type='text/javascript'>
                          var chartParams = {
                     - "element": "chart7d9e7b2133f2",
                     + "element": "chart144017eefeff",
                      "width":            800,
                      "height":            400,
                      "xkey": "year",
@@ -366,7 +366,7 @@
                      "pubid": "HtEfBTGE9r8C"
+                     }
                      ],
                     -"id": "chart7d9e7b2133f2",
                     +"id": "chart144017eefeff",
                      "labels": "cites"
                      },
                            chartType = "Bar"

docs/featuredarticles/index.xml

History View file @ 773e11e3

@@ -20,7 +20,7 @@
                            <guid>https://guangchuangyu.github.io/ggtree/featuredarticles/</guid>
                            <description>Let us know if you have published using ggtree and your publication will be featured here.
                     -    .rChart { display: block; margin-left: auto; margin-right: auto; width: 800px; height: 300px; }   var chartParams = { &#34;element&#34;: &#34;chart7d9e7b2133f2&#34;, &#34;width&#34;: 800, &#34;height&#34;: 400, &#34;xkey&#34;: &#34;year&#34;, &#34;ykeys&#34;: [ &#34;cites&#34; ], &#34;data&#34;: [ { &#34;year&#34;: 2016, &#34;cites&#34;: 1, &#34;</description>
                     +    .rChart { display: block; margin-left: auto; margin-right: auto; width: 800px; height: 300px; }   var chartParams = { &#34;element&#34;: &#34;chart144017eefeff&#34;, &#34;width&#34;: 800, &#34;height&#34;: 400, &#34;xkey&#34;: &#34;year&#34;, &#34;ykeys&#34;: [ &#34;cites&#34; ], &#34;data&#34;: [ { &#34;year&#34;: 2016, &#34;cites&#34;: 1, &#34;</description>
                          </item>
                        </channel>

docs/gallery/index.html

History View file @ 773e11e3

@@ -184,9 +184,9 @@
                     -<a  title="Documentation" href="../documentation/">
                     +<a  title="ggtree" href="../">
                     -	Documentation
                     +	ggtree
                      </a>
@@ -202,9 +202,9 @@
                     -<a  title="FAQ" href="../faq/">
                     +<a  title="Documentation" href="../documentation/">
                     -	FAQ
                     +	Documentation
                      </a>
@@ -220,9 +220,9 @@
                     -<a  title="Featured Articles" href="../featuredArticles/">
                     +<a  title="FAQ" href="../faq/">
                     -	Featured Articles
                     +	FAQ
                      </a>
@@ -238,15 +238,12 @@
                     -<a class="current" title="Gallery" href="../gallery/">
                     +<a  title="Featured Articles" href="../featuredArticles/">
                     -	Gallery
                     +	Featured Articles
                      </a>
                     -<ul id="scrollspy">
                     -</ul>
+                    -
                      </li>
@@ -259,12 +256,15 @@
                     -<a  title="ggtree" href="../">
                     +<a class="current" title="Gallery" href="../gallery/">
                     -	ggtree
                     +	Gallery
                      </a>
                     +<ul id="scrollspy">
                     +</ul>
+                    +
                      </li>
@@ -480,22 +480,6 @@ multiple sequence alignment with <a href="https://twitter.com/hashtag/phylogenet
                        <div class="next">
                     -      <a href="https://guangchuangyu.github.io/ggtree/" title="ggtree: visualization and annotation of phylogenetic trees">
                     -        <span class="direction">
                     -          Next
                     -        </span>
                     -        <div class="page">
                     -          <div class="stretch">
                     -            <div class="title">
                     -              ggtree: visualization and annotation of phylogenetic trees
                     -            </div>
                     -          </div>
                     -          <div class="button button-next" role="button" aria-label="Next">
                     -            <i class="icon icon-forward"></i>
                     -          </div>
                     -        </div>
                     -      </a>
+                    -
                        </div>
                      </nav>

site_src/ggtree.png

History View file @ 773e11e3

                     similarity index 100%
                     rename from site_src/ggtree.png
                     rename to docs/ggtree.png

docs/index.html

History View file @ 773e11e3

@@ -187,9 +187,9 @@
                     -<a  title="Documentation" href="./documentation/">
                     +<a  title="ggtree" href="./">
                     -	Documentation
                     +	ggtree
                      </a>
@@ -205,9 +205,9 @@
                     -<a  title="FAQ" href="./faq/">
                     +<a  title="Documentation" href="./documentation/">
                     -	FAQ
                     +	Documentation
                      </a>
@@ -223,9 +223,9 @@
                     -<a  title="Featured Articles" href="./featuredArticles/">
                     +<a  title="FAQ" href="./faq/">
                     -	Featured Articles
                     +	FAQ
                      </a>
@@ -241,9 +241,9 @@
                     -<a  title="Gallery" href="./gallery/">
                     +<a  title="Featured Articles" href="./featuredArticles/">
                     -	Gallery
                     +	Featured Articles
                      </a>
@@ -259,9 +259,9 @@
                     -<a  title="ggtree" href="./">
                     +<a  title="Gallery" href="./gallery/">
                     -	ggtree
                     +	Gallery
                      </a>
@@ -453,14 +453,14 @@ biocLite(&quot;ggtree&quot;)</code></pre>
                        <div class="next">
                     -      <a href="https://guangchuangyu.github.io/ggtree/faq/" title="FAQ">
                     +      <a href="https://guangchuangyu.github.io/ggtree/documentation/" title="Documentation">
                              <span class="direction">
                                Next
                              </span>
                              <div class="page">
                                <div class="stretch">
                                  <div class="title">
                     -              FAQ
                     +              Documentation
                                  </div>
                                </div>
                                <div class="button button-next" role="button" aria-label="Next">

docs/index.rmd

History View file @ 773e11e3

@@ -2,7 +2,7 @@
                      date: 2017-07-08T21:07:13+01:00
                      title: 'ggtree: visualization and annotation of phylogenetic trees'
                      type: index
                     -weight: 0
                     +weight: 1
                      ---

docs/index.xml

History View file @ 773e11e3

@@ -7,11 +7,21 @@
                          <generator>Hugo -- gohugo.io</generator>
                          <language>en-us</language>
                          <copyright>Released under the Artistic-2.0 license</copyright>
                     -    <lastBuildDate>Mon, 24 Jul 2017 00:11:02 +0100</lastBuildDate>
                     +    <lastBuildDate>Sat, 08 Jul 2017 21:07:13 +0100</lastBuildDate>
                      	<atom:link href="https://guangchuangyu.github.io/ggtree/index.xml" rel="self" type="application/rss+xml" />
                     +    <item>
                     +      <title>ggtree: visualization and annotation of phylogenetic trees</title>
                     +      <link>https://guangchuangyu.github.io/ggtree/</link>
                     +      <pubDate>Sat, 08 Jul 2017 21:07:13 +0100</pubDate>
+                    +
                     +      <guid>https://guangchuangyu.github.io/ggtree/</guid>
                     +      <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.
                     + Authors Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</description>
                     +    </item>
+                    +
                          <item>
                            <title>Documentation</title>
                            <link>https://guangchuangyu.github.io/ggtree/documentation/</link>
@@ -40,7 +50,7 @@ Sometimes I may write blog post to introduce new functions which is not availabl
                            <guid>https://guangchuangyu.github.io/ggtree/featuredarticles/</guid>
                            <description>Let us know if you have published using ggtree and your publication will be featured here.
                     -    .rChart { display: block; margin-left: auto; margin-right: auto; width: 800px; height: 300px; }   var chartParams = { &#34;element&#34;: &#34;chart7d9e7b2133f2&#34;, &#34;width&#34;: 800, &#34;height&#34;: 400, &#34;xkey&#34;: &#34;year&#34;, &#34;ykeys&#34;: [ &#34;cites&#34; ], &#34;data&#34;: [ { &#34;year&#34;: 2016, &#34;cites&#34;: 1, &#34;</description>
                     +    .rChart { display: block; margin-left: auto; margin-right: auto; width: 800px; height: 300px; }   var chartParams = { &#34;element&#34;: &#34;chart144017eefeff&#34;, &#34;width&#34;: 800, &#34;height&#34;: 400, &#34;xkey&#34;: &#34;year&#34;, &#34;ykeys&#34;: [ &#34;cites&#34; ], &#34;data&#34;: [ { &#34;year&#34;: 2016, &#34;cites&#34;: 1, &#34;</description>
                          </item>
                          <item>
@@ -52,15 +62,5 @@ Sometimes I may write blog post to introduce new functions which is not availabl
                            <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>
                          </item>
                     -    <item>
                     -      <title>ggtree: visualization and annotation of phylogenetic trees</title>
                     -      <link>https://guangchuangyu.github.io/ggtree/</link>
                     -      <pubDate>Sat, 08 Jul 2017 21:07:13 +0100</pubDate>
+                    -
                     -      <guid>https://guangchuangyu.github.io/ggtree/</guid>
                     -      <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.
                     - Authors Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</description>
                     -    </item>
+                    -
                        </channel>
                      </rss>
                     \ No newline at end of file

docs/sitemap.xml

History View file @ 773e11e3

@@ -2,6 +2,11 @@
                      <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"
                        xmlns:xhtml="http://www.w3.org/1999/xhtml">
                     +  <url>
                     +    <loc>https://guangchuangyu.github.io/ggtree/</loc>
                     +    <lastmod>2017-07-08T21:07:13+01:00</lastmod>
                     +  </url>
+                    +
                        <url>
                          <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
                          <lastmod>2017-07-24T00:11:02+01:00</lastmod>
@@ -22,11 +27,6 @@
                          <lastmod>2017-07-24T00:11:02+01:00</lastmod>
                        </url>
                     -  <url>
                     -    <loc>https://guangchuangyu.github.io/ggtree/</loc>
                     -    <lastmod>2017-07-08T21:07:13+01:00</lastmod>
                     -  </url>
+                    -
                        <url>
                          <loc>https://guangchuangyu.github.io/ggtree/categories/</loc>
                          <priority>0</priority>
@@ -63,7 +63,7 @@
                        <url>
                          <loc>https://guangchuangyu.github.io/ggtree/</loc>
                     -    <lastmod>2017-07-24T00:11:02+01:00</lastmod>
                     +    <lastmod>2017-07-08T21:07:13+01:00</lastmod>
                          <priority>0</priority>
                        </url>

site_src/config.toml

History View file @ 773e11e3

@@ -51,7 +51,7 @@ relativeurls = true
                      [[menu.main]]
                      	name   = "ggtree"
                      	url    = "/"
                     -	weight = 0
                     +	weight = 1
                      [[menu.main]]
                      	name   = "Documentation"

site_src/content/featuredArticles/index.html

History View file @ 773e11e3

@@ -28,12 +28,12 @@ weight: 30
                          height: 300px;
+                       }
                        </style>
                     -<div id="chart7d9e7b2133f2" class="rChart morris">
                     +<div id="chart144017eefeff" class="rChart morris">
                      </div>
                      <script type='text/javascript'>
                          var chartParams = {
                     - "element": "chart7d9e7b2133f2",
                     + "element": "chart144017eefeff",
                      "width":            800,
                      "height":            400,
                      "xkey": "year",
@@ -52,7 +52,7 @@ weight: 30
                      "pubid": "HtEfBTGE9r8C"
+                     }
                      ],
                     -"id": "chart7d9e7b2133f2",
                     +"id": "chart144017eefeff",
                      "labels": "cites"
                      },
                            chartType = "Bar"

site_src/content/index.html

History View file @ 773e11e3

@@ -2,7 +2,7 @@
                      date: 2017-07-08T21:07:13+01:00
                      title: 'ggtree: visualization and annotation of phylogenetic trees'
                      type: index
                     -weight: 0
                     +weight: 1
                      ---

site_src/content/index.rmd

History View file @ 773e11e3

@@ -2,7 +2,7 @@
                      date: 2017-07-08T21:07:13+01:00
                      title: 'ggtree: visualization and annotation of phylogenetic trees'
                      type: index
                     -weight: 0
                     +weight: 1
                      ---