Browse code

update docs

guangchuang yu authored on 23/01/2018 04:03:27
Showing 9 changed files

... ...
@@ -6,7 +6,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
6 6
 
7 7
 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
8 8
 
9
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--22-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
9
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
10 10
 
11 11
 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
12 12
 
... ...
@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
25 25
 
26 26
 **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.
27 27
 
28
-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-72-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
28
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-73-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
29 29
 
30 30
 ------------------------------------------------------------------------
31 31
 
... ...
@@ -443,6 +443,7 @@ d$label &lt;- as.numeric(d$label)
443 443
 d &lt;- d[d$label &gt; 80,]
444 444
 
445 445
 q + geom_text(data=d, aes(label=label))</code></pre>
446
+<p><a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/ZeR8YZKIzq8/g5RCB_MiAQAJ">Here is another exammple</a> for multiple bootstrap support values.</p>
446 447
 </div>
447 448
 </div>
448 449
 <div id="aesthetic-mapping" class="section level2">
449 450
Binary files a/docs/images/citation.png and b/docs/images/citation.png differ
... ...
@@ -346,7 +346,7 @@
346 346
 
347 347
 				<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>
348 348
 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
349
-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-23533/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-906/month-blue.svg?style=flat" alt="month" /></a></p>
349
+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.5-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-23533/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-906/month-blue.svg?style=flat" alt="month" /></a></p>
350 350
 <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>
351 351
 <div id="authors" class="section level2">
352 352
 <h2><i class="fa fa-user"></i> Authors</h2>
... ...
@@ -355,7 +355,7 @@
355 355
 <div id="citation" class="section level2">
356 356
 <h2><i class="fa fa-book"></i> Citation</h2>
357 357
 <p>Please cite the following article when using <code>ggtree</code>:</p>
358
-<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-327-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-72-blue.svg?style=flat" alt="citation" /></a></p>
358
+<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-327-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-73-blue.svg?style=flat" alt="citation" /></a></p>
359 359
 <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>
360 360
 </div>
361 361
 <div id="featured-articles" class="section level2">
362 362
new file mode 100644
... ...
@@ -0,0 +1,19 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/tree-utilities.R
3
+\name{getSubtree.df}
4
+\alias{getSubtree.df}
5
+\title{getSubtree.df}
6
+\usage{
7
+getSubtree.df(df, node)
8
+}
9
+\arguments{
10
+\item{df}{tree data.frame}
11
+
12
+\item{node}{id of starting node.}
13
+}
14
+\value{
15
+list of all child node id's from starting node.
16
+}
17
+\description{
18
+Get all children of node from df tree using breath-first.
19
+}
0 20
new file mode 100644
... ...
@@ -0,0 +1,20 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/tree-utilities.R
3
+\name{getSubtreeUnrooted}
4
+\alias{getSubtreeUnrooted}
5
+\title{getSubtreeUnrooted}
6
+\usage{
7
+getSubtreeUnrooted(tree, node)
8
+}
9
+\arguments{
10
+\item{tree}{ape phylo tree object}
11
+
12
+\item{node}{is the tree node id from which the subtrees are derived.}
13
+}
14
+\value{
15
+named list of subtrees with the root id of subtree and list of node id's making up subtree.
16
+}
17
+\description{
18
+Get all subtrees of specified node. This includes all ancestors and relatives of node and
19
+return named list of subtrees.
20
+}
... ...
@@ -106,6 +106,7 @@ d$label &lt;- as.numeric(d$label)
106 106
 d &lt;- d[d$label &gt; 80,]
107 107
 
108 108
 q + geom_text(data=d, aes(label=label))</code></pre>
109
+<p><a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/ZeR8YZKIzq8/g5RCB_MiAQAJ">Here is another exammple</a> for multiple bootstrap support values.</p>
109 110
 </div>
110 111
 </div>
111 112
 <div id="aesthetic-mapping" class="section level2">
... ...
@@ -173,6 +173,9 @@ q + geom_text(data=d, aes(label=label))
173 173
 ```
174 174
 
175 175
 
176
+[Here is another exammple](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/ZeR8YZKIzq8/g5RCB_MiAQAJ) for multiple bootstrap support values.
177
+
178
+
176 179
 ## <i class="fa fa-map-marker"></i> _aesthetic_ mapping
177 180
 
178 181
 ### <i class="fa fa-angle-double-right"></i> inherit _aes_
... ...
@@ -9,7 +9,7 @@ weight: 1
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 11
 <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-1.10.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-23533/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-906/month-blue.svg?style=flat" alt="month" /></a></p>
12
+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.5-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-23533/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-906/month-blue.svg?style=flat" alt="month" /></a></p>
13 13
 <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>
14 14
 <div id="authors" class="section level2">
15 15
 <h2><i class="fa fa-user"></i> Authors</h2>
... ...
@@ -18,7 +18,7 @@ weight: 1
18 18
 <div id="citation" class="section level2">
19 19
 <h2><i class="fa fa-book"></i> Citation</h2>
20 20
 <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-327-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-72-blue.svg?style=flat" alt="citation" /></a></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-327-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-73-blue.svg?style=flat" alt="citation" /></a></p>
22 22
 <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 23
 </div>
24 24
 <div id="featured-articles" class="section level2">