1. ggtree
  2. Commit f55f0c6838da52b89fd07d3cbb6a6460d0d26a81
Browse code

read.nhx supports newick file

guangchuang yu authored on 17/10/2016 03:02:31
Showing 10 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: ggtree
2 2 
 Type: Package
3 3 
 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.5.16
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+Version: 1.5.17
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 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
NEWS
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@@ -1,3 +1,8 @@
1 
+CHANGES IN VERSION 1.5.17
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+------------------------
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+ o read.nhx support newick file <2016-10-17, Mon>
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+   + https://github.com/GuangchuangYu/ggtree/issues/79
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+
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 CHANGES IN VERSION 1.5.16
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 ------------------------
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  o read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue>
R/NHX.R
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... ... 
@@ -15,7 +15,7 @@ read.nhx <- function(file) {
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         treetext <- paste0(treetext, collapse = '')
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     }
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     treetext %<>% gsub(" ", "",. )
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-
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+
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     phylo <- read.tree(text=treetext)
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     nnode <- phylo$Nnode + Ntip(phylo)
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     nlab <- paste("X", 1:nnode, sep="")
... ... 
@@ -32,25 +32,29 @@ read.nhx <- function(file) {
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     nhx.matches <- gregexpr("(\\w+)?(:?\\d*\\.?\\d*[Ee]?[\\+\\-]?\\d*)?\\[&&NHX.*?\\]", treetext)
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     matches <- nhx.matches[[1]]
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     match.pos <- as.numeric(matches)
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-    match.len <- attr(matches, 'match.length')
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-
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-    nhx_str <- substring(treetext, match.pos, match.pos+match.len-1)
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+    if (length(match.pos) == 1 && (match.pos == -1)) {
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+        nhx_stats <- data.frame(node = treeinfo$node)
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+    } else {
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+        match.len <- attr(matches, 'match.length')
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+
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+        nhx_str <- substring(treetext, match.pos, match.pos+match.len-1)
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-    ## nhx_features <- gsub("^(\\w+)?:?\\d*\\.?\\d*[Ee]?[\\+\\-]?\\d*", "", nhx_str) %>%
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-    nhx_features <- gsub("^[^\\[]*", "", nhx_str) %>%
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-        gsub("\\[&&NHX:", "", .) %>%
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+        ## nhx_features <- gsub("^(\\w+)?:?\\d*\\.?\\d*[Ee]?[\\+\\-]?\\d*", "", nhx_str) %>%
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+        nhx_features <- gsub("^[^\\[]*", "", nhx_str) %>%
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+            gsub("\\[&&NHX:", "", .) %>%
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             gsub("\\]", "", .)
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-
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-    nhx_stats <- get_nhx_feature(nhx_features)
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-    fields <- names(nhx_stats)
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-    for (i in ncol(nhx_stats)) {
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-        if(any(grepl("\\D+", nhx_stats[,i])) == FALSE) {
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-            ## should be numerical varialbe
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-            nhx_stats[,i] <- as.numeric(nhx_stats[,i])
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+
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+        nhx_stats <- get_nhx_feature(nhx_features)
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+        fields <- names(nhx_stats)
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+        for (i in ncol(nhx_stats)) {
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+            if(any(grepl("\\D+", nhx_stats[,i])) == FALSE) {
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+                ## should be numerical varialbe
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+                nhx_stats[,i] <- as.numeric(nhx_stats[,i])
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+            }
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         }
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+        nhx_stats$node <- node
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     }
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-    nhx_stats$node <- node
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-
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+
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     new("nhx",
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         file = filename(file),
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         fields = fields,
README.md
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1 1 
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
2 2 
 ===========================================================================================================================
3 3
4 
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.16-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) [![total](https://img.shields.io/badge/downloads-14940/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
4 
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.17-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) [![total](https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
5 5
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-[![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-2016--10--11-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) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![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-2016--10--17-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) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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@@ -17,7 +17,7 @@ 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***. *accepted*
19 19
20 
-[![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) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-125-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
20 
+[![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) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-187-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
21 21
22 22 
 ------------------------------------------------------------------------
23 23
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@@ -50,7 +50,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
50 50
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 ### Download stats
52 52
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-14940/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
53 
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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          +-------------------------+------------------------+-------------------------+----------------+
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          |                                                                                         *   |
docs/featuredArticles/index.html
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   }
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   </style>
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-<div id = 'chart1bce5e7d0c51' class = 'rChart morris'></div>
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+<div id = 'chartbfe1744ae9d' class = 'rChart morris'></div>
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 <script type='text/javascript'>
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     var chartParams = {
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 "pubid": "HtEfBTGE9r8C"
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docs/index.html
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
223 223 
 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.4.20-blue.svg?style=flat" /></a>
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-<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.5.16-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-15163/total-blue.svg?style=flat" /></a>
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+<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.5.17-blue.svg?style=flat" /></a>
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+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat" /></a>
226 226 
 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat" /></a></p>
227 227 
 <p>The <code>ggtree</code> package extending the <code>ggplot2</code> package. It based on grammar of graphics and takes all the good parts of <code>ggplot2</code>.  <code>ggtree</code> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
228 228 
 <code>ggtree</code> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
... ... 
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232 232 
 <p>Please cite the following article when using <code>ggtree</code>:</p>
233 233 
 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="doi" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>
234 234 
 <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat" /></a>
235 
-<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-125-blue.svg?style=flat" /></a></p>
235 
+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-187-blue.svg?style=flat" /></a></p>
236 236 
 <p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. <strong><em>Methods in Ecology and Evolution</em></strong>. <em>accepted</em>.</p>
237 237 
 <h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
238 238 
 <p><img alt="" src="./featured_img/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
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@@ -269,7 +269,7 @@ biocLite(&quot;ggtree&quot;)
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 <h4 id="bioconductor-packages"><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>
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 <ul>
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 <li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of lincRNAs and protein-coding genes</li>
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-<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic paritioning based ILR transform for metagenomics data</li>
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+<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li>
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 </ul>
274 274 
 <h4 id="other-applications"><i class="fa fa-angle-double-right"></i> Other applications</h4>
275 275 
 <ul>
docs/mkdocs/search_index.json
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     "docs": [
3 3 
         {
4 4 
             "location": "/",
5 
-            "text": "The \nggtree\n package extending the \nggplot2\n package. It based on grammar of graphics and takes all the good parts of \nggplot2\n.  \nggtree\n is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.\n\nggtree\n is released within the \nBioconductor\n project and the source code is hosted on \n GitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \nMethods in Ecology and Evolution\n. \naccepted\n.\n\n\n Featured Articles\n\n\n\n\n Find out more on \n \nFeatured Articles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor page\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages, please refer to the \nggtree-installation\n wiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore the tree visually\n\n\n\n\n Find out details and examples on \n \nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic paritioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n: Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n: Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you \nfollow the guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and",
5 
+            "text": "The \nggtree\n package extending the \nggplot2\n package. It based on grammar of graphics and takes all the good parts of \nggplot2\n.  \nggtree\n is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.\n\nggtree\n is released within the \nBioconductor\n project and the source code is hosted on \n GitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \nMethods in Ecology and Evolution\n. \naccepted\n.\n\n\n Featured Articles\n\n\n\n\n Find out more on \n \nFeatured Articles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor page\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages, please refer to the \nggtree-installation\n wiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore the tree visually\n\n\n\n\n Find out details and examples on \n \nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n: Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n: Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you \nfollow the guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and",
6 6 
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7 7 
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-            "text": "LINC : co-expression of lincRNAs and protein-coding genes  philr : Phylogenetic paritioning based ILR transform for metagenomics data",
55 
+            "text": "LINC : co-expression of lincRNAs and protein-coding genes  philr : Phylogenetic partitioning based ILR transform for metagenomics data",
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             "location": "/featuredArticles/",
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-            "text": "Let us know if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart1bce5e7d0c51\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart1bce5e7d0c51\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape \n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens \n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015 \n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species \n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976",
195 
+            "text": "Let us know if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chartbfe1744ae9d\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chartbfe1744ae9d\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape \n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens \n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015 \n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species \n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976",
196 196 
             "title": "Featured Articles"
197 197 
         },
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         {
docs/sitemap.xml
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mkdocs/docs/index.md
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
19 
-[![develVersion](https://img.shields.io/badge/devel%20version-1.5.16-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
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-[![total](https://img.shields.io/badge/downloads-15163/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![develVersion](https://img.shields.io/badge/devel%20version-1.5.17-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
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+[![total](https://img.shields.io/badge/downloads-15283/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 [![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
37 37 
 [![citation](https://img.shields.io/badge/cited%20by-1-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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-[![Altmetric](https://img.shields.io/badge/Altmetric-125-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![Altmetric](https://img.shields.io/badge/Altmetric-187-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
39 39
40 40 
 __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. *accepted*.
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 #### <i class="fa fa-angle-double-right"></i> Bioconductor packages
89 89 
 + [LINC](https://www.bioconductor.org/packages/LINC): co-expression of lincRNAs and protein-coding genes
90 
-+ [philr](https://www.bioconductor.org/packages/philr): Phylogenetic paritioning based ILR transform for metagenomics data
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++ [philr](https://www.bioconductor.org/packages/philr): Phylogenetic partitioning based ILR transform for metagenomics data
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 #### <i class="fa fa-angle-double-right"></i> Other applications
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 + [BreadCrumbs](https://bitbucket.org/biobakery/breadcrumbs): Collection of scripts for metagenomics analysis