1. ggtree
  2. Commit 4931b0273ab105cc45ecedb877bfc2ecbecd84e5
Browse code

reverse_x and reverse_y parameters for inset

guangchuang yu authored on 05/01/2017 03:23:11
Showing 11 changed files
DESCRIPTION
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 Package: ggtree
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 Type: Package
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 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.7.5
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+Version: 1.7.6
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 Authors@R: c(
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 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
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 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
NEWS
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+CHANGES IN VERSION 1.7.6
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+------------------------
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+ o inset support reverse scale <2017-01-05, Thu>
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+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/_JPfm71Z8nM/6gL93oxHFQAJ
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+
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 CHANGES IN VERSION 1.7.5
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 ------------------------
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  o disable labeling collapsed node as tip <2017-01-03, Tue>
R/inset.R
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 ##' @param hjust horizontal adjustment
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 ##' @param vjust vertical adjustment
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 ##' @param x x position, one of 'node' and 'branch'
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+##' @param reverse_x whether x axis was reversed by scale_x_reverse
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+##' @param reverse_y whether y axis was reversed by scale_y_reverse
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 ##' @return tree view with insets
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 ##' @export
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 ##' @author Guangchuang Yu
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-inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x="node") {
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+inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,
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+                  x="node", reverse_x=FALSE, reverse_y=FALSE) {
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+
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     df <- tree_view$data[as.numeric(names(insets)),]
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     x <- match.arg(x, c("node", "branch", "edge"))
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@@ -25,6 +29,10 @@ inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x=
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     xx <- xx - hjust
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     yy <- yy - vjust
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+    if (reverse_x)
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+        xx <- -xx
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+    if (reverse_y)
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+        yy <- -yy
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     for (i in seq_along(insets)) {
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         tree_view %<>% subview(insets[[i]],
README.md
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 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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 ===========================================================================================================================
4 4
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.6-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.5-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) [![total](https://img.shields.io/badge/downloads-19096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.6-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-19191/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1177/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
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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--12--30-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-2017--01--05-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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 **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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-[![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-284-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![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-287-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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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) [![total](https://img.shields.io/badge/downloads-19096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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-19191/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1177/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-       0 +   *   *   *                                                                                 +
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-       2015                  2015.5                  2016                  2016.5                  2017
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+       0 +   *   *  *                                                                                  +
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+         ++---------------------+---------------------+---------------------+---------------------+----+
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+        2015                 2015.5                 2016                 2016.5                 2017
docs/featuredArticles/index.html
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   }
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   </style>
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-<div id = 'chart464a137dd257' class = 'rChart morris'></div>
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+<div id = 'chart6b52366c186' class = 'rChart morris'></div>
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 <script type='text/javascript'>
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
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 "pubid": "HtEfBTGE9r8C"
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 }
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 ],
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-"id": "chart464a137dd257",
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 "labels": "cites"
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 },
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docs/index.html
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 <p><img src="https://raw.githubusercontent.com/GuangchuangYu/ggtree/master/logo.png" align="right" /></p>
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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-<p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.6-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-1.7.5-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-19152/total-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat" /></a></p>
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+<p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.7-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-1.7.6-blue.svg?style=flat" /></a>
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248 248 
 <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.
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 <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>
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 <h2 id="authors"><i class="fa fa-user"></i> Authors</h2>
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 <p>Please cite the following article when using <code>ggtree</code>:</p>
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 <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>
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 <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>
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-<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-284-blue.svg?style=flat" /></a></p>
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+<a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-287-blue.svg?style=flat" /></a></p>
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 <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>
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 <h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
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 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
docs/mkdocs/search_index.json
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         },
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         {
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             "location": "/featuredArticles/",
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-            "text": "Let us know\n 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\": \"chart464a137dd257\",\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\": \"chart464a137dd257\",\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",
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+            "text": "Let us know\n 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\": \"chart6b52366c186\",\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\": \"chart6b52366c186\",\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",
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             "title": "Featured Articles"
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docs/sitemap.xml
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
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-     <lastmod>2017-01-03</lastmod>
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+     <lastmod>2017-01-05</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>
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-     <lastmod>2017-01-03</lastmod>
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+     <lastmod>2017-01-05</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
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-     <lastmod>2017-01-03</lastmod>
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+     <lastmod>2017-01-05</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
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-     <lastmod>2017-01-03</lastmod>
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+     <lastmod>2017-01-05</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>
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-     <lastmod>2017-01-03</lastmod>
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+     <lastmod>2017-01-05</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
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-     <lastmod>2017-01-03</lastmod>
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+     <lastmod>2017-01-05</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>
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-     <lastmod>2017-01-03</lastmod>
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+     <lastmod>2017-01-05</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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man/inset.Rd
History View file @ 4931b027
... ... 
@@ -5,7 +5,7 @@
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 \title{inset}
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 \usage{
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 inset(tree_view, insets, width = 0.1, height = 0.1, hjust = 0,
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-  vjust = 0, x = "node")
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+  vjust = 0, x = "node", reverse_x = FALSE, reverse_y = FALSE)
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 }
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 \arguments{
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 \item{tree_view}{tree view}
... ... 
@@ -21,6 +21,10 @@ inset(tree_view, insets, width = 0.1, height = 0.1, hjust = 0,
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 \item{vjust}{vertical adjustment}
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 \item{x}{x position, one of 'node' and 'branch'}
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+
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+\item{reverse_x}{whether x axis was reversed by scale_x_reverse}
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+
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+\item{reverse_y}{whether y axis was reversed by scale_y_reverse}
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 }
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 \value{
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 tree view with insets
mkdocs/docs/featuredArticles.md
History View file @ 4931b027
... ... 
@@ -36,10 +36,10 @@
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   }
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   </style>
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-<div id = 'chart464a137dd257' class = 'rChart morris'></div>
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+<div id = 'chart6b52366c186' class = 'rChart morris'></div>
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 <script type='text/javascript'>
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     var chartParams = {
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- "element": "chart464a137dd257",
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+ "element": "chart6b52366c186",
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
... ... 
@@ -53,7 +53,7 @@
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 "pubid": "HtEfBTGE9r8C"
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 }
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 ],
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-"id": "chart464a137dd257",
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+"id": "chart6b52366c186",
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 "labels": "cites"
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 },
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       chartType = "Bar"
mkdocs/docs/index.md
History View file @ 4931b027
... ... 
@@ -20,10 +20,10 @@
20 20
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
22 22
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.6-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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-[![develVersion](https://img.shields.io/badge/devel%20version-1.7.5-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
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-[![total](https://img.shields.io/badge/downloads-19152/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.7-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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+[![develVersion](https://img.shields.io/badge/devel%20version-1.7.6-blue.svg?style=flat)](https://github.com/GuangchuangYu/ggtree)
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+[![total](https://img.shields.io/badge/downloads-19191/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![month](https://img.shields.io/badge/downloads-1177/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 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.
... ... 
@@ -40,7 +40,7 @@ Please cite the following article when using `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)
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 [![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)
43 
-[![Altmetric](https://img.shields.io/badge/Altmetric-284-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![Altmetric](https://img.shields.io/badge/Altmetric-287-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
44 44
45 45 
 __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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