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README.Rmd
--- output: md_document: variant: markdown_github html_preview: false --- <!-- README.md is generated from README.Rmd. Please edit that file --> # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data ```{r echo=FALSE, results="hide", message=FALSE} #library("txtplot") library("badger") library("ypages") library("ggplot2") ``` <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /> `r badge_bioc_release("ggtree", "green")` `r badge_devel("guangchuangyu/ggtree", "green")` [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) `r badge_bioc_download("ggtree", "total", "blue")` `r badge_bioc_download("ggtree", "month", "blue")` [![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-`r gsub('-', '--', Sys.Date())`-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) [![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) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors) 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. [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>. + [Documentation](https://guangchuangyu.github.io/ggtree/documentation/) + [FAQ](https://guangchuangyu.github.io/ggtree/faq/) + [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/) + [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) ----------------------------------------------------- Please cite the following article when using `ggtree`: __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. 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. `r badge_doi("10.1111/2041-210X.12628", "green")` `r badge_altmetric("10533079", "green")` ---------------------------------------------------------------------------------------- ### Citation `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")` ```{r echo=F, comment=NA} d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C') ## txtplot(d$year, d$cites) ## library("ggalt") ## p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') + p <- ggplot(d, aes(year, cites)) + geom_segment(aes(xend=year, yend=0)) + geom_point(size=3, color='firebrick') + theme_minimal() + xlab(NULL) + ylab(NULL) + labs(title="Citation", caption="data from Google Scholar") ggsave(p, file="docs/citation.png", width=8, height=4) ``` <img src="docs/citation.png" width="890"/> ### Download stats `r badge_download_bioc("ggtree")` `r badge_bioc_download("ggtree", "total", "blue")` `r badge_bioc_download("ggtree", "month", "blue")` ```{r echo=F, message=F, comment=NA} x <- dlstats::bioc_stats("ggtree") x <- x[-nrow(x), ] # last month data is not complete ## txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25) p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() + theme_minimal() +xlab(NULL) + ylab(NULL) + labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor") ggsave(p, file="docs/dlstats.png", width=8, height=4) ``` <img src="docs/dlstats.png" width="890"/> ## Contributors This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md). <a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a> ## Backers Thank you to all our backers! 🙏 [[Become a backer](https://opencollective.com/ggtree#backer)] <a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a> ## Sponsors Support this project by becoming a sponsor. Your logo will show up here with a link to your website. [[Become a sponsor](https://opencollective.com/ggtree#sponsor)] <a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>