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AllClasses.R 100644 12 kb
AllGenerics.R 100644 6 kb
Date.R 100644 1 kb
MRCA.R 100644 2 kb
NJ.R 100644 2 kb
RAxML.R 100644 3 kb
ape.R 100644 3 kb
as.polytomy.R 100644 1 kb
clade-functions.R 100644 8 kb
codeml.R 100644 2 kb
codeml_mlc.R 100644 2 kb
experimental_function.R 100644 9 kb
facet_plot.R 100644 1 kb
geom_balance.R 100644 6 kb
geom_cladelabel.R 100644 9 kb
geom_cladelabel2.R 100644 11 kb
geom_hilight.R 100644 4 kb
geom_hilight_encircle.R 100644 10 kb
geom_label.R 100644 4 kb
geom_point.R 100644 5 kb
geom_range.R 100644 2 kb
geom_segment.R 100644 3 kb
geom_strip.R 100644 7 kb
geom_taxalink.R 100644 2 kb
geom_text.R 100644 4 kb
geom_tiplab.R 100644 5 kb
geom_tree.R 100644 8 kb
geom_treescale.R 100644 5 kb
ggtree-package.R 100644 0 kb
ggtree.R 100644 3 kb
gheatmap.R 100644 4 kb
hyphy.R 100644 8 kb
inset.R 100644 4 kb
layout.R 100644 1 kb
method-drop-tip.R 100644 3 kb
method-fortify.R 100644 23 kb
method-get-tree.R 100644 3 kb
method-groupClade.R 100644 3 kb
method-groupOTU.R 100644 7 kb
method-gzoom.R 100644 3 kb
method-identify.R 100644 1 kb
method-print.R 100644 0 kb
method-reroot.R 100644 2 kb
method-scale-color.R 100644 4 kb
method-show.R 100644 6 kb
msaplot.R 100644 4 kb
multiplot.R 100644 1 kb
operator.R 100644 4 kb
paml.R 100644 12 kb
paml_rst.R 100644 4 kb
phangorn.R 100644 5 kb
phylip.R 100644 1 kb
phylopic.R 100644 5 kb
plot.R 100644 9 kb
r8s.R 100644 2 kb
rescale_tree.R 100644 0 kb
subview.R 100644 3 kb
theme.R 100644 4 kb
tidytree.R 100644 48 kb
treeio.R 100644 0 kb
utilities.R 100644 13 kb
xlim.R 100644 1 kb
zzz.R 100644 1 kb
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") library("yyplot") ``` <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")` `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")` ---------------------------------------------------------------------------------------- ### Citation ```{r echo=F, comment=NA} p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C') ggsave(p, file="docs/images/citation.png", width=8, height=4) ``` <img src="docs/images/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/images/dlstats.png", width=8, height=4) ``` <img src="docs/images/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>