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<!-- 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)
[![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)


[![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-`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)



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"/>