forked from YuLab-SMU/ggtree
-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.Rmd
90 lines (58 loc) · 4.34 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
---
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("ypages")
```
`r badge_release("ggtree", "green")`
`r badge_devel("ggtree", "green")`
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
`r badge_download("ggtree", "total", "blue")`
`r badge_download("ggtree", "month", "blue")`
<img src="logo.png" align="right" />
[](http://www.repostatus.org/#active)
[](https://codecov.io/gh/GuangchuangYu/ggtree)
[)`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
[](https://github.com/GuangchuangYu/ggtree/network)
[](https://github.com/GuangchuangYu/ggtree/stargazers)
[](https://awesome-r.com/#awesome-r-graphic-displays)
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
[](https://travis-ci.org/GuangchuangYu/ggtree)
[](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
[](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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.
[](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
-----------------------------------------------------
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_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
`r badge_altmetric("10533079", "green")`
----------------------------------------------------------------------------------------
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)
### Citation
`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
```{r echo=F, comment=NA}
d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
txtplot(d$year, d$cites)
```
### Download stats
`r badge_download_bioc("ggtree")`
`r badge_download("ggtree", "total", "blue")`
`r badge_download("ggtree", "month", "blue")`
```{r echo=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)
```