README.Rmd

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output: 
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    variant: gfm
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```{r, include = FALSE}
knitr::opts_chunk$set(
  fig.path = "man/figures/REAMED-",
  message = FALSE,
  warning = FALSE
)
```
#  ggmsa:a visual exploration tool for multiple sequence alignment and associated data <img src="man/figures/logo.png" height="140" align="right" />

```{r echo=FALSE, results="hide", message=FALSE}
library(badger)
```

```{r, echo = FALSE, results='asis'}
cat(
	badge_devel("YuLab-SMU/ggmsa", "blue"),
	badge_lifecycle("experimental", "orange"),
	badge_license("Artistic-2.0")
)
```
<!-- badges: start -->
<!-- [![CRAN_Release_Badge](https://www.r-pkg.org/badges/version-ago/ggmsa)](https://cran.r-project.org/package=ggmsa)-->
<!-- [![CRAN_Download_Badge](https://cranlogs.r-pkg.org/badges/grand-total/ggmsa?color=green)](https://cran.r-project.org/package=ggmsa)-->
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`ggmsa` is designed for visualization and annotation of multiple sequence alignment. It implements functions to visualize publication-quality multiple sequence alignments (protein/DNA/RNA) in R extremely simple and powerful. 

For details, please visit <http://yulab-smu.top/ggmsa/>


##  :hammer: Installation

The released version from `Bioconductor`

```{r eval=FALSE}
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggmsa")
```

Alternatively, you can grab the development version from github using devtools:

```{r eval=FALSE}
if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")
```


##  :bulb: Quick Example 

```{r fig.height = 2.5, fig.width = 11, message=FALSE, warning=FALSE, dpi=300}
library(ggmsa)
protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")
ggmsa(protein_sequences, start = 221, end = 280, char_width = 0.5, seq_name = TRUE) + geom_seqlogo() + geom_msaBar()
```


##  :books: Learn more

Check out the guides for learning everything there is to know about all the different features:

- [Getting Started](https://yulab-smu.github.io/ggmsa/articles/ggmsa.html)
- [Annotations](https://yulab-smu.github.io/ggmsa/articles/guides/Annotations.html)
- [Color Schemes and Font Families](https://yulab-smu.github.io/ggmsa/articles/guides/Color_schemes_And_Font_Families.html)
- [Theme](https://yulab-smu.github.io/ggmsa/articles/guides/MSA_theme.html)
- [Other Modules](https://yulab-smu.github.io/ggmsa/articles/guides/Other_Modules.html)
- [View Modes](https://yulab-smu.github.io/ggmsa/articles/guides/View_modes.html)

##  :runner: Author

- [Guangchuang Yu](https://guangchuangyu.github.io)  Professor, PI 
- [Lang Zhou](https://github.com/nyzhoulang)  Master's Student
- [Shuangbin Xu](https://github.com/xiangpin)  PhD Student

**YuLab**  <https://yulab-smu.top/>

**Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University**



## :sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to abide
by the terms outlined in the [Contributor Code of Conduct](https://github.com/YuLab-SMU/ggmsa/blob/master/CONDUCT.md).