# _Gviz_ - Plotting data and annotation information along genomic coordinates

## Software status

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|                     | Bioc ([release](https://bioconductor.org/packages/release/bioc/html/Gviz.html)) | Bioc ([devel](https://bioconductor.org/packages/devel/bioc/html/Gviz.html)) |
|:--------------------|----------------------------------------------------------------------------:|--------------------------------------------------------------------------------:|
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| GitHub Last Commit  | [![GitHub last commit (Bioconductor-release)](https://img.shields.io/github/last-commit/ivanek/Gviz/RELEASE_3_17)](https://github.com/ivanek/Gviz/tree/RELEASE_3_17) | [![GitHub last commit (Bioconductor-devel)](https://img.shields.io/github/last-commit/ivanek/Gviz/devel)](https://github.com/ivanek/Gviz/tree/devel/) |
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| Coverage            | [![Codecov.io (Bioconductor-release)](https://codecov.io/github/ivanek/Gviz/coverage.svg?branch=RELEASE_3_17)](https://codecov.io/gh/ivanek/Gviz/branch/RELEASE_3_17) | [![Codecov.io (Bioconductor-devel)](https://codecov.io/github/ivanek/Gviz/coverage.svg?branch=devel)](https://codecov.io/github/ivanek/Gviz) |

## Authors

- Florian Hahne
- Steffen Durinck
- Robert Ivanek
- Arne Mueller
- Steve Lianoglou
- Ge Tan 
- Lance Parsons
- Shraddha Pai

## Overview

![Gviz UCSC like screenshot](vignettes/Gviz-example.png)

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the [biomaRt](https://bioconductor.org/packages/biomaRt/) and the [rtracklayer](https://bioconductor.org/packages/rtracklayer/) packages to perform live annotation queries to [Ensembl](https://www.ensembl.org/) and [UCSC](https://genome.ucsc.edu) and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

## Installation

#### Release version

```
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Gviz", version = "release")
```

#### Developmental version

```
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Gviz", version = "devel")
```

#### Github

```
if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("ivanek/Gviz")
```
## Usage

For detailed instructions check the package vignette 
([release](https://bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.html) 
or 
[developmental](https://bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.html) 
version). Or check the [GitHub.io page](https://ivanek.github.io/Gviz/).

## Citation 

- Hahne F, Ivanek R (2016). "Statistical Genomics: Methods and Protocols." In Mathé E, Davis S (eds.), chapter Visualizing Genomic Data Using Gviz and Bioconductor, 335–351. Springer New York, New York, NY. ISBN 978-1-4939-3578-9, doi: [10.1007/978-1-4939-3578-9_16](https://dx.doi.org/10.1007/978-1-4939-3578-9_16).
