https://github.com/g3viz/g3viz
Lollipop-diagram to interactively visualize genetic mutations
https://github.com/g3viz/g3viz
bioinformatics genomics-visualization lollipop-plot variants visualize-mutation-data
Last synced: 3 months ago
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Lollipop-diagram to interactively visualize genetic mutations
- Host: GitHub
- URL: https://github.com/g3viz/g3viz
- Owner: G3viz
- License: other
- Created: 2018-08-01T02:34:58.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-09-10T04:23:40.000Z (over 1 year ago)
- Last Synced: 2026-01-12T00:24:22.798Z (5 months ago)
- Topics: bioinformatics, genomics-visualization, lollipop-plot, variants, visualize-mutation-data
- Language: JavaScript
- Homepage: https://g3viz.github.io/g3viz/
- Size: 65.2 MB
- Stars: 33
- Watchers: 1
- Forks: 19
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
# G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram
**Date: 2024-09-04**
[](https://travis-ci.org/G3viz/g3viz)
[](https://CRAN.R-project.org/package=g3viz)
[](https://cran.r-project.org/package=g3viz)
## Live demo
- [x] [Short introduction](https://g3viz.github.io/g3viz/)
- [x] [Chart themes](https://g3viz.github.io/g3viz/chart_themes.html)
## Introduction
Intuitively and effectively visualizing genetic mutation data can help researchers to better understand genomic data and validate findings. `G3viz` is an R package which provides an easy-to-use lollipop-diagram tool. It enables users to interactively visualize detailed translational effect of genetic mutations in RStudio or a web browser, without having to know any HTML5/JavaScript technologies.
The features of `g3viz` include
- Interactive (zoom & pan, tooltip, brush selection tool, and interactive legend)
- Highlight and label positional mutations
- 8 ready-to-use chart themes
- Highly customizable with over 50 chart options and over 35 color schemes
- Save charts in PNG or high-quality SVG format
- Built-in function to retrieve protein domain information and resolve gene isoforms
- Built-in function to map genetic mutation type (a.k.a, variant classification) to mutation class
## Install `g3viz`
Install from R repository
```r
# install package
install.packages("g3viz", repos = "http://cran.us.r-project.org")
```
or install development version from github
```r
# Check if "devtools" installed
if("devtools" %in% rownames(installed.packages()) == FALSE){
install.packages("devtools")
}
# install from github
devtools::install_github("g3viz/g3viz")
```
## Reference
Guo, X., *et al*. (2020). G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram. **Bioinformatics**, 36(3), 928-929.
## What's new
1.2.0
- [x] Updated Pfam (v37.0) (date: 2024-07-29)
- [x] Updated UniProtKB (date: 2024-07-29)
- [x] Updated `hgnc2pfam.df.rda` (date: 2024-07-29)
1.1.5
- [x] Updated getMutationsFromCbioportal (date: 2022-06-23)
- [x] Remove Dependency cgdsr; Add Dependency cBioPortalData (date: 2022-06-23)
- [x] Updated `hgnc2pfam.df.rda` (date: 2022-06-24)