G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram

Date: 2022-08-19

Live demo

• Short introduction
• Chart themes

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

# install package
install.packages("g3viz", repos = "http://cran.us.r-project.org")

or install development version from github

# 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

1.1.3

• Updated Pfam version 33.1 (date: 2020-08-24)
• Updated UniProt (date: 2020-08-24)
• add "prepare_data" folder to instruct how to create hgnc2pfam.df.rda data

1.1.5

• Updated getMutationsFromCbioportal (date: 2022-06-23)
• Remove Dependency cgdsr; Add Dependency cBioPortalData (date: 2022-06-23)
• Updated hgnc2pfam.df.rda (date: 2022-06-24)