BioCircos.R

Simple htmlwidgets binding R commands to the BioCircos.js library


Introduction

This package allows to implement in ‘R’ Circos-like visualizations of genomic data, as proposed by the BioCircos.js JavaScript library, based on the JQuery and D3 technologies.
For a complete list of all the parameters available, please refer to the package documentation.

Motivation

The amount of data produced nowadays in a lot of different fields assesses the relevance of reactive analyses and interactive display of the results. This especially true in biology, where the cost of sequencing data has dropped must faster than the Moore’s law prediction. New ways of integrating different level of information and accelerating the interpretation are therefore needed.

The integration challenge appears to be of major importance, as it allows a deeper understanding of the biological phenomena happening, that cannot be observed in the single analyses independently.

This package aims at offering an easy way of producing Circos-like visualizations to face distinct challenges :

The terminology used here arises from genomics but this tool may be of interest for different situations where different positional or temporal informations must be combined.

Installation

To install this package, you can use CRAN (the central R package repository) to get the last stable release or build the last development version directly from the GitHub repository.

From CRAN

install.packages('BioCircos')

From Github

# You need devtools for that
if (!require('devtools')){install.packages('devtools')}
devtools::install_github('lvulliard/BioCircos.R', build_vignettes = TRUE))

Compatibility and troubleshooting

Since the visualizations are powered by JavaScript, they are affected by the environment in which they are displayed.
If nothing shows up in a shiny application or an Rmarkdown document, try to update your web browser. See the vignettes for examples of BioCircos plots that should be correctly displayed.

Obseved behavior

Tutorial

See the vignettes to learn how to use BioCircos visualizations.

vignette('BioCircos')

Original work

BioCircos.js : an Interactive Circos JavaScript Library for Biological Data Visualization on Web Applications.

https://github.com/YaCui/Biocircos.js

http://bioinfo.ibp.ac.cn/biocircos/

http://www.ncbi.nlm.nih.gov/pubmed/26819473

Documentation: http://bioinfo.ibp.ac.cn/biocircos/document/index.html

Modifications

The following features have been added to the original BioCircos.js library, based on version 1.1.2:

Contact

To report bugs, request features or for any question or remark regarding this package, please use the GitHub page or contact Loan Vulliard.

Credits

The creation and implementation of the BioCircos.js JavaScript library is an independent work attributed to Ya Cui and Xiaowei Chen.
This work is described in the following scientific article: BioCircos.js: an Interactive Circos JavaScript Library for Biological Data Visualization on Web Applications. Cui, Y., et al. Bioinformatics. (2016).

This package relies on several open source projects other R packages, and is made possible thanks to shiny and htmlwidgets.

The package heatmaply was used as a model for this vignette, as well as for the htmlwidgets configuration.