interacCircos

The interacCircos package is designed for the generation of interactive Circos plot

Introduction

The interacCircos package is inspired by circosJS, BioCircos.js and NG-Circos.

circosJS, BioCircos.js and NG-Circos are developed in JavaScript to provide a framework for displaying the interactive Circos plot in website.

For these 3 JavaScript library, plot are all drawn through different JS functions(back-end) and displayed through HTML element(front-end), which requires users be familiar with JavaScript language and HTML language very much. Besides, the way of data input in JavaScript is not user-friendly, especially for data with millions of rows.

We integrate the modules of circosJS, BioCircos.js and NG-Circos into this R package: interacCircos, based on htmlwidgets framework.

Features

• 21 modules(Arc, Auxilirayline, Background, Bubble, Chord,chord.p, Cnv, Combination, Compare, Gene, Heatmap, Histogram, Legend, Line, Link, Lollipop, Redirect, Scatter, Snp, Text, Wig) of circosJS, BioCircos.js and NG-Circos are available at interacCircos. All modules from different libraries are now presented in R function and compatible to each other.

• Instead of transforming data using python script of manually, the data can be directly input into interacCircos through data.frame format, which is one of the most common data type of R and can easily cooperate with other R packages.

• interacCircos is much more programming friendly. Users can draw a multi-track interactive Circos plot in at least 2 steps, as easy as drawing a plot using ggplot2.

Installation

By devtools

    # Via devtools
    if (!require('devtools')){install.packages('devtools')}
    devtools::install_github('mrcuizhe/interacCircos')
    
    # htmlwidgets, RColorBrewer, plyr are required !  

By Bioconductor:

    #Via Bioconductor
    if (!requireNamespace("BiocManager", quietly = TRUE))
            install.packages("BiocManager")
    
    BiocManager::install("interacCircos")

    # htmlwidgets, RColorBrewer, plyr are required !  
    # Bioconductor version: ≥ Release (3.13)
    # R version ≥ 4.1

Documentation

Documentation is available at

• interacCircos-documentation

Or

• interacCircos-pdf

Citation

Please cite interacCircos: an R package based on JavaScript libraries for the generation of interactive circos plots for publication

Contact

Please contact mrcuizhe@gmail.com for help