论文信息 - interacCircos: an R package based on JavaScript libraries for the generation of interactive circos plots

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

SUMMARY JavaScript-based Circos libraries have been widely implemented to generate interactive Circos plots in web applications. However, these libraries require either local installation, which requires the compilation of extra libraries, or extra data processing procedures to prepare input and configuration for each track of plot, which limits the utility and capability of integration with powerful R packages. In this report, we present interacCircos, an R package for creating interactive Circos plots through the integration of JavaScript-based libraries. interacCircos can simply and flexibly implement 14 track-plot functions and 7 auxiliary functions for presenting large-scale genomic data in interactive Circos plots. AVAILABILITY AND IMPLEMENTATION InteracCircos and its manual are freely available at https://github.com/mrcuizhe/interacCircos. The online documentation is available at https://mrcuizhe.github.io/interacCircos_documentation/index.html under the GPL license. We thank the teams of BioCircos.js, BioCircos.R, NGCircos and circosJS for sharing the code.

[1] Steven J. M. Jones,et al. Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[2] Mathieu Blanchette,et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution , 2013, Nature Genetics.

[3] K. Pillen,et al. A nested association mapping population identifies multiple small effect QTL conferring resistance against net blotch (Pyrenophora teres f. teres) in wild barley , 2017, PloS one.

[4] Nikos Darzentas,et al. Circoletto: visualizing sequence similarity with Circos , 2010, Bioinform..

[5] Jianjun Luo,et al. BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications , 2016, Bioinform..

[6] Hongen Zhang,et al. RCircos: an R package for Circos 2D track plots , 2013, BMC Bioinformatics.

[7] Hui Xiao,et al. NG-Circos: next-generation Circos for data visualization and interpretation , 2020, NAR genomics and bioinformatics.

[8] Jeffrey Heer,et al. SpanningAspectRatioBank Easing FunctionS ArrayIn ColorIn Date Interpolator MatrixInterpola NumObjecPointI Rectang ISchedu Parallel Pause Scheduler Sequen Transition Transitioner Transiti Tween Co DelimGraphMLCon IData JSONCon DataField DataSc Dat DataSource Data DataUtil DirtySprite LineS RectSprite , 2011 .

[9] Yves D'Aubenton-Carafa,et al. CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data , 2014, BMC Bioinformatics.