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Open Access Highly Accessed Software

RCircos: an R package for Circos 2D track plots

Hongen Zhang, Paul Meltzer and Sean Davis*

Author Affiliations

Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 6138, 37 Convent Drive, Bethesda, MD 20892-4265, USA

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BMC Bioinformatics 2013, 14:244  doi:10.1186/1471-2105-14-244

Published: 10 August 2013

Abstract

Background

Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional relationships between genomic intervals. Running Circos requires extra data processing procedures to prepare plot data files and configure files from datasets, which limits its capability of integrating directly with other software tools such as R. Recently published R Bioconductor package ggbio provides a function to display genomic data in circular layout based on multiple other packages, which increases its complexity of usage and decreased the flexibility in integrating with other R pipelines.

Results

We implemented an R package, RCircos, using only R packages that come with R base installation. The package supports Circos 2D data track plots such as scatter, line, histogram, heatmap, tile, connectors, links, and text labels. Each plot is implemented with a specific function and input data for all functions are data frames which can be objects read from text files or generated with other R pipelines.

Conclusion

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

Keywords:
Software; RCircos; R package; Circos; Genomic data visualization