RCircos: an R package for Circos 2D track plots

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.

Figure 1

RCircos image showing human chromosome ideogram with data tracks for connectors, gene labels, heatmap, scatter plot, line plot, histogram, tiles, and link lines.

Figure 2

Combination of RCircos plot and other R graphics plot. Mouse and rat chromosome ideograms, heatmaps, and link lines are drawn with RCircos with two input datasets. Title, legend, and color key are added with function calls of R graphics package.