- Open Access
RCircos: an R package for Circos 2D track plots
© Zhang et al.; licensee BioMed Central Ltd. 2013
- Received: 18 March 2013
- Accepted: 7 August 2013
- Published: 10 August 2013
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.
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.
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.
- R package
- Genomic data visualization
Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional relationships between genomic intervals . Although many tools for genomic data visualization have been developed [2-5], Circos is commonly used by the genome research community to present large-scale multi-sample genomic research data (http://circos.ca/in_literature/scientific/). While Circos is powerful and flexible in displaying genomic data it requires extra data procedures to prepare plot data files and configuration files from datasets, which limits its capability of integrating directly with other software tools such as R, one of the most commonly used toolsets in processing and statistical analysis of genomic data.
Recently, Yin et al.  published a Bioconductor package, ggbio, that includes a function to display genomic data in a circular layout and covers many of the basic Circos-like plots. The ggbio package relies on multiple other packages and offers some integration with other Bioconductor packages. However, ggbio is somewhat complex (but powerful) and relies on high-level plotting packages. RCircos was developed as a simple and flexible approach to Circos-like plots that uses base R graphics.
To make Circos 2D track plots simple and flexible, we implemented an R package, RCircos, that relies on base graphics and R data structures. With RCircos, Circos 2D track plots could be easily generated and the procedures can be effectively integrated with other R pipelines including graphics output manipulation.
Packages used to build RCircos are all included in the R base installation (http://www.r-project.org/). Graphics functionality is accomplished using base R graphics. No other package is required unless input data is associated with special data structure such as GenomicRanges objects and need to be processed separately.
To reduce the complexity of the usage, all functions in RCircos use a simple data frame as input. The first three columns of the data frame are genomic position data in the order of chromosome name, start position, and end position followed by one or more data columns except of link data which requires paired chromosome positions for each row. Data set in data frame is directly passed to the plot function without need of further processing. Sample data are included in the package to show the input data formats and can be easily explored with data(package = “RCircos”) function.
We follow the layout paradigm set forth by Circos and arrange data plots by tracks. The core track is the chromosome ideogram track with highlighting and labels. Data plot tracks can be placed inside or outside of chromosome ideogram track. A set of parameters is used to control the plot pattern such as chromosome width, number of base pairs per chromosome unit, track height, and point type. These parameters are initialized prior to plotting but can be customized to meet the requirements of different plot types.
RCircos is designed such that each type of Circos 2D track plot is drawn with a separate and dedicated function call. To make RCircos more flexible in integrating with other R pipelines, we chose low level plot functions of R including points(), lines(), polygon(), and text() to implement graphic plot functions of RCircos. All RCircos plots work on an existing plot facilitating plot customization using standard R plot functionality.
RCircos implements most of Circos 2D track plots including scatter, line, histogram, heatmaps, tiles, connectors, and text labels. We use the chromosome ideogram tables from UCSC genome browser to generate chromosome ideogram images and currently human, mouse, and rat are available in RCircos, but other species can be supported if relevant ideogram table is provided in a same format as cytoBandIdeo table in the UCSC genome browser .
The RCircos package provides simple and flexible functionality to generate Circos 2D track plots with R and can be easily integrated into other R data processing and graphic manipulation pipelines to present large-scale multi-sample genomic research data.
The package and source code of RCircos are available for download and install from CRAN website (http://www.r-project.org) with the license of GPL (> = 2).
HZ designed and implemented the software package, and wrote manuscript. SD participated in the software design and drafted the manuscript. PM revised the manuscript critically. All authors read and approved the final manuscript.
This study was supported by NCI intramural research Funding in Center for Cancer Research, National Cancer Institute, National Institutes of Health, USA. The package was developed and tested with the Biowulf Linux cluster at the National Institutes of Health, Bethesda, MD. (http://biowulf.nih.gov).
- Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19: 1639-1645. 10.1101/gr.092759.109.PubMed CentralView ArticlePubMedGoogle Scholar
- Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T: Visualizing genomes: techniques and challenges. Nat Methods. 2010, 7 (3 Suppl): S5-S15.View ArticlePubMedGoogle Scholar
- Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N: Visualizing multidimensional cancer genomics data. Genome Med. 2013, 5 (1): 9-10.1186/gm413.PubMed CentralView ArticlePubMedGoogle Scholar
- Miller CA, Anthony J, Meyer MM, Marth G: Scribl: An HTML5 Canvas-based graphics library for visualizing genomic data over the web. Bioinformatics. 2013, 29: 381-383. 10.1093/bioinformatics/bts677.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhu Z, Niu B, Chen J, Wu S, Sun S, Li W: MGAviewer: A desktop visualization tool for analysis of metagenomics alignment data. Bioinformatics. 2013, 29: 122-123. 10.1093/bioinformatics/bts567.PubMed CentralView ArticlePubMedGoogle Scholar
- Yin T, Cook D, Lawrence M: ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol. 2012, 13: R77-10.1186/gb-2012-13-8-r77.PubMed CentralView ArticlePubMedGoogle Scholar
- Kuhn RM, Haussler D, Kent WJ: The UCSC genome browser and associated tools. Brief Bioinform. 2012, 10.1093/bib/bbs038.Google Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.