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      circlize implements and enhances circular visualization in R

      Author(s): , , , ,
      Publication date Created:
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      Journal: Bioinformatics
      Publisher: Oxford University Press (OUP)

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          Abstract

          Circular layout is an efficient way for the visualization of huge amounts of genomic information. Here we present the circlize package, which provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding genomic patterns behind multi-dimensional data.

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          Circos: an information aesthetic for comparative genomics.

          Martin Krzywinski, Jacqueline Schein, Inanç Birol … (2009)
          We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
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            RCircos: an R package for Circos 2D track plots

            Hongen Zhang, Paul Meltzer, Sean Davis (2013)
            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.
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              ggbio: an R package for extending the grammar of graphics for genomic data

              Tengfei Yin, Dianne Cook, Michael Lawrence (2012)
              We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data. The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. The methods leverage the statistical functionality available in R, the grammar of graphics and the data handling capabilities of the Bioconductor project. The plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. The ggbio R package is available at http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html.
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                Author and article information

                Journal
                Title: Bioinformatics
                Publisher: Oxford University Press (OUP)
                ISSN (Electronic): 1460-2059
                ISSN (Print): 1367-4803
                Publication date Created: October 2014
                Publication date Created: October 01 2014
                Publication date Created: June 14 2014
                Publication date (Print): October 2014
                Publication date (Print): October 01 2014
                Publication date (Electronic): June 14 2014
                Volume: 30
                Issue: 19
                Pages: 2811-2812
                Article
                DOI: 10.1093/bioinformatics/btu393
                PubMed ID: 24930139
                SO-VID: 004acaf3-a8a8-4e80-88d7-f247c027ba16
                Copyright © © 2014
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