ggbio: an R package for extending the grammar of graphics for genomic data
1 Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
2 Department of Statistics, Iowa State University, Ames, IA 50011, USA
3 Department of Bioinformatics, Genentech, 1 Dna Way South San Francisco, CA 94080, USA
Genome Biology 2012, 13:R77 doi:10.1186/gb-2012-13-8-r77Published: 31 August 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 webcite.