ggbio: an R package for extending the grammar of graphics for genomic data

By Tengfei Yin, D. Cook, Michael F. Lawrence. Genome Biology, 2012

299 citations recorded by the source corpus.

We introduce ggbio, a new methodology to visualize and explore genomics annotationsand high-throughput data. The plots provide detailed views of genomic regions,summary views of sequence alignments and splicing patterns, and genome-wide overviewswith karyogram, circular and grand linear layouts. The methods leverage thestatistical functionality available in R, the grammar of graphics and the datahandling capabilities of the Bioconductor project. The plots are specified within amodular framework that enables users to construct plots in a systematic way, and aregenerated directly from Bioconductor data structures. The ggbio R package isavailable athttp://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5573edbdc0eaa778b3f7ff25f9818f7f63b93311

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Citations in the corpus

circlize implements and enhances circular visualization in R (2014, background): “Received on March 25, 2014; revised on June 4, 2014; accepted on June 11, 2014”
karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data (2017, background): “Circos (Krzywinski et al. , 2009) produces highly customizable high quality circular plots, as does it’s R counterpart RCircos (Zhang et al. , 2013).”
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants (2014, unknown): “R VCF objects can be visualized with packages such as ggbio (Yin et al ., 2012).”
Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression (2014, methodology): “Circular plots were created using the ggbio R package (65), and local association plots were generated with LocusZoom (66).”
RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms (2019, methodology): “Although few R packages, like GenomeGraphs (Durinck et al. 2009), ggbio (Yin et al. 2012), IdeoViz (Pai & Ren 2014), chromPlot (Orostica & Verdugo 2016) and chromDraw (Janecka & Lysak 2016), and JavaScript libraries, like Ideogram.js (Weitz et al. 2017) and karyotypeSVG (Prlic 2017), have been…”
RCircos: an R package for Circos 2D track plots (2013, methodology): “[6] 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.”
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases (2014, background): “A few program libraries [14-17] have been developed to facilitate the calculation and plotting of coverage from NGS data, but they require a user to have substantial programming skills and involve a steep learning curve.”