RCircos: an R package for Circos 2D track plots

By Hongen Zhang, Paul S. Meltzer, Sean Davis. BMC Bioinformatics, 2013

853 citations recorded by the source corpus.

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.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/12ce8cb4e7a7b1cb7d09510830e226d5493f06aa

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In Artificial Intelligence

1. Zuguang Gu

In Molecular Biology

1. Zuguang Gu
2. Bernat Gel
3. Eduard Serra
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5. D. Huebschmann
6. Peter B. Becker

Citations in the corpus

• 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 ites R counterpart RCircos (Zhang et al. , 2013).”
• Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. (2018, neutral): “2.0 Zhang et al., 2013 https://cran.r-project.org/web/packages/RCircos/index.html ANNOVAR v2018Apr16 Wang et al., 2010 http://annovar.openbioinformatics.org/en/latest/ Cell 174, 1–12.e1–e3, July 26, 2018 e1 Please cite this article in press as: Quigley et al., Genomic Hallmarks and Structural…”
• 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”