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SOFIA: an R package for enhancing genetic visualization with Circos

Luis Diaz-Garcia, Giovanny Covarrubias-Pazaran, Brandon Schlautman, Juan Zalapa
doi: https://doi.org/10.1101/088377
Luis Diaz-Garcia
1University of Wisconsin, Department of Horticulture, Madison, Wisconsin, United States of America
2Instituto Nacional de Investigaciones Forestales y Agrícolas y Pecuarias, Aguascalientes, Mexico
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  • For correspondence: jezalapa@wisc.edu diaz.antonio@inifap.gob.mx
Giovanny Covarrubias-Pazaran
1University of Wisconsin, Department of Horticulture, Madison, Wisconsin, United States of America
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Brandon Schlautman
3The Land Institute, Salina, Kansas, United States of America.
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Juan Zalapa
1University of Wisconsin, Department of Horticulture, Madison, Wisconsin, United States of America
4USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin
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  • For correspondence: jezalapa@wisc.edu diaz.antonio@inifap.gob.mx
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Abstract

Visualization of data from any stage of genetic and genomic research is one of the most useful approaches for detecting potential errors, ensuring accuracy and reproducibility, and presentation of the resulting data. Currently software such as Circos, ClicO FS, and RCircos, among others, provide tools for plotting a variety of genetic data types in a concise manner for data exploration and presentation. However, each of the programs have one or more disadvantages that limit their usability in data exploration or construction of publication quality figures, such as inflexibility in formatting and configuration, reduced image quality, lack of potential for automation, or requirements of high-level computational expertise. Therefore, we developed the R package SOFIA, which leverages the capabilities of Circos by manipulating data, preparing configuration files, and running the Perl-native Circos directly from the R environment with minimal user intervention. The advantages of integrating both R and Circos into SOFIA are numerous. R is a very powerful, mid-level programming language widely used among the genetic and genomic research community, while Circos has proven to be a novel software for arranging genomic data to create aesthetical publication quality circular figures. Producing Circos figures in R with SOFIA is simple, requires minimal coding experience, even for complex figures that incorporate high-dimensional genetic information, and allows simultaneous analysis and visual exploration of genomic and genetic data in a single programming environment.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 17, 2016.
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SOFIA: an R package for enhancing genetic visualization with Circos
Luis Diaz-Garcia, Giovanny Covarrubias-Pazaran, Brandon Schlautman, Juan Zalapa
bioRxiv 088377; doi: https://doi.org/10.1101/088377
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SOFIA: an R package for enhancing genetic visualization with Circos
Luis Diaz-Garcia, Giovanny Covarrubias-Pazaran, Brandon Schlautman, Juan Zalapa
bioRxiv 088377; doi: https://doi.org/10.1101/088377

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