OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

Abstract

Summary: OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label figures. Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves. Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats. In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization.

Availability and implementation: OmicCircos is available through Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html. An extensive vignette in the package describes installation, data formatting, and workflow procedures. The software is open source under the Artistic-2.0 license.

Keywords: R package; circular plot; genomic variation.

Figure 1

Circular plots by OmicCircos of expression, CNV, and fusion proteins in 15 Her2 subtype samples from TCGA breast cancer data. Circular tracks from outside to inside: genome positions by chromosomes (black lines are cytobands), expression heatmap of 2000 most variable genes whose locations are indicated by elbow connectors, CNVs (red: gain, blue: loss), correlation p-values between expression and CNV, fusion proteins (intra/inter chromosomes: red/blue). Chromosomes 1–22 are shown in the right half of the circle. Zoomed chromosomes 11 and 17 are displayed in the left half. The circle arc was drawn using trigonometric functions. The fusion protein links were plotted with the Bézier curve algorithm.

Figure 2

Integration of circular plots by OmicCircos and clusters from R of TCGA breast cancer data. Circular tracks from outside to inside: genome positions by chromosomes (black lines are cytobands), CNVs in Basal, Her2, Luminal A (LumA) and Luminal B (LumB) subtypes with 15 samples in each track (red: gain; blue: loss), in the center, four clusters from principle component analysis (PCA) of the gene expression data with R packages in the bioconductor.