RCircos: an R package for Circos 2D track plots

Abstract

BackgroundCircos 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.ResultsWe 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.ConclusionRCircos 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.

Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma

“…Delly [29] was used to identify genomic rearrangements in the LO data using default parameter settings. We used Rcircos [30] to visualize the genomic rearrangements in a Circos plot.…”

Familial resemblances in blood leukocyte DNA methylation levels

“…We used RCircos package in R software to make the Circos plot. 34 Finally, we used the IPA system (Ingenuity Ò Systems, www.ingenuity.com) to analyze pathways overrepresented among genes of significant and FDR-corrected significant probes. Using a right-tailed Fisher's exact test, IPA measured the likelihood that genes belong to specific overrepresented pathways.…”

DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID

“…DMRs were detected using RRBSseeqer with parameters of 250bp maximum distance between DMCs, minimum of 5 DMCs per region and 10% total methylation difference for region. Ideogram was generated using the ggbio package (Yin et al, 2012) and UCSC GRCm38 CytoBand data from the RCircos package (Zhang et al, 2013). Epigenetic diversity and diverse CpG hotspots were calculated as described in Supplemental Experimental Procedures.…”