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Circos Plots - Usage Guide

Overview

Create circular genome visualizations with multiple data tracks for CNVs, gene fusions, Hi-C contacts, and multi-omics summaries.

Prerequisites

# Circos (Perl)
conda install -c bioconda circos

# pyCircos (Python)
pip install pyCircos

# circlize (R)
install.packages('circlize')

Quick Start

Tell your AI agent what you want to do:

  • "Create a circos plot of my CNV data"
  • "Visualize gene fusions as links between chromosomes"
  • "Make a circular genome plot with expression data"

Example Prompts

CNV Visualization

"Create a circos plot showing copy number gains in red and losses in blue"

"Add a CNV heatmap track to my genome circle"

Gene Fusions

"Draw arcs connecting fusion breakpoints between chromosomes"

"Visualize structural variants as links in a circos plot"

Hi-C and Chromatin

"Show Hi-C contact frequencies as links between regions"

"Create a circos plot of chromatin interactions"

Multi-omics Summary

"Layer variant, expression, and methylation data around the genome"

"Create a summary circos with multiple data tracks"

What the Agent Will Do

  1. Initialize genome coordinates (hg38/mm10)
  2. Add chromosome ideograms as outer track
  3. Add data tracks (bars, heatmaps, scatter)
  4. Draw links for interactions/fusions
  5. Export as SVG/PNG

Common Use Cases

  • CNV Visualization: Show copy number gains (red) and losses (blue) as bars or heatmap tracks
  • Gene Fusions: Display fusion breakpoints as arcs connecting two genomic positions
  • Hi-C Contacts: Visualize chromatin interactions as links between genomic regions
  • Multi-omics Summary: Layer multiple data types around the genome

Tips

  • Track order: Outermost = chromosome ideograms, inner tracks = data
  • Use interspace parameter to separate chromosomes
  • Keep color schemes consistent across tracks
  • Export as SVG for publication, PNG for quick viewing
  • Use circlize (R) for fastest prototyping

Related Skills

  • data-visualization/genome-tracks - Linear track plots
  • hi-c-analysis/contact-visualization - Hi-C specific plots