bio-data-visualization-circos-plots

name	bio-data-visualization-circos-plots
description	Build circular genome visualizations using circlize (R), pyCirclize (Python), or Circos (Perl CLI) with ideogram tracks, multi-data tracks (scatter, histogram, heatmap), chord/link arcs for interactions, and explicit circos.clear() between plots. Covers when circular is appropriate vs when Cartesian wins (Cleveland-McGill 1984), karyograms, and chromosome adjacency in chord diagrams. Use when adjacency on the circle conveys meaning — chromosome-level overview, structural variants, Hi-C interactions, cross-genome comparisons.
origin	openai4s
category	bioskills/data-visualization
metadata	{"tool_type":"mixed","primary_tool":"circlize","third_party":{"name":"GPTomics/bioSkills","repository":"https://github.com/GPTomics/bioSkills","commit":"d91ed3d563019e649dc854c56ccd62551359488a","license":"MIT"}}

Version Compatibility

Reference examples tested with: circlize 0.4.16+ (R), pyCirclize 1.4+ (Python), Circos 0.69-9 (Perl CLI), ComplexHeatmap 2.18+ (uses circlize for color mapping).

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name
• Python: pip show <package> then help(module.function)

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Circular Genome Plots (Circos)

"Make a circos plot" -> Render genome chromosomes around a circle with stacked tracks (histogram, scatter, heatmap) and arcs/chords showing interactions. Krzywinski 2009 Genome Res 19:1639 introduced the genre for genome-scale comparative views. The single decision that matters: does the circular layout convey meaning that Cartesian cannot?

• R: circlize::circos.initializeWithIdeogram + circos.genomicTrack* (Gu 2014)
• Python: pyCirclize.Gcircle
• CLI: Circos (Perl); config-driven; most flexible but steepest learning

The Single Most Important Modern Insight -- Circular Plots Often Hide What Cartesian Reveals

Cleveland-McGill 1984 J Am Stat Assoc 79:531 effectiveness rankings establish that position-on-common-scale (Cartesian) is the most accurate visual channel; circular position requires mental "unwrapping" and impairs precise value comparison. Heer-Bostock 2010 CHI replicated the ranking in modern crowd studies. Use circular only when adjacency on the circle conveys meaning that linear cannot.

Use circular ONLY when:

• Chromosome adjacency matters (whole-genome SVs, Hi-C contacts where genome circularity is the geometry)
• Pairwise interactions between many entities (chord diagrams; chromosome translocations)
• Aesthetic / overview infographic for cover figure

Do NOT use circular for:

• Comparing values across categories (Cartesian bar/dot wins)
• Time series (linear axis wins)
• Anything where precise value reading matters

The circos plot is a beautiful but dangerous default. The most-cited published critique is the genre being applied where it adds no information.

circlize (R) — Modern Default

Goal: Render a multi-track circos plot with ideograms, gene-density histogram, variant-density heatmap, and inter-chromosomal SV links.

Approach: Initialize with chromosome ideograms via circos.initializeWithIdeogram; add tracks with circos.genomicTrack + appropriate panel function; add links with circos.link; always call circos.clear() after the plot completes.

library(circlize)

# 1. Initialize with hg38 ideograms
pdf('circos.pdf', width = 8, height = 8)
circos.par(start.degree = 90,             # 12 o'clock start
           gap.degree = c(rep(1, 23), 5)) # bigger gap before chr1 for visual break
# hg38 specifically benefits from explicit chromosome.index to skip unmapped contigs
circos.initializeWithIdeogram(species = 'hg38',
                               chromosome.index = paste0('chr', c(1:22, 'X', 'Y')),
                               plotType = c(  


circos.genomicDensitygene_bed col   track.height  


circos.genomicHeatmapvariant_bed
                       col  colorRamp2   
                       heatmap_height   side  


circos.genomicTrackcnv_bed ylim   
                     panel.fun  region value ... 
                         circos.genomicPointsregion value
                                              col  ifelsevalue   
                                                           ifelsevalue    
                                              pch   cex  
                     
                     track.height  


 i  nrowsv_df 
    circos.linksv_dfchr1i sv_dfstart1i sv_dfend1i
                sv_dfchr2i sv_dfstart2i sv_dfend2i
                col   lwd  



circos.clear
dev.off

The circos.clear() Trap

circos.par() settings (start.degree, gap.degree, canvas.xlim, canvas.ylim, clock.wise, circle.margin) are GLOBAL state. After a plot completes, those settings persist into the next plot.

Forgetting circos.clear() produces:

• Next circos.par() calls silently fail to take effect (warning, easily missed in loops)
• Re-initialization may error or render at wrong angles
• Loop-rendered figures inherit state from the previous iteration

Always call circos.clear() after every plot. Make it the last line of the plotting block alongside dev.off().

pyCirclize (Python)

from pycirclize import Circos
import matplotlib.pyplot as plt

sectors = {'chr1': 248956422, 'chr2': 242193529, ...}
circos = Circos(sectors, space=2)                       # space = degree gap between sectors

for sector in circos.sectors:
    sector.text(sector.name, r=110, size=8)
    # outer ideogram
    sector.axis(r_lim=(95, 100), fc='lightgrey')
    # data track
    track = sector.add_track((75, 90))
    track.bar(positions, heights, width=bin_size, color='#0072B2')

# Inter-sector links (chord diagram)
circos.link(('chr1', 1e8, 1.1e8), ('chr5', 2e8, 2.1e8),
            color='#888888', alpha=0.5)

fig = circos.plotfig()
fig.savefig('circos_py.pdf', bbox_inches='tight')

pyCirclize is a younger package than circlize but actively developed (Shimoyama 2024+). API more Pythonic than circlize-via-rpy2.

Circos CLI (Perl) — Most Powerful, Steepest Curve

# config: circos.conf with karyotype, ideogram, plots, links sections
circos -conf circos.conf -outputfile output.png

Circos (Krzywinski 2009) is the original; supports unlimited tracks and arbitrary geometries via configuration. For publication-grade complex figures the Perl tool remains the most powerful. For Python/R workflows, circlize/pyCirclize are more accessible.

Decision Tree by Use Case

Use case	Recommended	Why
Whole-genome CNV summary	circlize/pyCirclize	Standard genre
SV link diagram	Chord arcs in circos	Inter-chromosomal adjacency
Hi-C contact summary at chromosome level	circos heatmap track	Adjacency matters
Per-sample mutation overview	Circular karyogram	Aesthetic; comparable to OncoPrint
Cohort-wide gene expression comparison	NOT circular	Use heatmap (Cartesian wins)
Time-series of any kind	NOT circular	Use line plot
Pathway diagram	NOT circular	Use Cytoscape

Ideogram + Karyogram Without Circos

For per-chromosome data display where circularity is not required, karyoploteR (Gel 2017 Bioinformatics 33:3088) renders linear ideograms with stacked data tracks — often the better choice for CNV per-chromosome views.

library(karyoploteR)
kp <- plotKaryotype(genome = 'hg38', chromosomes = c('chr1', 'chr7', 'chr17'))
kpAddBaseNumbers(kp)
kpLines(kp, data = cnv_gr, y = cnv_gr$log2)
kpAddCytobandLabels(kp)

See copy-number/cnv-visualization for karyoploteR in depth.

Per-Method Failure Modes

circos.clear() forgotten in a loop

Trigger: Plotting multiple circos figures in a for loop without circos.clear() between.

Mechanism: circos.par settings (gap.degree, start.degree, clock.wise) persist across plots.

Symptom: Plots 2..N inherit state from plot 1; gap sizes, rotation differ unexpectedly.

Fix: End every plot block with circos.clear(). Make it a hygiene rule.

Using circular when Cartesian would be better

Trigger: "Circos plot of gene expression across 20 conditions."

Mechanism: Circular impairs value comparison (Cleveland-McGill 1984; Heer-Bostock 2010).

Symptom: Reviewer or coauthor says "I can't tell which condition is highest."

Fix: Use clustered heatmap. Reserve circos for genome-adjacency or chord-diagram use cases.

Too many links produce a black blob

Trigger: Plotting 10000+ chord links between chromosomes.

Mechanism: Overlap saturates the center; no individual link visible.

Symptom: Center of circos is uniformly dark.

Fix: Filter to top-confidence links; OR color-bin by interaction strength with alpha; OR aggregate to chromosome-level summary then link.

Sector ordering arbitrary

Trigger: Default sector order is input order.

Mechanism: circlize / pyCirclize do not auto-order chromosomes 1..22, X, Y.

Symptom: Chromosomes appear in genome-build-file order.

Fix: Explicit chromosome.index = c(paste0('chr', 1:22), 'chrX', 'chrY').

Wrong species ideogram

Trigger: species = 'hg19' when data is hg38-coordinate.

Mechanism: circlize fetches cytoband data per species; mismatch renders correct ideogram but wrong banding for the data.

Symptom: Cytoband boundaries don't match published references.

Fix: Match species to data coordinate system. For non-standard genomes, supply custom cytoband file. For species = 'hg38' specifically, always pass chromosome.index = paste0('chr', c(1:22, 'X', 'Y')) to skip unmapped contigs (jokergoo/circlize issue #46).

Ideogram covers data track

Trigger: Default ideogram track height too large; data track squeezed.

Mechanism: circos.initializeWithIdeogram uses ~5% of radius; left-over for data.

Symptom: Data values invisible because track is too narrow.

Fix: Reduce cytoband.height in initialization; OR use plotType = c('axis', 'labels') to omit ideogram entirely.

Chromosome label collisions for small chromosomes

Trigger: Default label position; small chromosomes (chr21, chr22, chrY) have overlapping labels.

Mechanism: Labels drawn at sector midpoints regardless of sector width.

Symptom: Labels overlap.

Fix: circos.par(gap.degree = c(rep(1, 22), 10, 10, 10)) for larger gaps before small chromosomes; OR reduce label font size.

Reconciliation

Pattern	Cause	Action
circlize and pyCirclize differ in default rotation	Different start-angle convention	Set start.degree=90 (R) / equivalent (Python) explicitly
Cytoband colors don't match UCSC	Different species cytoband source	Verify species; for custom genomes supply band file
Inter-sector links arc the "long way around"	Default arc direction	Some chord packages support direction = 'short'

Quantitative Thresholds

Threshold	Value	Source
Max sectors readable	~30	Visualization practical
Max links before blob	~5000	Practical; depends on alpha
Cytoband.height default	0.05 of radius	circlize default
When circular adds value	Adjacency-meaningful only	Cleveland-McGill 1984

Common Errors

Error / symptom	Cause	Solution
Subsequent plots use wrong rotation	circos.clear() forgotten	Always end with circos.clear()
Chromosomes out of order	Default = input order	Explicit chromosome.index
Cytoband mismatch	Wrong species	Match species to data coords
Center of circos black	Too many links	Filter or aggregate
Reviewer asks "why circular?"	Cartesian would have been clearer	Migrate to heatmap unless adjacency matters
Small-chromosome label overlap	Default label position	Larger gap.degree before small sectors

References

• Cleveland WS, McGill R. 1984. Graphical perception: theory, experimentation, and application to the development of graphical methods. J Am Stat Assoc 79(387):531-554.
• Gel B, Serra E. 2017. karyoploteR: an R/Bioconductor package to plot customizable genomes. Bioinformatics 33(19):3088-3090.
• Gu Z, Gu L, Eils R, Schlesner M, Brors B. 2014. circlize implements and enhances circular visualization in R. Bioinformatics 30(19):2811-2812.
• Heer J, Bostock M. 2010. Crowdsourcing graphical perception: using Mechanical Turk to assess visualization design. Proc CHI 203-212.
• Krzywinski M, Schein J, Birol I, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639-1645.
• Shimoyama Y. 2024. pyCirclize: Circular visualization in Python. GitHub https://github.com/moshi4/pyCirclize

Related Skills

• copy-number/cnv-visualization - karyoploteR linear alternative for CNV
• variant-calling/structural-variant-calling - SV data for circos links
• hi-c-analysis/hic-visualization - Hi-C contact data circular display
• data-visualization/genome-tracks - Linear track alternative
• data-visualization/color-palettes - Sector and link palettes