Circos: an information aesthetic for comparative genomics

Abstract

We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.

Figure 5.

Copy number whole-genome profiles of five follicular lymphoma tumor samples generated from the Affymetrix Mapping 500K array. Samples are represented in each of the five histograms in tracks A–E. A crop of histogram region F is shown in the center of the figure to demonstrate the structure of each histogram track. The central thick line (G) represents the average probe value across 250 adjacent probes. The area between this line and y = 0 is filled with green or red depending on whether the average value is positive (i.e., increased copy number value) or negative (decreased copy number value), respectively. Variability within each 250-probe set is shown in histogram components H and I, which show the maximum and minimum of three-probe average values within the set, respectively. The area under the maximum and minimum traces is filled with a lighter green or red, respectively.

Figure 6.

Copy number profiles for chromosomes 6 and 17 of five follicular lymphoma tumor samples generated from the Affymetrix Mapping 500K array. Probe values were averaged across 20 adjacent probes. Several regions showing large copy number changes are shown on ideograms with an expanded scale. The structure of the histogram track is the same as used in Figure 5. Regions A and B on chromosomes 6 are shown at 10× magnification on ideograms C and D, respectively, with ribbons E connecting these regions with their zoomed ideograms. Similarly, region F on chromosome 17 is shown at 5× magnification as ideogram G. Regions H and I on ideogram G are shown at 40× magnification on ideograms J and K, respectively. Individual probe values are shown as scatterplots on ideograms J and K.

Figure 7.

Copy number profiles for chromosomes 6 and 17 of five follicular lymphoma tumor samples generated from the Affymetrix Mapping 500K array. Regions of interest A and B on chromosomes 6 and J and K on chromosomes 17 (corresponding to similarly labeled zoomed ideograms in Fig. 6) are magnified by a continuous scale expansion in these regions. Individual probe values are shown as a scatterplot in the vicinity of regions J and K.