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Open Access Highly Accessed Methodology article

Visualization of three-way comparisons of omics data

Richard Baran13, Martin Robert1*, Makoto Suematsu2, Tomoyoshi Soga1 and Masaru Tomita1

Author Affiliations

1 Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan

2 Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan

3 Present address: Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia

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BMC Bioinformatics 2007, 8:72  doi:10.1186/1471-2105-8-72

Published: 5 March 2007



Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However, the current color-codings limit the visualizations to single datasets or pairwise comparisons.


We propose a color-coding approach for the representation of three-way comparisons. The approach is based on the HSB (hue, saturation, brightness) color model. The three compared values are assigned specific hue values from the circular hue range (e.g. red, green, and blue). The hue value representing the three-way comparison is calculated according to the distribution of three compared values. If two of the values are identical and one is different, the resulting hue is set to the characteristic hue of the differing value. If all three compared values are different, the resulting hue is selected from a color gradient running between the hues of the two most distant values (as measured by the absolute value of their difference) according to the relative position of the third value between the two. The saturation of the color representing the three-way comparison reflects the amplitude (or extent) of the numerical difference between the two most distant values according to a scale of interest. The brightness is set to a maximum value by default but can be used to encode additional information about the three-way comparison.


We propose a novel color-coding approach for intuitive visualization of three-way comparisons of omics data.