Thursday, 4 August 2016

Plotting multi-set intersections

Most of my research uses the chick model of refractive error, but at the moment I’m working to characterize the overlap in transcriptome and proteomics findings across the range of model species used in my field. The GeneOverlap R package has been a great tool for testing the overlap between my gene lists, however, I recently came across the SuperExactTest R package that provides some additional neat options for testing and visualizing multi-set intersections.

I used SuperExactTest to make the circular plot below showing intersections between differentially-expressed protein lists from tilapia, chick, mouse, guinea pig, and tree shrew. The five tracks in the middle represent the five protein lists, with individual blocks showing the presence (fill) or absence (no fill) of the protein sets in each intersection. The height of the bars on the outermost track is proportional to the intersection size (also indicated by the number next to each bar), and the fill colour of the outermost bars represents the statistical significance of the intersection. I’ve ordered this plot from lowest to highest p-value; the arrow on the right points to the most significant intersection (six shared protein findings between guinea pig and tree shrew).

If you’re interested, check out the paper ‘Efficient Test and Visualization of Multi-Set Intersections’ (Wang et al., 2015), which describes the theoretical framework for the SuperExactTest package.


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  2. Hi Nina,
    Nice plot. I'm also starting to use SuperExactTest and I'm wondering how you managed to program the different colours of the inner circles. Or did you change them by hand in an illustrator program?

    1. Hi Mark,
      Yes, I exported the vector figure and changed the colors in Illustrator. It's probably possible in R, but I generally find exporting and using Illustrator easier (especially if you're only doing a few figures with a given program).


    2. Thanks Nina. Yes, I agree. That's also my preferred way unless I have a huge figure, like now... :-)
      Thanks, anyway, really nice figure