Visualizing genetic variation

By Razib Khan | February 12, 2013 5:31 am

I’ve been thinking about how best to visualize PCA/MDS type of results, which allow for the two dimensional representation of genetic variation. Below are a few of my efforts with a data set I have. You can see the individuals in gray, but also ellipses which cover ~95% of the distribution of a given population.

Please click the images for a larger version. They represent coordinate 1 on the y axis and 2 on the z axis derive from a multidimesional scaling representing identity by state across individuals.

CATEGORIZED UNDER: Genomics, Geography
MORE ABOUT: Genetics, Genomics

Comments (3)

  1. ohwilleke

    It may just be my ideosyncreatic shortcomings of my own color vision, but the hue gradations in the legend are far too fine grained for me to discern and connect to the chart. I guess I was more an eight or twelve crayon package kid than a sixty-four crayon package kid.
    This matters because the broad color regions in the legend don’t line up linearly on the PCA chart.
    The 95% circles are great, but there are just too many of them to process meaningfully. Perhaps the circles could be annotated with three letter codes or something.

  2. razibkhan

    appreciate the suggestions!

  3. Attaching labels to each box, even if they’re just abbreviations, would make things a bit easier. But this is a very promising approach and I’m glad you’re following up on it.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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