Visualizing Europe genetically

By Razib Khan | February 13, 2013 5:54 am

This is a follow up to my post from yesterday. In case you care about the technical details (after I clean this stuff up I will put it on GitHub) I’m using R’s adehabitat package to create a 95% distribution curve after smoothing with kernel density. The goal is to give you a better intuition about where the populations are dispersed across two dimensional visualizations of genetic variation.

Thinking about how to plot text, I came up with a quick hack, which just used the initial data and found the median x and y position. That explains why some of the labels are shifted so, in populations with a huge range the label position is going to be sensitive to not being smoothed (if you know how to pull out the centroid out of the kver, tell!). I’ve given them colors and also used black. The latter actually seems to be clearer!

Note: This is not just for fun, as I plan to start rolling out results and methods from some of the data sets I have more regularly in the near future.


CATEGORIZED UNDER: Genetics, Genomics
  • https://delicious.com/robertford Robert Ford

    Much better

  • ohwilleke

    Agreed. With those modification it is a very clear and easy to understand presentation.

  • adsf

    You should definitly check out the directlabels package http://directlabels.r-forge.r-project.org/ for automatic label positioning

  • Gnnit

    I think you switched the Tuscans and the Spaniards, normally it’s the spaniards who are closer to French than Tuscans. Check that.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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 http://www.razib.com

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