South Asian PCA 3D Plot

Posted by Zack on January 12, 2012

Here's a 3-D plot of my South Asian PCA run, showing the first three principal components.

The principal components have been scaled according to their respective eigenvalues. The plot is rotating about the vertical 1st eigenvector.

</p> <p>Your browser does not support frames. Go <a href="http://www.harappadna.org/wp-content/uploads/2012/01/ref3_c_m_hap_sa.pcaplot.html">here</a> to see the animation.</p> <p>

You can find out your position on the plot by using the dropdown below the plot and selecting your Harappa ID.

PCA3d, harappa, reference, south asia

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18 Comments.

HRP15 January 12, 2012 at 12:12 pm

My ID is missing 🙁
When i want to select it, i cant find it.
- AV January 13, 2012 at 10:28 am
  
  This is a South-Asian 3D PCA plot, HRP15.
  
  Anyway, awesome work Zack! The particpants plus all the available reference populations together on one PCA plot makes for great reference.
- Zack January 13, 2012 at 10:49 am
  
  As I mentioned here, this run includes only those whose ref3 admixture results had more than 50% South Asian + Onge.
HRP15 January 13, 2012 at 1:41 pm

Hi Zack. Thanks for reply. Will you make a run on gypsies, to elaborate more on their origins?
- Zack January 17, 2012 at 12:29 pm
  
  Yes, now that I have a few Romany participants, I am going to do a group analysis for them.
HRP15 January 17, 2012 at 2:37 pm

Cool. Thanks
JK January 31, 2012 at 10:35 pm

Awesome 3 D PCA plot, this is quite a amazing tool. Great job Zack!
AV February 19, 2012 at 4:38 am

Hi Zack. Is it possible to make an option; wherein you can choose multiple participants from the drop down bar to be illustrated on the PCA plot?
- AV February 19, 2012 at 8:11 pm
  
  And also, the option of removing certain populations from the plot.
  - Zack February 20, 2012 at 5:27 pm
    
    I have been thinking about such features. But it will probably take some time.
mac September 1, 2012 at 9:34 pm

Hey Zack, I'm wondering if you could update your PCA 3d plot on page 5 with the newer participants? I mean the ones that are HRP0197-HRP0253.
air December 31, 2012 at 4:56 pm

Fascinating studies Zack.
What is a good reference to learn the science behind these studies ?
Thanks
MSG February 6, 2013 at 2:56 pm

Hello Zack,

I'm wondering if you could possibly update this 3D PCA plot with newer participants?
- Zack February 6, 2013 at 3:59 pm
  
  I will, though not sure when.
air February 6, 2013 at 6:52 pm

Zack what are the weights of the constituents of the three principal components ?
Thanks
- Zack February 7, 2013 at 3:42 pm
  
  Here
  - air February 7, 2013 at 6:27 pm
    
    Thanks Zack. What are the linear weights of each of the components in the eigenvectors....just for the first 2 or 3 eigen vectors ?
    - Zack February 9, 2013 at 7:23 pm
      
      Listed in that link.

Harappa Ancestry Project

Genetics and South Asia