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Thread: New 3D PCAs - South Asian focus

  1. #1
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    New 3D PCAs - South Asian focus

    Been bored so I've been messing around on Vahaduo's new 3D PCA tools. Like academic PCAs, these new 3D jawns use unscaled data. First thing I wanted to check was the MENA PCA. Obviously as they are 3D a total idea of the PCA will be missed without exploring them yourself.


    First: X=PC1 Y=PC2 Z=PC 3 and the colour of the component gradient = PC3.

    Annotation 2020-09-06 175157.png

    Second: X=PC1 Y=PC2 Z=PC4 Colour=PC4

    Annotation 2020-09-06 175855.png

    Interestingly, if my supposed ancestry [Harappa/what has been suggested in the other thread] was Khoja/Memon/Khatri etc, I'd be plotting with agentlime/Lollybolly etc as they exhibit a clear Copper Age Iranian pull [please correct me if I'm wrong]. Instead, like misanthropy bros, its more of a Yemen/Saudi/Egyptian-like pull. However, there may be more than one stream of ancestry at play, so I understand that. Next PCA will be various groups plotting on a South Asian PCA along with the individuals in my sheets. If anyone got any requests then holla
    Last edited by ThaYamamoto; 09-07-2020 at 11:58 PM.

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    Here's a South Asian only PCA X=PC1 Y=PC2 Z=PC3 COLOUR=PC3. Tried as many angles and orbital perspectives.

    Annotation 2020-09-08 030135.png

    Annotation 2020-09-08 030427.png

    Annotation 2020-09-08 030559.png

    Annotation 2020-09-08 030926.png

    Annotation 2020-09-08 031111.png

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    Quote Originally Posted by ThaYamamoto View Post
    Next PCA will be various groups plotting on a South Asian PCA along with the individuals in my sheets. If anyone got any requests then holla
    I have no idea how PCA's work or how to interpret them. I can share my coordinates if someone is willing to help me interpret the results.
    G25 Neolithic model

    "sample": "kamil154",
    "distance": 2.2284,
    "Ganj_Dareh_N": 41,
    "Barcin_N": 18,
    "Simulated_AASI_NW_by_DMXX": 17,
    "Karelia_HG": 10.5,
    "GEO_CHG": 3.5,
    "Tyumen_HG": 3,
    "LAO_Hoabinhian": 2.5,
    "LapaDoSanto_9600BP": 2.5,
    "Boshan_N": 2

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    Quote Originally Posted by kamil154 View Post
    I have no idea how PCA's work or how to interpret them. I can share my coordinates if someone is willing to help me interpret the results.
    I'd explain it terribly, hopefully someone can be kind enough to do so!

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    Quote Originally Posted by ThaYamamoto View Post
    Here's a South Asian only PCA X=PC1 Y=PC2 Z=PC3 COLOUR=PC3. Tried as many angles and orbital perspectives.

    Annotation 2020-09-08 030135.png

    Annotation 2020-09-08 030427.png

    Annotation 2020-09-08 030559.png

    Annotation 2020-09-08 030926.png

    Annotation 2020-09-08 031111.png
    unscaled is not good at all for PCAs , David I remember also pointed that out, this was almost 2 years back.

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    Kamil_scaled,0.0774,0.004062,-0.108234,0.064277,-0.068628,0.04518,-0.006345,-0.003692,-0.009408,-0.01221,-0.009581,0.003147,-0.005798,-0.00234,0.016151,0.005038,-0.004955,-0.00076,-0.002388,-0.011506,0.001497,-0.007048,-0.001602,-0.001446,0.008861

    Kamil,0.0068,0.0004,-0.0287,0.0199,-0.0223,0.0162,-0.0027,-0.0016,-0.0046,-0.0067,-0.0059,0.0021,-0.0039,-0.0017,0.0119,0.0038,-0.0038,-0.0006,-0.0019,-0.0092,0.0012,-0.0057,-0.0013,-0.0012,0.0074
    G25 Neolithic model

    "sample": "kamil154",
    "distance": 2.2284,
    "Ganj_Dareh_N": 41,
    "Barcin_N": 18,
    "Simulated_AASI_NW_by_DMXX": 17,
    "Karelia_HG": 10.5,
    "GEO_CHG": 3.5,
    "Tyumen_HG": 3,
    "LAO_Hoabinhian": 2.5,
    "LapaDoSanto_9600BP": 2.5,
    "Boshan_N": 2

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    Quote Originally Posted by pegasus View Post
    unscaled is not good at all for PCAs , David I remember also pointed that out, this was almost 2 years back.
    Yeah Vahaduo already cleared this up on the blog - it scales automatically or where deemed necessary. The results are almost identical to the scaled-only 2D PCA. That's why David posted about it. 2 weeks ago.

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    Quote Originally Posted by ThaYamamoto View Post
    Yeah Vahaduo already cleared this up on the blog - it scales automatically or where deemed necessary. The results are almost identical to the scaled-only 2D PCA. That's why David posted about it. 2 weeks ago.
    Thats good. I have not used it , I just look at the 3D one and it made me dizzy

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    Quote Originally Posted by ThaYamamoto View Post
    If anyone got any requests then holla
    Do include me in the next run if you are willing/able to. I'd like to know where I cluster in relation to some of the other users.
    G25 Neolithic model

    "sample": "kamil154",
    "distance": 2.2284,
    "Ganj_Dareh_N": 41,
    "Barcin_N": 18,
    "Simulated_AASI_NW_by_DMXX": 17,
    "Karelia_HG": 10.5,
    "GEO_CHG": 3.5,
    "Tyumen_HG": 3,
    "LAO_Hoabinhian": 2.5,
    "LapaDoSanto_9600BP": 2.5,
    "Boshan_N": 2

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