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Thread: UMAP of (sub)modern Europeans

  1. #211
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    Here are Jessie_mom and RVBLAKE
    Jessie_mom(JM) is hard to find. Look at 0.047, 3.799

    RVBLAKE.png

    Here are the nearest neighbors:

    Jessie_mom 'JM'
    [1] "Jessie" "England_Saxon:I0159"
    [3] "ITA_Collegno_MA:CL146" "England_Saxon:NO3423"
    [5] "French_Brittany:French24400" "jadegregM"
    [7] "English_Cornwall:HG00259" "VK2020_ISL_Hringsdalur_VA:VK127"
    [9] "English_Cornwall:HG00160"

    RVBLAKE 'r'
    [1] "English_Cornwall:HG00239" "English:English1" "Aaroon1916_mom"
    [4] "English:English3" "French_Brittany:Rennes_B_6" "VK2020_SWE_Skara_VA:VK398"
    [7] "VK2020_Faroes_EM:VK25" "VK2020_DNK_Jutland_VA:VK329" "English:HG02215"

  2. The Following 8 Users Say Thank You to Huijbregts For This Useful Post:

     Aroon1916 (10-17-2020),  Bygdedweller (10-17-2020),  evon (10-17-2020),  FionnSneachta (10-17-2020),  jadegreg (10-17-2020),  Jessie (10-18-2020),  JMcB (10-17-2020),  sktibo (10-17-2020)

  3. #212
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    Quote Originally Posted by anglesqueville View Post
    Well, OK. If I add Finn and his parents to Margaryan-Vadim spreadsheet, I get for Finn this list of distances:

    0.00872707 finn_mom
    0.00897550 finn_dad
    0.01079630 VK219
    0.01170854 VK290
    0.01280781 VK489
    0.01327479 VK40
    0.01360625 VK373
    0.01369306 VK173
    0.01400429 VK174
    0.01401678 VK316
    0.01404920 VK33
    0.01415309 VK172
    0.01426289 VK134
    0.01433004 VK238
    0.01484251 VK393
    0.01484992 VK486
    0.01502198 VK320
    0.01508310 VK23
    0.01515124 VK334
    0.01518321 VK323
    0.01532514 VK281
    0.01534764 VK401
    0.01546932 VK364
    0.01562626 VK101
    0.01598781 VK291

    The euclidean distance is maybe not very reliable, but at least it is able to localize Finn's parents in a sensical way. If now I apply umap to the same spreadsheet, I get this:

    Attachment 40380

    Please, explain.
    Thanks Angles. But that's really mission impossible. Because they are from a Viking context, applied to the Finns.
    In the UMAP case it should be the ones who are belonging to the 'same subcluster' as the Finn's.
    That needs an additional analysis to show if this is likely or not.

  4. #213
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    Quote Originally Posted by Huijbregts View Post
    Here are Jessie_mom and RVBLAKE
    Jessie_mom(JM) is hard to find. Look at 0.047, 3.799

    RVBLAKE.png

    Here are the nearest neighbors:

    Jessie_mom 'JM'
    [1] "Jessie" "England_Saxon:I0159"
    [3] "ITA_Collegno_MA:CL146" "England_Saxon:NO3423"
    [5] "French_Brittany:French24400" "jadegregM"
    [7] "English_Cornwall:HG00259" "VK2020_ISL_Hringsdalur_VA:VK127"
    [9] "English_Cornwall:HG00160"

    RVBLAKE 'r'
    [1] "English_Cornwall:HG00239" "English:English1" "Aaroon1916_mom"
    [4] "English:English3" "French_Brittany:Rennes_B_6" "VK2020_SWE_Skara_VA:VK398"
    [7] "VK2020_Faroes_EM:VK25" "VK2020_DNK_Jutland_VA:VK329" "English:HG02215"
    Thank you so much!

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  6. #214
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    Quote Originally Posted by anglesqueville View Post
    Well, OK. If I add Finn and his parents to Margaryan-Vadim spreadsheet, I get for Finn this list of distances:

    0.00872707 finn_mom
    0.00897550 finn_dad
    0.01079630 VK219
    0.01170854 VK290
    0.01280781 VK489
    0.01327479 VK40
    0.01360625 VK373
    0.01369306 VK173
    0.01400429 VK174
    0.01401678 VK316
    0.01404920 VK33
    0.01415309 VK172
    0.01426289 VK134
    0.01433004 VK238
    0.01484251 VK393
    0.01484992 VK486
    0.01502198 VK320
    0.01508310 VK23
    0.01515124 VK334
    0.01518321 VK323
    0.01532514 VK281
    0.01534764 VK401
    0.01546932 VK364
    0.01562626 VK101
    0.01598781 VK291

    The euclidean distance is maybe not very reliable, but at least it is able to localize Finn's parents in a sensical way. If now I apply umap to the same spreadsheet, I get this:

    Attachment 40380

    Please, explain.
    It is ease to mistune an UMAP model.

    In #178 you wrote:
    I really can't understand why Euclidean distances would be less "reliable" in dim 25 than in dim 2 or 3 or n. A distance is a distance, period. But drop it. We discussed all of this about t-sne and it almost ended in a fight. Obviously the same will happen here if we start. So... just drop it.
    What are you after?

  7. #215
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    Hello, FionnSneachta and Huijbregts, looks like we're sharing real estate.

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  9. #216
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    Thanks Huijbregts! Very interesting. Seems like I'm occupying my own little island up there. ^^
    Quote Originally Posted by evon View Post
    The odd thing I now noticed is the placement of Bygdedweller and FionnSneachta, while I can understand Bygdedweller as a Eastern Norwegian, I am having a hard time with FionnSeachta contra her relatives.
    Yes, I noticed that too. Definitely surprised me, but I see the plot stretching and changing orientation as new samples are being added, so who knows. However, I did notice FionnSneachta has affinity with Greenland and Iceland-samples in the nearest neighbor-results, similar to me. And the only reliable pattern I can deduce from the plot is that the samples seem to get increasingly Northern-like as we move upwards the UMAP2-axis on the plot. It would be interesting to see members plotted on the G25 North Europe PCA for comparison.
    Quote Originally Posted by jadegreg View Post
    I was thinking that I was beginning to understand the splits if one goes to the original orientation in the first post, but again, Bygdedweller and FionnSneachta's placements on the left side???.........nope....I've got nothing, Well, nothing that makes any sense. Maybe the 'fork' leading to three apparent separating clusters is actually misleading.
    That seems plausible. Maybe it's just an artifact of the algorithm that the samples are being stretched out this way, as the empty areas in-between the forks are a bit wide.

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  11. #217
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    Quote Originally Posted by Huijbregts View Post
    Here are Jessie_mom and RVBLAKE
    Jessie_mom(JM) is hard to find. Look at 0.047, 3.799

    RVBLAKE.png

    Here are the nearest neighbors:

    Jessie_mom 'JM'
    [1] "Jessie" "England_Saxon:I0159"
    [3] "ITA_Collegno_MA:CL146" "England_Saxon:NO3423"
    [5] "French_Brittany:French24400" "jadegregM"
    [7] "English_Cornwall:HG00259" "VK2020_ISL_Hringsdalur_VA:VK127"
    [9] "English_Cornwall:HG00160"

    RVBLAKE 'r'
    [1] "English_Cornwall:HG00239" "English:English1" "Aaroon1916_mom"
    [4] "English:English3" "French_Brittany:Rennes_B_6" "VK2020_SWE_Skara_VA:VK398"
    [7] "VK2020_Faroes_EM:VK25" "VK2020_DNK_Jutland_VA:VK329" "English:HG02215"
    My mother (AM) has company

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  13. #218
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    Quote Originally Posted by sktibo View Post
    If we look at this plot in terms of southern/continental to northern I think it makes sense, with KM being at the continental most end and FM being northern-most. We have Norwegian and Irish members sharing the northern space towards the top right.

    And I do not mean this is absolutely perfect for everyone when interpreted this way, so please don't quote me saying something like "but this doesn't work for me"

    I'm pointing out that's the pattern I see when I look at this data: Northern/ extreme insular component top right to continental like component bottom left. I'd draw a line but I'm on my phone - visualise a diagonal line running across the NW cluster
    That seems like a perfectly reasonable assumption. But what do you think is going on with the branch/cluster shared by Hujibregts, FionnSneachta and Bygdedwelle. Similarly, the branch/cluster that I myself and Radboud are in. I would really be interested in your thoughts.

    I was thinking the original orientation made the most sense with respect to geography of the populations

    UMAP1.2.png as opposed to

    UMAP3.22.png

    But now I'm not sure....
    Last edited by jadegreg; 10-17-2020 at 10:00 PM.

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  15. #219
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    Thanks Hujibregts for plotting me! Was wondering if you would be able to plot my mum as well?

    DMACmom,0.012,0.0135,0.0166,0.0131,0.0113,0.0057,0 .0001,0.0008,0.005,0.0029,-0.0034,0.0022,-0.0085,-0.0112,0.0166,0.0036,-0.001,0.0004,-0.0002,0.0088,0.0035,0.003,-0.0012,0.0089,0.0017

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  17. #220
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    Quote Originally Posted by Bygdedweller View Post
    Thanks Huijbregts! Very interesting. Seems like I'm occupying my own little island up there. ^^

    Yes, I noticed that too. Definitely surprised me, but I see the plot stretching and changing orientation as new samples are being added, so who knows. However, I did notice FionnSneachta has affinity with Greenland and Iceland-samples in the nearest neighbor-results, similar to me. And the only reliable pattern I can deduce from the plot is that the samples seem to get increasingly Northern-like as we move upwards the UMAP2-axis on the plot. It would be interesting to see members plotted on the G25 North Europe PCA for comparison.
    I didn't notice that the plot was stretching, but that makes sense when I was trying to align my position with the original plot in the first post. However, I wasn't sure if Hujibregts had removed the thrre smaller populations from the original plot, for the later ones with Anthrogenica members.

    I think that's a good idea with respect to plotting the individual members on the North Europe PCA. See if that helps make sense of this......

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