{"id":36584,"date":"2011-01-18T13:06:39","date_gmt":"2011-01-18T21:06:39","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=9203"},"modified":"2011-01-24T07:01:48","modified_gmt":"2011-01-24T15:01:48","slug":"admixture-vs-mds-visualization-is-just-visualization","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2011\/01\/18\/admixture-vs-mds-visualization-is-just-visualization\/","title":{"rendered":"ADMIXTURE vs. MDS, visualization is just visualization"},"content":{"rendered":"<p>Dienekes did another <a href=\"http:\/\/dodecad.blogspot.com\/2011\/01\/clusters-galore-results-k64-for-dodecad.html\">run of his data with K = 64<\/a>. He posted a <a href=\"https:\/\/docs.google.com\/leaf?id=0B7AJcY18g2GaZGIxOTRhNjMtY2JjNS00MDdlLWEwNWQtNzViNjliMDdhOTc2&amp;hl=en&amp;authkey=CNiC1ZwC\">huge plot<\/a> with the two largest dimensions of variation. He also posted an accompanying spreadsheet with the coordinates of where the Dodecad samples were. So I found my own position pretty quickly. Before going to that, I thought I&#8217;d repost a comparison between myself, the HapMap Gujaratis, the North Kannadi sample, and the HGDP Uygurs. This is at K = 10 in ADMIXTURE from Dodecad.<br \/>\n<a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/01\/meADMIXTURE.png\"><img decoding=\"async\" src=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/01\/meADMIXTURE.png\" alt=\"\" class=\"alignnone size-thumbnail wp-image-9204\" \/><\/a><\/p>\n<p>OK, with that in mind, here&#8217;s the full MDS with the two largest components of genetic variation. I&#8217;ve added large labels. Also, click the image for a larger file so you can read the small labels.<\/p>\n<p>\n<a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/01\/MDS_DOD307.png\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/01\/MDS_DOD307-300x300.png\" alt=\"\" width=\"300\" height=\"300\" class=\"alignleft size-medium wp-image-9205\" \/><\/a>One thing that jumps out at me is the tight clustering of very populous groups such as Europeans. The East Asians and Yoruba samples aren&#8217;t as representative of their macro-region, so that makes some sense. But the Dodecad Ancestry Project has a lot of West Eurasian groups, so the affinity there is still striking. I am basically a touch off the &#8220;North Kannadi&#8221; cluster, a little toward &#8230;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Dienekes did another run of his data with K = 64. He posted a huge plot with the two largest dimensions of variation. He also posted an accompanying spreadsheet with the coordinates of where the Dodecad samples were. So I found my own position pretty q&#8230;<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[290,780,4,82,1000],"tags":[],"class_list":["post-36584","post","type-post","status-publish","format-standard","hentry","category-admixture","category-dodecad","category-genetics","category-genomics","category-mds"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/36584","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/comments?post=36584"}],"version-history":[{"count":6,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/36584\/revisions"}],"predecessor-version":[{"id":36801,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/36584\/revisions\/36801"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=36584"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=36584"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=36584"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}