{"id":1683,"date":"2008-08-13T13:00:46","date_gmt":"2008-08-13T11:00:46","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/?p=1683"},"modified":"2008-08-19T12:14:31","modified_gmt":"2008-08-19T10:14:31","slug":"the-pointillism-gwa-plot","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2008\/08\/the-pointillism-gwa-plot\/","title":{"rendered":"The pointillism GWA plot"},"content":{"rendered":"<p><a href=\"https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2008\/08\/genomeplots.png\" data-rel=\"key-image-0\" data-rl_title=\"\" data-rl_caption=\"\"><img decoding=\"async\" src=\"https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2008\/08\/genomeplots-150x150.png\" alt=\"\" title=\"\" style=\"display:inline;float:left;margin-right:20px\"\/><\/a><br \/>\nThe experts in the field will immediately notice  what I am suggesting here &#8211; an improved GWA plot that does not take into account p values alone but also effect sizes. I was experimenting some time with <em><a href=\"http:\/\/www3.interscience.wiley.com\/cgi-bin\/fulltext\/119398126\/HTMLSTART\">smile plots<\/a><\/em> but finally ended with this bubble plot. Bubble size for 0.5&lt;OR&gt;2 is set to a minimum while all other ORs get increasing bubbles (BTW use for OR&lt;1 a 1\/OR transformation beforehand). Chromosomal colors are from a self defined palette using the <em>colorRampPalette<\/em> function in R which makes it look like <a href=\"http:\/\/www.webexhibits.org\/colorart\/jatte.html\">pointillism<\/a> art. The real question: <strong>Did the previous GWA p value screening miss some important effects?<\/strong> For example the important dot at x=4 and y=4?<\/p>\n\n<p>&nbsp;<\/p>\n<div class=\"bottom-note\">\n  <span class=\"mod1\">CC-BY-NC Science Surf , accessed 05.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"<p>The experts in the field will immediately notice what I am suggesting here &#8211; an improved GWA plot that does not take into account p values alone but also effect sizes. I was experimenting some time with smile plots but finally ended with this bubble plot. Bubble size for 0.5&lt;OR&gt;2 is set to a minimum &hellip; <a href=\"https:\/\/www.wjst.de\/blog\/sciencesurf\/2008\/08\/the-pointillism-gwa-plot\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">The pointillism GWA plot<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[2012,1114,2013],"class_list":["post-1683","post","type-post","status-publish","format-standard","hentry","category-genetics-biology","tag-bubble-size","tag-gwa","tag-introduction-new-plot-type"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1683","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=1683"}],"version-history":[{"count":0,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1683\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=1683"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=1683"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=1683"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}