{"id":433,"date":"2025-07-10T20:07:38","date_gmt":"2025-07-10T20:07:38","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=433"},"modified":"2025-07-11T00:40:48","modified_gmt":"2025-07-11T00:40:48","slug":"drawing-a-qq-plot","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2025\/07\/10\/drawing-a-qq-plot\/","title":{"rendered":"How to draw a QQ plot"},"content":{"rendered":"\n<p>This post will explain how to draw a QQ plot using QTLmax Workbench. When you perform GWAS calculations in QTLmax, the following result files are generated:<\/p>\n\n\n\n<ol start=\"1\" class=\"wp-block-list\">\n<li><strong>genotype.ped<\/strong><\/li>\n\n\n\n<li><strong>genotype.map<\/strong><\/li>\n\n\n\n<li><strong>pvalues<\/strong><\/li>\n\n\n\n<li><strong>pvalues_map.csv<\/strong><\/li>\n<\/ol>\n\n\n\n<p>To draw a QQ plot using QTLmax, you only need file #3: <strong>pvalues<\/strong>.<br>Figure 1 shows the QQ plot drawing tab selected within the QTLmax Workbench program. This tab presents several configuration options. If you prefer not to select each setting individually, simply click the <strong>[Load demo]<\/strong> button; most of the settings will then be configured automatically. (Figure 1)<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"590\" src=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_006-2-1024x590.png\" alt=\"\" class=\"wp-image-577\" srcset=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_006-2-1024x590.png 1024w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_006-2-300x173.png 300w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_006-2-768x443.png 768w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_006-2-1536x885.png 1536w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_006-2.png 1798w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>(Figure1)<br>After replacing the demo data with your own, you&#8217;re free to change the settings to your desired values. <strong>Selecting the color for the points to be displayed on the QQ plot is mandatory.<\/strong> Once all settings are finalized, click the <strong>[Visualize]<\/strong> button, and you&#8217;ll see the QQ plot generated (Figure 2).<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"590\" src=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_007-2-1024x590.png\" alt=\"\" class=\"wp-image-578\" srcset=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_007-2-1024x590.png 1024w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_007-2-300x173.png 300w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_007-2-768x443.png 768w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_007-2-1536x885.png 1536w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-Workbench_007-2.png 1798w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>(Figure 2)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This post will explain how to draw a QQ plot using QTLmax Workbench. When you perform GWAS calculations in QTLmax, the following result files are generated: To draw a QQ plot using QTLmax, you only need file #3: pvalues.Figure 1 shows the QQ plot drawing tab selected within the QTLmax Workbench program. This tab presents [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"categories":[1],"tags":[],"class_list":["post-433","post","type-post","status-publish","format-standard","hentry","category-guide"],"_links":{"self":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/433","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/comments?post=433"}],"version-history":[{"count":7,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/433\/revisions"}],"predecessor-version":[{"id":635,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/433\/revisions\/635"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=433"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=433"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=433"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}