<\/title> \n<meta charset=\"utf-8\"> \n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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#33ab01;margin-right:5px;}.ad{text-decoration:none;color:#d6d4d4;font-size:12px;}.msgBodyReply{padding-top:5px;}.userName span{float:right;color:#afafaf;font-size:14px;}code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;}.code-snippet__fix{font-size:14px;margin:10px 0;display:block;color:#333;position:relative;background-color:rgba(0,0,0,0.03);border:1px solid #f0f0f0;border-radius:2px;display:-webkit-box;display:-webkit-flex;display:flex;padding-left:25px;line-height:26px}.code-snippet__fix code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;font-family:Consolas,\"Liberation 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solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);width: 100%;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;vertical-align: top;width: 70.0348%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70.0348% !important;\">\n<section style=\"margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: 29.9652%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 29.9652% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;line-height: 0;\">\n<section>\n<section style=\"display: inline-block;vertical-align: middle;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 0;\">\n<section style=\"width: 111px;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1.75em;text-indent: 0em;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;height: auto;width: 111px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_Xkz3aJGClianeaJMFaPKsbDRmfsHNw-6.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3URAEIyVaH5J7WwYnm1GpxBmYrwXkz3aJGClianeaJMFaPKsbDRmfsHNw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"400\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 10px 0% 8px;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;font-size: 14px;\" powered-by=\"xiumi.us\">\n<\/span>hello\uff0c\u4eca\u5929\u5c0f\u679c\u6765\u6559\u5927\u5bb6\u5982\u4f55\u5bf9KEGG\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\u901a\u8fc7ggplot2\u5b9e\u73b0\u53ef\u89c6\u5316\u5e76\u7ed8\u5236\u5bf9\u5e94\u7684KEGG\u901a\u8def\u7f51\u7edc\u56fe \uff0c\u8ba9\u4f60\u7684\u5206\u6790\u7ed3\u679c\u66f4\u52a0\u7f8e\u89c2\uff01<\/span>\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/span><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n1. <\/span><\/em><\/strong>\u51c6\u5907\u9700\u8981\u7684R\u5305<\/em><\/span><\/strong><\/p>\n <\/p>\n\u5148\u6765\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\u6211\u4eec\u4eca\u5929\u7528\u5230\u7684R\u5305\uff0c\u5206\u522b\u662fDOSE\u3001clusterProfiler\u3001org.Hs.eg.db\u3001ggplot2\u3001tidyverse\u4ee5\u53caenrichplot\u5305\u3002\u540c\u5b66\u4eec\u8981\u63d0\u524d\u4e0b\u8f7d\u597d\u54e6\uff01\u5728\u8fd9\u91cc\u5c0f\u679c\u4e3a\u5927\u5bb6\u7b80\u5355\u7684\u4ecb\u7ecd\u4e00\u4e0b\u5176\u4e2d\u51e0\u4e2aR\u5305\uff1a<\/span><o:p><\/o:p><\/p>\n1.DOSE\uff1a<\/span><\/strong>DOSE\u5305\u4e3b\u8981\u7528\u4e8e\u57fa\u56e0\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff0c\u5b83\u80fd\u591f\u901a\u8fc7\u6bd4\u8f83\u8f93\u5165\u7684\u57fa\u56e0\u5217\u8868\u4e0e\u5df2\u77e5\u7684\u57fa\u56e0\u529f\u80fd\u6ce8\u91ca\u4fe1\u606f\uff0c\u627e\u51fa\u5728\u7279\u5b9a\u529f\u80fd\u7c7b\u522b\u4e2d\u5bcc\u96c6\u7684\u57fa\u56e0\u3002<\/span><o:p><\/o:p><\/p>\n2.clusterProfiler\uff1a<\/span><\/strong>clusterProfiler\u662f\u4e00\u4e2a\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u7684R\u5305\uff0c\u4e3b\u8981\u7528\u4e8e\u529f\u80fd\u6ce8\u91ca\u548c\u5bcc\u96c6\u5206\u6790\u3002\u5b83\u63d0\u4f9b\u4e86\u9488\u5bf9\u591a\u79cd\u751f\u7269\u6570\u636e\u7c7b\u578b\u7684\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\uff0c\u5305\u62ecGO\u3001KEGG\u3001Reactome\u7b49\u3002\u8be5\u5305\u8fd8\u63d0\u4f9b\u4e86\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u4f7f\u7528\u6237\u80fd\u591f\u66f4\u597d\u5730\u7406\u89e3\u548c\u89e3\u91ca\u529f\u80fd\u5bcc\u96c6\u7ed3\u679c\u3002<\/span><o:p><\/o:p><\/p>\n3.org.Hs.eg.db\uff1a<\/strong>org.Hs.eg.db\u662f\u4e00\u4e2aR\u8bed\u8a00\u4e2d\u7528\u4e8e\u4eba\u7c7b\u57fa\u56e0\u6ce8\u91ca\u7684\u6570\u636e\u5e93\u5305\u3002\u5b83\u63d0\u4f9b\u4e86\u5bf9\u4eba\u7c7b\u57fa\u56e0\u7ec4\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u5305\u62ec\u57fa\u56e0ID\u3001\u57fa\u56e0\u540d\u79f0\u3001\u57fa\u56e0\u7b26\u53f7\u3001\u901a\u8def\u4fe1\u606f\u7b49\u3002\u4f7f\u7528org.Hs.eg.db\u5305\uff0c\u7528\u6237\u53ef\u4ee5\u5c06\u57fa\u56e0ID\u8f6c\u6362\u4e3a\u6613\u8bfb\u7684\u57fa\u56e0\u7b26\u53f7\uff0c\u4ece\u800c\u66f4\u5bb9\u6613\u7406\u89e3\u548c\u89e3\u91ca\u529f\u80fd\u5bcc\u96c6\u7ed3\u679c\u3002<\/span><o:p><\/o:p><\/p>\n4.tidyverse\uff1a<\/span><\/strong>tidyverse\u662f\u4e00\u4e2a\u7531\u591a\u4e2aR\u5305\u7ec4\u6210\u7684\u96c6\u5408\uff0c\u65e8\u5728\u63d0\u4f9b\u4e00\u5957\u4e00\u81f4\u4e14\u6613\u4e8e\u4f7f\u7528\u7684\u6570\u636e\u5904\u7406\u548c\u53ef\u89c6\u5316\u5de5\u5177\u3002\u8fd9\u4e9b\u5305\u5305\u62ecggplot2\u3001dplyr\u3001tidyr\u3001readr\u7b49\u3002\u5176\u4e2d\uff0cggplot2\u662f\u7528\u4e8e\u6570\u636e\u53ef\u89c6\u5316\u7684\u91cd\u8981\u7ec4\u6210\u90e8\u5206\uff0c\u63d0\u4f9b\u4e86\u5f3a\u5927\u4e14\u7075\u6d3b\u7684\u7ed8\u56fe\u529f\u80fd\uff0c\u4f7f\u7528\u6237\u80fd\u591f\u521b\u5efa\u9ad8\u8d28\u91cf\u7684\u56fe\u8868\uff0c\u7528\u4e8e\u6570\u636e\u63a2\u7d22\u548c\u5c55\u793a\u3002<\/span><o:p><\/o:p><\/p>\n5.enrichplot\uff1a<\/span><\/strong>enrichplot\u662f\u4e00\u4e2a\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u7684R\u5305\uff0c\u4e3b\u8981\u7528\u4e8e\u529f\u80fd\u5bcc\u96c6\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u3002\u5b83\u63d0\u4f9b\u4e86\u591a\u79cd\u7ed8\u56fe\u51fd\u6570\uff0c\u53ef\u4ee5\u7ed8\u5236\u57fa\u56e0\u96c6\u7684\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\uff0c\u5982GO\u6761\u5f62\u56fe\u3001KEGG\u901a\u8def\u7f51\u7edc\u56fe\u7b49\u3002enrichplot\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u53c2\u6570\u8bbe\u7f6e\uff0c\u4ee5\u6ee1\u8db3\u7528\u6237\u5bf9\u7ed3\u679c\u53ef\u89c6\u5316\u7684\u4e2a\u6027\u5316\u9700\u6c42\u3002 <\/span><\/p>\n\uff08<span style=\"text-decoration: underline;color: rgb(0, 122, 170);font-family: system-ui, -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.544px;text-wrap: wrap;background-color: rgb(255, 255, 255);\">\u5173\u6ce8\u5c0f\u679c\u56de\u590d111\u9886\u53d6\u76f8\u5173\u6587\u4ef6\u54df\uff01<\/span>\uff09<\/span><\/strong><\/span><\/p>\n <\/span><\/p>\n <\/span><\/p>\n2. KEGG\u5bcc\u96c6\u5206\u6790<\/span><\/em><\/strong><\/p>\nenrichKEGG\u8fdb\u884c\u5bcc\u96c6\u5206\u6790<\/strong><\/span><o:p><\/o:p><\/p>\n\u9996\u5148\uff0c\u52a0\u8f7dDOSE\u5305\u5e76\u4f7f\u7528\u8be5\u5305\u4e2d\u7684\u57fa\u56e0\u96c6\u4f5c\u4e3a\u6211\u4eec\u5206\u6790\u7684\u5bf9\u8c61\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"kotlin\"><code>library(\"DOSE\"<\/span>)<\/span><\/code><code>data<\/span>(geneList, package<\/span> = \"DOSE\"<\/span>)<\/span><\/code><code>g_list <- names(geneList)[1<\/span>:100<\/span>]<\/span><\/code><code>head(g_list)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.08285163776493257\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_qeibXrdVicHIicPPZ5bGCLO0cA6Fdg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHve0sYGRSYOdz66Pc4RhPa6xq2icHqeibXrdVicHIicPPZ5bGCLO0cA6Fdg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"519\" style=\"\"><\/p>\n <\/p>\n\u5229\u7528enrichKEGG\u51fd\u6570<\/span><\/strong><\/span>\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u5bf9\u6307\u5b9a\u7684\u57fa\u56e0\u5217\u8868\u8fdb\u884cKEGG\u901a\u8def\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u8bbe\u7f6ep-value\u548cq-value\u7684\u9608\u503c\u3002<o:p><\/o:p><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>library(\"clusterProfiler\")<\/span><\/code><code>library(\"org.Hs.eg.db\")<\/span><\/code><code> <\/span><\/code><code>ek <-<\/span> enrichKEGG<\/span>(gene<\/span> = g_list,<\/span><\/span><\/span><\/code><code> organism<\/span> = \"hsa\"<\/span>,<\/span><\/code><code> pvalueCutoff<\/span> = 0.05,<\/span><\/span><\/code><code> qvalueCutoff<\/span> = 0.05)<\/span><\/span><\/code><code>write.table<\/span>(ek<\/span>, file<\/span> = \"ek.txt\"<\/span>, sep<\/span> = \"t\"<\/span>, quote<\/span> = FALSE,<\/span> row.names<\/span> = FALSE)<\/span><\/span><\/code><\/pre>\n<\/section>\n <\/p>\n\u6ce8\u610f\uff1a<\/span><\/strong><\/span><\/span><\/p>\n\u00b7pvalueCutoff = 0.05\uff1a<\/span><\/span><\/strong><\/span>\u8bbe\u7f6ep-value\u7684\u9608\u503c\uff0c\u7528\u4e8e\u7b5b\u9009\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u4e2d\u7edf\u8ba1\u663e\u8457\u7684\u901a\u8def\u3002\u5728\u8fd9\u91cc\uff0c\u8bbe\u5b9a\u4e3a0.05\uff0c\u5373p-value\u5c0f\u4e8e0.05\u7684\u901a\u8def\u88ab\u8ba4\u4e3a\u662f\u663e\u8457\u5bcc\u96c6\u7684\u901a\u8def\u3002<\/span><o:p><\/o:p><\/p>\n\u00b7<\/span>qvalueCutoff = 0.05\uff1a<\/span><\/strong><\/span>\u8bbe\u7f6eq-value\u7684\u9608\u503c\uff0cq-value\u662f\u7ecf\u8fc7FDR\u6821\u6b63\u7684p-value\uff0c\u7528\u4e8e\u63a7\u5236\u591a\u91cd\u5047\u8bbe\u68c0\u9a8c\u7684\u9519\u8bef\u53d1\u73b0\u7387\u3002\u540c\u6837\uff0c\u8bbe\u5b9a\u4e3a0.05\uff0c\u5373q-value\u5c0f\u4e8e0.05\u7684\u901a\u8def\u88ab\u8ba4\u4e3a\u662f\u663e\u8457\u5bcc\u96c6\u7684\u901a\u8def\u3002<\/span><o:p><\/o:p><\/p>\n\u81f3\u6b64\u6211\u4eec\u5df2\u7ecf\u5b8c\u6210\u4e86\u5bcc\u96c6\u5206\u6790\u7684\u6d41\u7a0b\uff0c\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5206\u6790\u7684\u7ed3\u679c\u5427\uff01<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6695526695526696\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_uyp5SWWnsPicOakSc4OjBT7rpNmcUw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHxuKWT4NeYsUkzzhgF0ho2SJpOuyp5SWWnsPicOakSc4OjBT7rpNmcUw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n<\/span><o:p><\/o:p><\/p>\n\u9700\u8981\u6ce8\u610f\u7684\u662f\u7ed3\u679c\u4e2d<\/span>geneID\u4e3a<\/span>EntrezID\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code>head<\/span>(ek<\/span>@result<\/span>$geneID<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.1927007299270073\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_59XZAQ7kbG6EQWDDrhhCJ0VSKjSXxQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHX8cmAOsFN5ewHYcCJ64tqcfo59XZAQ7kbG6EQWDDrhhCJ0VSKjSXxQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"685\" style=\"\"><\/p>\n <\/p>\n\u5c06<\/span>EntrezID\u8f6c\u6362\u4e3a<\/span>Symbol<\/span><\/strong><\/span><\/p>\n\u4f7f\u7528setReadable\u51fd\u6570\u5c06EntrezID\u8f6c\u6362\u4e3aSymbol\uff1a<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>ek2<\/span> <- setReadable(ek,<\/span><\/code><code> OrgDb = \"org.Hs.eg.db\"<\/span>,<\/span><\/code><code> keyType = \"ENTREZID\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.17604617604617603\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_2SElrUiaAR7icRYGThDhyPpXzpturA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHHxfDV4kAOO81F25P57ADUKyVn52SElrUiaAR7icRYGThDhyPpXzpturA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n <\/p>\nggplot2\u53ef\u89c6\u5316\u7ed3\u679c<\/span><\/strong><\/span><\/span><\/strong><o:p><\/o:p><\/span><\/strong><\/p>\n\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u901a\u8fc7\u5b89\u88c5<\/span>tidyverse<\/span>\u5305\u5e76\u8bfb\u53d6\u4fdd\u5b58\u7684\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u6587\u672c\u6587<\/span>\u4ef6\uff0c\u5bf9\u8868\u683c\u8fdb\u884c\u5904\u7406\u548c\u8ba1\u7b97<\/span>Enrichment Factor<\/span>\uff0c\u5728\u8fd9\u91cc\u5c0f\u679c\u7528<\/span>tidyverse<\/span>\u5305<\/span>\u7684<\/span>separate<\/span>\u51fd\u6570\u5c06<\/span>GeneRatio<\/span>\u548c<\/span>BgRatio<\/span>\u7684\u5206\u5b50\u5206\u6bcd\u5148\u5206\u5f00\uff0c\u518d\u8fdb\u884c\u8ba1\u7b97\uff1a<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code>library(tidyverse)<\/span><\/code><code>ek.rt <- read.table(\"ek.txt\"<\/span>, header = TRUE, sep = \"t\"<\/span>, quote = \"\"<\/span>) <\/span><\/code><code>ek.rt <- separate(data = ek.rt, col = GeneRatio, into<\/span> = c(\"GR1\"<\/span>, \"GR2\"<\/span>), sep = \"\/\"<\/span>)<\/span><\/code><code>ek.rt <- separate(data = ek.rt, col = BgRatio, into<\/span> = c(\"BR1\"<\/span>, \"BR2\"<\/span>), sep = \"\/\"<\/span>)<\/span><\/code><code>ek.rt <- mutate(ek.rt, enrichment_factor = (as<\/span>.numeric(GR1) \/ as<\/span>.numeric(GR2)) \/ (as<\/span>.numeric(BR1) \/ as<\/span>.numeric(BR2)))<\/span><\/code><\/pre>\n<\/section>\n\u7b5b\u9009\u51fa\u524d<\/span>10\u4e2a\u901a\u8def\u8fdb\u884c\u53ef\u89c6\u5316\uff1a<\/span><\/span><o:p><\/o:p><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>ek.rt10 <-<\/span> ek.rt<\/span> %><\/span>% filter(row_number() >= 1, row_number() <=<\/span> 10<\/span>)<\/span><\/span><\/code><\/pre>\n<\/section>\n <\/p>\nggplot2\u7ed8\u5236<\/span>dotplot<\/span><\/span><\/strong><\/span><o:p><\/o:p><\/span><\/strong><\/p>\n\u4f7f\u7528<\/span>ggplot2\u5305\u7ed8\u5236<\/span>Enrichment Factor\u4e0e<\/span>KEGG term\u4e4b\u95f4\u7684\u5173\u7cfb\u56fe\uff1a<\/span><\/span><o:p><\/o:p><\/span><\/p>\n<\/span><\/span><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cpp\"><code>library(\"ggplot2\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>p <- ggplot(ek.rt10, aes(enrichment_factor, fct_reorder(factor(Description), enrichment_factor))) + <\/span><\/code><code> geom_point(aes(size = Count, color = -1<\/span> * log10<\/span>(pvalue))) +<\/span><\/code><code> scale_color_gradient(low = \"green\"<\/span>, high = \"red\"<\/span>) + <\/span><\/code><code> labs<\/span>(color = expression(-log<\/span>[10<\/span>](p_value)), size = \"Count\"<\/span>,<\/span><\/code><code> x = \"Enrichment Factor\"<\/span>, y = \"KEGG term\"<\/span>, title = \"KEGG enrichment\"<\/span>) + <\/span><\/code><code> theme_bw()<\/span><\/code><code>ggsave(\"er.rt10_KEGG.png\"<\/span>, width = 6<\/span>, height = 4<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u6548\u679c\u56fe\u5427\uff01<\/span><o:p><\/o:p><\/span><\/p>\n<\/span><\/span><\/strong><\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6666666666666666\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_hf78KpwQnqn0CIzSHw2P6nKuMERJww.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHfoyS3JJkNI0Cto1nJ1YiaFlKUhf78KpwQnqn0CIzSHw2P6nKuMERJww\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n<\/span><\/span><\/strong><\/span><\/p>\n <\/p>\n\u7ed8\u5236<\/span>KEGG\u901a\u8def\u7f51\u7edc\u56fe<\/span><\/span><\/strong><\/span><\/span><\/strong><\/span><o:p><\/o:p><\/span><\/strong><\/p>\n\u4f7f\u7528<\/span>enrichplot\u5305\u7684<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:var(--monospace);mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:11.0000pt;mso-font-kerning:0.0000pt;background:rgb(243,244,244);mso-shading:rgb(243,244,244);\">cnetplot<\/span>\u51fd\u6570\u7ed8\u5236<\/span>KEGG\u901a\u8def\u7f51\u7edc\u56fe\uff0c\u5e76\u5c06\u7ed3\u679c\u4fdd\u5b58\u4e3a<\/span>PDF<\/span>\u6587\u4ef6\u3002<\/span><\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>library<\/span>(\"enrichplot\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>pdf<\/span>(file = \"net-pathway.pdf\"<\/span>, width = 8, height = 10) <\/span><\/code><code>cnetplot<\/span>(ek2)<\/span><\/code><code>dev<\/span>.off<\/span>()<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"font-size: 16px;\">\n\u6548\u679c\u56fe\u5982\u4e0b\uff1a<\/span><o:p><\/o:p><\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1.241112828438949\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_GYIRAqeda96BgvbXrGFtXEQOg4gQ6w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHneFwqa7eGibQMQPCz9BiaraXj6GYIRAqeda96BgvbXrGFtXEQOg4gQ6w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"647\" style=\"\"><\/p>\n <\/p>\n\u4ee5\u4e0a\u6559\u7a0b\u5c0f\u679c\u4ecb\u7ecd\u4e86\u5982\u4f55\u4f7f\u7528<\/span>R\u8bed\u8a00\u4e2d\u7684<\/span>DOSE\u548c<\/span>clusterProfiler\u5305\u8fdb\u884c\u57fa\u56e0\u96c6\u7684<\/span>KEGG\u901a\u8def\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u901a\u8fc7<\/span>ggplot2\u548c<\/span>enrichplot\u5b9e\u73b0\u53ef\u89c6\u5316\u5316\u3002\u901a\u8fc7\u8fd9\u4e9b\u4ee3\u7801\uff0c\u4f60\u53ef\u4ee5\u5c06\u81ea\u5df1\u7684\u57fa\u56e0\u5217\u8868\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u8fdb\u4e00\u6b65\u5c06\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\u4ee5\u5e2e\u52a9\u89e3\u91ca\u548c\u7406\u89e3\u6570\u636e\u54e6\uff01\u600e\u4e48\u6837\uff0c\u4f60\u5b66\u4f1a\u4e86\u561b\uff1f<\/span><\/span><\/span><\/p>\n<\/span><\/span><o:p><\/o:p><\/span><\/p>\n\u673a\u5668\u5b66\u4e60\u76f8\u5173\u5176\u4ed6\u5206\u6790\u5185\u5bb9\u6b22\u8fce\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/span><\/strong><\/span> 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data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<\/body> \n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"ggplot2 \u4e4b\u4f5c\uff1a\u591a\u5f69\u548c\u8c10\u7684\u901a\u8def\u5bcc\u96c6\u53ef\u89c6\u5316\u4e4b\u65c5 \uff01 \u539f\u521b \u5c0f\u679c &nbsp 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{"id":57382,"date":"2024-06-16T19:13:53","date_gmt":"2024-06-16T11:13:53","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=57382"},"modified":"2024-06-16T19:13:53","modified_gmt":"2024-06-16T11:13:53","slug":"ggplot2-%e4%b9%8b%e4%bd%9c%ef%bc%9a%e5%a4%9a%e5%bd%a9%e5%92%8c%e8%b0%90%e7%9a%84%e9%80%9a%e8%b7%af%e5%af%8c%e9%9b%86%e5%8f%af%e8%a7%86%e5%8c%96%e4%b9%8b%e6%97%85-%ef%bc%81-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=57382","title":{"rendered":"ggplot2 \u4e4b\u4f5c\uff1a\u591a\u5f69\u548c\u8c10\u7684\u901a\u8def\u5bcc\u96c6\u53ef\u89c6\u5316\u4e4b\u65c5 \uff01"},"content":{"rendered":"

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rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);width: 100%;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;vertical-align: top;width: 70.0348%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70.0348% !important;\">\n<section style=\"margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: 29.9652%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 29.9652% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;line-height: 0;\">\n<section>\n<section style=\"display: inline-block;vertical-align: middle;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 0;\">\n<section style=\"width: 111px;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1.75em;text-indent: 0em;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;height: auto;width: 111px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_Xkz3aJGClianeaJMFaPKsbDRmfsHNw-6.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPdqELib8iaLzsvaTzaicfA3URAEIyVaH5J7WwYnm1GpxBmYrwXkz3aJGClianeaJMFaPKsbDRmfsHNw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"400\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 10px 0% 8px;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;font-size: 14px;\" powered-by=\"xiumi.us\">\n<\/span>hello\uff0c\u4eca\u5929\u5c0f\u679c\u6765\u6559\u5927\u5bb6\u5982\u4f55\u5bf9KEGG\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\u901a\u8fc7ggplot2\u5b9e\u73b0\u53ef\u89c6\u5316\u5e76\u7ed8\u5236\u5bf9\u5e94\u7684KEGG\u901a\u8def\u7f51\u7edc\u56fe \uff0c\u8ba9\u4f60\u7684\u5206\u6790\u7ed3\u679c\u66f4\u52a0\u7f8e\u89c2\uff01<\/span>\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/span><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n1. <\/span><\/em><\/strong>\u51c6\u5907\u9700\u8981\u7684R\u5305<\/em><\/span><\/strong><\/p>\n <\/p>\n\u5148\u6765\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\u6211\u4eec\u4eca\u5929\u7528\u5230\u7684R\u5305\uff0c\u5206\u522b\u662fDOSE\u3001clusterProfiler\u3001org.Hs.eg.db\u3001ggplot2\u3001tidyverse\u4ee5\u53caenrichplot\u5305\u3002\u540c\u5b66\u4eec\u8981\u63d0\u524d\u4e0b\u8f7d\u597d\u54e6\uff01\u5728\u8fd9\u91cc\u5c0f\u679c\u4e3a\u5927\u5bb6\u7b80\u5355\u7684\u4ecb\u7ecd\u4e00\u4e0b\u5176\u4e2d\u51e0\u4e2aR\u5305\uff1a<\/span><o:p><\/o:p><\/p>\n1.DOSE\uff1a<\/span><\/strong>DOSE\u5305\u4e3b\u8981\u7528\u4e8e\u57fa\u56e0\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff0c\u5b83\u80fd\u591f\u901a\u8fc7\u6bd4\u8f83\u8f93\u5165\u7684\u57fa\u56e0\u5217\u8868\u4e0e\u5df2\u77e5\u7684\u57fa\u56e0\u529f\u80fd\u6ce8\u91ca\u4fe1\u606f\uff0c\u627e\u51fa\u5728\u7279\u5b9a\u529f\u80fd\u7c7b\u522b\u4e2d\u5bcc\u96c6\u7684\u57fa\u56e0\u3002<\/span><o:p><\/o:p><\/p>\n2.clusterProfiler\uff1a<\/span><\/strong>clusterProfiler\u662f\u4e00\u4e2a\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u7684R\u5305\uff0c\u4e3b\u8981\u7528\u4e8e\u529f\u80fd\u6ce8\u91ca\u548c\u5bcc\u96c6\u5206\u6790\u3002\u5b83\u63d0\u4f9b\u4e86\u9488\u5bf9\u591a\u79cd\u751f\u7269\u6570\u636e\u7c7b\u578b\u7684\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\uff0c\u5305\u62ecGO\u3001KEGG\u3001Reactome\u7b49\u3002\u8be5\u5305\u8fd8\u63d0\u4f9b\u4e86\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u4f7f\u7528\u6237\u80fd\u591f\u66f4\u597d\u5730\u7406\u89e3\u548c\u89e3\u91ca\u529f\u80fd\u5bcc\u96c6\u7ed3\u679c\u3002<\/span><o:p><\/o:p><\/p>\n3.org.Hs.eg.db\uff1a<\/strong>org.Hs.eg.db\u662f\u4e00\u4e2aR\u8bed\u8a00\u4e2d\u7528\u4e8e\u4eba\u7c7b\u57fa\u56e0\u6ce8\u91ca\u7684\u6570\u636e\u5e93\u5305\u3002\u5b83\u63d0\u4f9b\u4e86\u5bf9\u4eba\u7c7b\u57fa\u56e0\u7ec4\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u5305\u62ec\u57fa\u56e0ID\u3001\u57fa\u56e0\u540d\u79f0\u3001\u57fa\u56e0\u7b26\u53f7\u3001\u901a\u8def\u4fe1\u606f\u7b49\u3002\u4f7f\u7528org.Hs.eg.db\u5305\uff0c\u7528\u6237\u53ef\u4ee5\u5c06\u57fa\u56e0ID\u8f6c\u6362\u4e3a\u6613\u8bfb\u7684\u57fa\u56e0\u7b26\u53f7\uff0c\u4ece\u800c\u66f4\u5bb9\u6613\u7406\u89e3\u548c\u89e3\u91ca\u529f\u80fd\u5bcc\u96c6\u7ed3\u679c\u3002<\/span><o:p><\/o:p><\/p>\n4.tidyverse\uff1a<\/span><\/strong>tidyverse\u662f\u4e00\u4e2a\u7531\u591a\u4e2aR\u5305\u7ec4\u6210\u7684\u96c6\u5408\uff0c\u65e8\u5728\u63d0\u4f9b\u4e00\u5957\u4e00\u81f4\u4e14\u6613\u4e8e\u4f7f\u7528\u7684\u6570\u636e\u5904\u7406\u548c\u53ef\u89c6\u5316\u5de5\u5177\u3002\u8fd9\u4e9b\u5305\u5305\u62ecggplot2\u3001dplyr\u3001tidyr\u3001readr\u7b49\u3002\u5176\u4e2d\uff0cggplot2\u662f\u7528\u4e8e\u6570\u636e\u53ef\u89c6\u5316\u7684\u91cd\u8981\u7ec4\u6210\u90e8\u5206\uff0c\u63d0\u4f9b\u4e86\u5f3a\u5927\u4e14\u7075\u6d3b\u7684\u7ed8\u56fe\u529f\u80fd\uff0c\u4f7f\u7528\u6237\u80fd\u591f\u521b\u5efa\u9ad8\u8d28\u91cf\u7684\u56fe\u8868\uff0c\u7528\u4e8e\u6570\u636e\u63a2\u7d22\u548c\u5c55\u793a\u3002<\/span><o:p><\/o:p><\/p>\n5.enrichplot\uff1a<\/span><\/strong>enrichplot\u662f\u4e00\u4e2a\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u7684R\u5305\uff0c\u4e3b\u8981\u7528\u4e8e\u529f\u80fd\u5bcc\u96c6\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u3002\u5b83\u63d0\u4f9b\u4e86\u591a\u79cd\u7ed8\u56fe\u51fd\u6570\uff0c\u53ef\u4ee5\u7ed8\u5236\u57fa\u56e0\u96c6\u7684\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\uff0c\u5982GO\u6761\u5f62\u56fe\u3001KEGG\u901a\u8def\u7f51\u7edc\u56fe\u7b49\u3002enrichplot\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u53c2\u6570\u8bbe\u7f6e\uff0c\u4ee5\u6ee1\u8db3\u7528\u6237\u5bf9\u7ed3\u679c\u53ef\u89c6\u5316\u7684\u4e2a\u6027\u5316\u9700\u6c42\u3002 <\/span><\/p>\n\uff08<span style=\"text-decoration: underline;color: rgb(0, 122, 170);font-family: system-ui, -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.544px;text-wrap: wrap;background-color: rgb(255, 255, 255);\">\u5173\u6ce8\u5c0f\u679c\u56de\u590d111\u9886\u53d6\u76f8\u5173\u6587\u4ef6\u54df\uff01<\/span>\uff09<\/span><\/strong><\/span><\/p>\n <\/span><\/p>\n <\/span><\/p>\n2. KEGG\u5bcc\u96c6\u5206\u6790<\/span><\/em><\/strong><\/p>\nenrichKEGG\u8fdb\u884c\u5bcc\u96c6\u5206\u6790<\/strong><\/span><o:p><\/o:p><\/p>\n\u9996\u5148\uff0c\u52a0\u8f7dDOSE\u5305\u5e76\u4f7f\u7528\u8be5\u5305\u4e2d\u7684\u57fa\u56e0\u96c6\u4f5c\u4e3a\u6211\u4eec\u5206\u6790\u7684\u5bf9\u8c61\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"kotlin\"><code>library(\"DOSE\"<\/span>)<\/span><\/code><code>data<\/span>(geneList, package<\/span> = \"DOSE\"<\/span>)<\/span><\/code><code>g_list <- names(geneList)[1<\/span>:100<\/span>]<\/span><\/code><code>head(g_list)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.08285163776493257\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_qeibXrdVicHIicPPZ5bGCLO0cA6Fdg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHve0sYGRSYOdz66Pc4RhPa6xq2icHqeibXrdVicHIicPPZ5bGCLO0cA6Fdg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"519\" style=\"\"><\/p>\n <\/p>\n\u5229\u7528enrichKEGG\u51fd\u6570<\/span><\/strong><\/span>\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u5bf9\u6307\u5b9a\u7684\u57fa\u56e0\u5217\u8868\u8fdb\u884cKEGG\u901a\u8def\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u8bbe\u7f6ep-value\u548cq-value\u7684\u9608\u503c\u3002<o:p><\/o:p><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>library(\"clusterProfiler\")<\/span><\/code><code>library(\"org.Hs.eg.db\")<\/span><\/code><code> <\/span><\/code><code>ek <-<\/span> enrichKEGG<\/span>(gene<\/span> = g_list,<\/span><\/span><\/span><\/code><code> organism<\/span> = \"hsa\"<\/span>,<\/span><\/code><code> pvalueCutoff<\/span> = 0.05,<\/span><\/span><\/code><code> qvalueCutoff<\/span> = 0.05)<\/span><\/span><\/code><code>write.table<\/span>(ek<\/span>, file<\/span> = \"ek.txt\"<\/span>, sep<\/span> = \"t\"<\/span>, quote<\/span> = FALSE,<\/span> row.names<\/span> = FALSE)<\/span><\/span><\/code><\/pre>\n<\/section>\n <\/p>\n\u6ce8\u610f\uff1a<\/span><\/strong><\/span><\/span><\/p>\n\u00b7pvalueCutoff = 0.05\uff1a<\/span><\/span><\/strong><\/span>\u8bbe\u7f6ep-value\u7684\u9608\u503c\uff0c\u7528\u4e8e\u7b5b\u9009\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u4e2d\u7edf\u8ba1\u663e\u8457\u7684\u901a\u8def\u3002\u5728\u8fd9\u91cc\uff0c\u8bbe\u5b9a\u4e3a0.05\uff0c\u5373p-value\u5c0f\u4e8e0.05\u7684\u901a\u8def\u88ab\u8ba4\u4e3a\u662f\u663e\u8457\u5bcc\u96c6\u7684\u901a\u8def\u3002<\/span><o:p><\/o:p><\/p>\n\u00b7<\/span>qvalueCutoff = 0.05\uff1a<\/span><\/strong><\/span>\u8bbe\u7f6eq-value\u7684\u9608\u503c\uff0cq-value\u662f\u7ecf\u8fc7FDR\u6821\u6b63\u7684p-value\uff0c\u7528\u4e8e\u63a7\u5236\u591a\u91cd\u5047\u8bbe\u68c0\u9a8c\u7684\u9519\u8bef\u53d1\u73b0\u7387\u3002\u540c\u6837\uff0c\u8bbe\u5b9a\u4e3a0.05\uff0c\u5373q-value\u5c0f\u4e8e0.05\u7684\u901a\u8def\u88ab\u8ba4\u4e3a\u662f\u663e\u8457\u5bcc\u96c6\u7684\u901a\u8def\u3002<\/span><o:p><\/o:p><\/p>\n\u81f3\u6b64\u6211\u4eec\u5df2\u7ecf\u5b8c\u6210\u4e86\u5bcc\u96c6\u5206\u6790\u7684\u6d41\u7a0b\uff0c\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5206\u6790\u7684\u7ed3\u679c\u5427\uff01<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6695526695526696\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_uyp5SWWnsPicOakSc4OjBT7rpNmcUw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHxuKWT4NeYsUkzzhgF0ho2SJpOuyp5SWWnsPicOakSc4OjBT7rpNmcUw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n<\/span><o:p><\/o:p><\/p>\n\u9700\u8981\u6ce8\u610f\u7684\u662f\u7ed3\u679c\u4e2d<\/span>geneID\u4e3a<\/span>EntrezID\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code>head<\/span>(ek<\/span>@result<\/span>$geneID<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.1927007299270073\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_59XZAQ7kbG6EQWDDrhhCJ0VSKjSXxQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHX8cmAOsFN5ewHYcCJ64tqcfo59XZAQ7kbG6EQWDDrhhCJ0VSKjSXxQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"685\" style=\"\"><\/p>\n <\/p>\n\u5c06<\/span>EntrezID\u8f6c\u6362\u4e3a<\/span>Symbol<\/span><\/strong><\/span><\/p>\n\u4f7f\u7528setReadable\u51fd\u6570\u5c06EntrezID\u8f6c\u6362\u4e3aSymbol\uff1a<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>ek2<\/span> <- setReadable(ek,<\/span><\/code><code> OrgDb = \"org.Hs.eg.db\"<\/span>,<\/span><\/code><code> keyType = \"ENTREZID\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.17604617604617603\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_2SElrUiaAR7icRYGThDhyPpXzpturA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHHxfDV4kAOO81F25P57ADUKyVn52SElrUiaAR7icRYGThDhyPpXzpturA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n <\/p>\nggplot2\u53ef\u89c6\u5316\u7ed3\u679c<\/span><\/strong><\/span><\/span><\/strong><o:p><\/o:p><\/span><\/strong><\/p>\n\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u901a\u8fc7\u5b89\u88c5<\/span>tidyverse<\/span>\u5305\u5e76\u8bfb\u53d6\u4fdd\u5b58\u7684\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u6587\u672c\u6587<\/span>\u4ef6\uff0c\u5bf9\u8868\u683c\u8fdb\u884c\u5904\u7406\u548c\u8ba1\u7b97<\/span>Enrichment Factor<\/span>\uff0c\u5728\u8fd9\u91cc\u5c0f\u679c\u7528<\/span>tidyverse<\/span>\u5305<\/span>\u7684<\/span>separate<\/span>\u51fd\u6570\u5c06<\/span>GeneRatio<\/span>\u548c<\/span>BgRatio<\/span>\u7684\u5206\u5b50\u5206\u6bcd\u5148\u5206\u5f00\uff0c\u518d\u8fdb\u884c\u8ba1\u7b97\uff1a<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code>library(tidyverse)<\/span><\/code><code>ek.rt <- read.table(\"ek.txt\"<\/span>, header = TRUE, sep = \"t\"<\/span>, quote = \"\"<\/span>) <\/span><\/code><code>ek.rt <- separate(data = ek.rt, col = GeneRatio, into<\/span> = c(\"GR1\"<\/span>, \"GR2\"<\/span>), sep = \"\/\"<\/span>)<\/span><\/code><code>ek.rt <- separate(data = ek.rt, col = BgRatio, into<\/span> = c(\"BR1\"<\/span>, \"BR2\"<\/span>), sep = \"\/\"<\/span>)<\/span><\/code><code>ek.rt <- mutate(ek.rt, enrichment_factor = (as<\/span>.numeric(GR1) \/ as<\/span>.numeric(GR2)) \/ (as<\/span>.numeric(BR1) \/ as<\/span>.numeric(BR2)))<\/span><\/code><\/pre>\n<\/section>\n\u7b5b\u9009\u51fa\u524d<\/span>10\u4e2a\u901a\u8def\u8fdb\u884c\u53ef\u89c6\u5316\uff1a<\/span><\/span><o:p><\/o:p><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>ek.rt10 <-<\/span> ek.rt<\/span> %><\/span>% filter(row_number() >= 1, row_number() <=<\/span> 10<\/span>)<\/span><\/span><\/code><\/pre>\n<\/section>\n <\/p>\nggplot2\u7ed8\u5236<\/span>dotplot<\/span><\/span><\/strong><\/span><o:p><\/o:p><\/span><\/strong><\/p>\n\u4f7f\u7528<\/span>ggplot2\u5305\u7ed8\u5236<\/span>Enrichment Factor\u4e0e<\/span>KEGG term\u4e4b\u95f4\u7684\u5173\u7cfb\u56fe\uff1a<\/span><\/span><o:p><\/o:p><\/span><\/p>\n<\/span><\/span><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cpp\"><code>library(\"ggplot2\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>p <- ggplot(ek.rt10, aes(enrichment_factor, fct_reorder(factor(Description), enrichment_factor))) + <\/span><\/code><code> geom_point(aes(size = Count, color = -1<\/span> * log10<\/span>(pvalue))) +<\/span><\/code><code> scale_color_gradient(low = \"green\"<\/span>, high = \"red\"<\/span>) + <\/span><\/code><code> labs<\/span>(color = expression(-log<\/span>[10<\/span>](p_value)), size = \"Count\"<\/span>,<\/span><\/code><code> x = \"Enrichment Factor\"<\/span>, y = \"KEGG term\"<\/span>, title = \"KEGG enrichment\"<\/span>) + <\/span><\/code><code> theme_bw()<\/span><\/code><code>ggsave(\"er.rt10_KEGG.png\"<\/span>, width = 6<\/span>, height = 4<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u6548\u679c\u56fe\u5427\uff01<\/span><o:p><\/o:p><\/span><\/p>\n<\/span><\/span><\/strong><\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6666666666666666\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_hf78KpwQnqn0CIzSHw2P6nKuMERJww.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHfoyS3JJkNI0Cto1nJ1YiaFlKUhf78KpwQnqn0CIzSHw2P6nKuMERJww\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n<\/span><\/span><\/strong><\/span><\/p>\n <\/p>\n\u7ed8\u5236<\/span>KEGG\u901a\u8def\u7f51\u7edc\u56fe<\/span><\/span><\/strong><\/span><\/span><\/strong><\/span><o:p><\/o:p><\/span><\/strong><\/p>\n\u4f7f\u7528<\/span>enrichplot\u5305\u7684<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:var(--monospace);mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:11.0000pt;mso-font-kerning:0.0000pt;background:rgb(243,244,244);mso-shading:rgb(243,244,244);\">cnetplot<\/span>\u51fd\u6570\u7ed8\u5236<\/span>KEGG\u901a\u8def\u7f51\u7edc\u56fe\uff0c\u5e76\u5c06\u7ed3\u679c\u4fdd\u5b58\u4e3a<\/span>PDF<\/span>\u6587\u4ef6\u3002<\/span><\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>library<\/span>(\"enrichplot\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>pdf<\/span>(file = \"net-pathway.pdf\"<\/span>, width = 8, height = 10) <\/span><\/code><code>cnetplot<\/span>(ek2)<\/span><\/code><code>dev<\/span>.off<\/span>()<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"font-size: 16px;\">\n\u6548\u679c\u56fe\u5982\u4e0b\uff1a<\/span><o:p><\/o:p><\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1.241112828438949\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_GYIRAqeda96BgvbXrGFtXEQOg4gQ6w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxOIcovR5Pf0DaZvcbtd2DHneFwqa7eGibQMQPCz9BiaraXj6GYIRAqeda96BgvbXrGFtXEQOg4gQ6w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"647\" style=\"\"><\/p>\n <\/p>\n\u4ee5\u4e0a\u6559\u7a0b\u5c0f\u679c\u4ecb\u7ecd\u4e86\u5982\u4f55\u4f7f\u7528<\/span>R\u8bed\u8a00\u4e2d\u7684<\/span>DOSE\u548c<\/span>clusterProfiler\u5305\u8fdb\u884c\u57fa\u56e0\u96c6\u7684<\/span>KEGG\u901a\u8def\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u901a\u8fc7<\/span>ggplot2\u548c<\/span>enrichplot\u5b9e\u73b0\u53ef\u89c6\u5316\u5316\u3002\u901a\u8fc7\u8fd9\u4e9b\u4ee3\u7801\uff0c\u4f60\u53ef\u4ee5\u5c06\u81ea\u5df1\u7684\u57fa\u56e0\u5217\u8868\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u8fdb\u4e00\u6b65\u5c06\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\u4ee5\u5e2e\u52a9\u89e3\u91ca\u548c\u7406\u89e3\u6570\u636e\u54e6\uff01\u600e\u4e48\u6837\uff0c\u4f60\u5b66\u4f1a\u4e86\u561b\uff1f<\/span><\/span><\/span><\/p>\n<\/span><\/span><o:p><\/o:p><\/span><\/p>\n\u673a\u5668\u5b66\u4e60\u76f8\u5173\u5176\u4ed6\u5206\u6790\u5185\u5bb9\u6b22\u8fce\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/span><\/strong><\/span> 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data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<\/body> \n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"ggplot2 \u4e4b\u4f5c\uff1a\u591a\u5f69\u548c\u8c10\u7684\u901a\u8def\u5bcc\u96c6\u53ef\u89c6\u5316\u4e4b\u65c5 \uff01 \u539f\u521b \u5c0f\u679c &nbsp 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