{"id":59732,"date":"2024-06-17T08:42:25","date_gmt":"2024-06-17T00:42:25","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59732"},"modified":"2024-06-17T08:42:25","modified_gmt":"2024-06-17T00:42:25","slug":"%e5%8d%81%e5%88%86%e9%92%9fgsea%e4%bb%8e%e5%8e%9f%e7%90%86%e5%88%b0%e7%bb%98%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59732","title":{"rendered":"\u5341\u5206\u949fGSEA\u4ece\u539f\u7406\u5230\u7ed8\u56fe"},"content":{"rendered":"


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center;\"><strong><em><span style=\"font-size: 20px;\">GSEA\u539f\u7406<\/span><\/em><\/strong><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">GSEA\uff08Gene Set Enrichment Analysis\uff09\u662f\u4e00\u79cd\u7528\u4e8e\u5206\u6790\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u8ba1\u7b97\u65b9\u6cd5\uff0c\u65e8\u5728\u63ed\u793a\u57fa\u56e0\u96c6\u5728\u7279\u5b9a\u751f\u7269\u5b66\u8fc7\u7a0b\u6216\u75be\u75c5\u4e2d\u7684\u529f\u80fd\u5bcc\u96c6\u60c5\u51b5\u3002\u5b83\u662f\u4e00\u79cd\u5e7f\u6cdb\u5e94\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u548c\u7cfb\u7edf\u751f\u7269\u5b66\u7814\u7a76\u7684\u5de5\u5177\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">GSEA\u7684\u57fa\u672c\u539f\u7406\u662f\u901a\u8fc7\u5c06\u57fa\u56e0\u6839\u636e\u5176\u8868\u8fbe\u6a21\u5f0f\u8fdb\u884c\u6392\u5e8f\uff0c\u7136\u540e\u8ba1\u7b97\u9884\u5b9a\u4e49\u7684\u57fa\u56e0\u96c6\u5728\u6392\u5e8f\u5217\u8868\u4e2d\u7684\u5bcc\u96c6\u7a0b\u5ea6\u3002\u8fd9\u4e9b\u57fa\u56e0\u96c6\u53ef\u4ee5\u662f\u4e0e\u7279\u5b9a\u751f\u7269\u5b66\u8fc7\u7a0b\u3001\u7ec6\u80de\u4fe1\u53f7\u901a\u8def\u3001\u75be\u75c5\u76f8\u5173\u7684\u57fa\u56e0\u96c6\u5408\uff0c\u6216\u8005\u662f\u6765\u81ea\u516c\u5171\u6570\u636e\u5e93\uff08\u5982\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u6570\u636e\u5e93\uff09\u4e2d\u7684\u5df2\u77e5\u57fa\u56e0\u96c6\u3002\u901a\u8fc7\u6bd4\u8f83\u57fa\u56e0\u96c6\u5728\u6392\u5e8f\u5217\u8868\u4e2d\u7684\u5bcc\u96c6\u7a0b\u5ea6\uff0c\u53ef\u4ee5\u786e\u5b9a\u54ea\u4e9b\u57fa\u56e0\u96c6\u4e0e\u7814\u7a76\u5174\u8da3\u76f8\u5173\u3002GSEA\u7684\u4f18\u70b9\u5728\u4e8e\u5b83\u4e0d\u4ec5\u8003\u8651\u5355\u4e2a\u57fa\u56e0\u7684\u8868\u8fbe\u53d8\u5316\uff0c\u800c\u4e14\u5173\u6ce8\u6574\u4e2a\u57fa\u56e0\u96c6\u7684\u5bcc\u96c6\u60c5\u51b5\u3002\u8fd9\u79cd\u65b9\u6cd5\u5bf9\u4e8e\u7814\u7a76\u590d\u6742\u7684\u751f\u7269\u5b66\u8fc7\u7a0b\u548c\u75be\u75c5\u673a\u5236\u975e\u5e38\u6709\u7528\uff0c\u56e0\u4e3a\u5b83\u80fd\u591f\u6355\u6349\u5230\u591a\u4e2a\u57fa\u56e0\u7684\u534f\u540c\u8c03\u63a7\u548c\u529f\u80fd\u76f8\u5173\u6027\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5c0f\u679c\u6709\u8bdd\u8981\u8bb2\uff1a\u5728\u8fdb\u884c\u7ed8\u56fe\u7684\u8fc7\u7a0b\u4e2d\uff0c\u6f02\u4eae\u7684\u56fe\u5f62\u662f\u6b21\u8981\u7684\uff0c\u6b63\u786e\u7684\u5206\u6790\u624d\u662f\u91cd\u8981\u7684\u4e00\u73af\u3002<\/span><\/p>\n<p><span style=\"text-decoration: underline;color: rgb(178, 178, 178);\"><em><span style=\"color: rgb(178, 178, 178);text-decoration: underline;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u516c\u4f17\u53f7\u56de\u590d\u201c111\u201d\u9886\u53d6\u76f8\u5173\u4ee3\u7801\uff0c\u4ee3\u7801\u7f16\u53f7\uff1a231001<\/span><\/em><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3888888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_IlmBAWe69EMUPMhNEgrv6NXX85lJxg-24.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwyrj7kbUR3ULG9ZUbLrLkgibzL8qUpQROfe8ebc3gNSnu1dIlmBAWe69EMUPMhNEgrv6NXX85lJxg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><strong><em><span style=\"font-size: 20px;\">GSEA\u5b9e\u8df5<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">1.<span style=\"font-family:Helvetica Neue, Helvetica, Hiragino Sans GB, Microsoft YaHei, Arial, sans-serif;\">\u52a0\u8f7d\u5b89\u88c5\u5404\u79cd\u5305<\/span><\/span><\/em><\/strong><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><em><span style=\"font-size: 20px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><strong style=\"text-align: justify;letter-spacing: 0.034em;\"><span style=\"font-family: "Open Sans";color: rgb(51, 51, 51);\"><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><\/span><\/span><\/strong><\/span><\/em><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><br \/><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code><span class=\"code-snippet_outer\">rm(list = ls())<\/span><\/code><code><span class=\"code-snippet_outer\">devtools::install_github(\"nicolash2\/gggsea\")<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::<span class=\"code-snippet__keyword\">install<\/span>(<span class=\"code-snippet__string\">\"GSVA\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::<span class=\"code-snippet__keyword\">install<\/span>(<span class=\"code-snippet__string\">\"enrichplot\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::<span class=\"code-snippet__keyword\">install<\/span>(<span class=\"code-snippet__string\">\"GSEABase\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::<span class=\"code-snippet__keyword\">install<\/span>(<span class=\"code-snippet__string\">\"clusterProfiler\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(gggsea)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(GSVA)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(enrichplot)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(<span class=\"code-snippet__string\">'GSEABase'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(clusterProfiler)<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">2. <span style=\"letter-spacing: 0.544px;\">\u57fa\u56e0\u6392\u5e8f\u4fe1\u606f<\/span><\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;white-space: normal;font-size: 16px;\"><o:p><\/o:p><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\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=\"bash\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6570\u636e\u7684\u51c6\u5907\u81f3\u5c11\u5305\u542b\u4e24\u5217\u4e3alogFC\u548cSYMBOL ID\uff0c\u6839\u636elogFC\u6392\u5e8f\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">deg<- read.csv(<span class=\"code-snippet__string\">\"\/Users\/sansan\/Desktop\/\u8f6f\u6587\/deg.csv\"<\/span>,header = T,na.strings = T)<span class=\"code-snippet__comment\">#\u8fd9\u91cc\u9009\u62e9\u5408\u9002\u7684\u65b9\u6cd5read.delim()\u6216\u8005read.table()\u8fdb\u884c\u5012\u5165\u6570\u636e\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">alldiff <- deg[order(deg<span class=\"code-snippet__variable\">$logFC<\/span>,decreasing = T),]<\/span><\/code><code><span class=\"code-snippet_outer\">id <- alldiff<span class=\"code-snippet__variable\">$logFC<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">names(id) <- alldiff<span class=\"code-snippet__variable\">$gene_name<\/span><span class=\"code-snippet__comment\">#\u8fd9\u91cc\u9700\u8981\u586b\u5165\u4f60\u5b58\u50a8genename\u7684\u5217<\/span><\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1.7365853658536585\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_4PLxk5QfERibllfcXHts9WBQZGBcfw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAztctFDciaTgXQTByLub6rkEyLHmcahic9ud4hkmWm6ictoFOdl4PLxk5QfERibllfcXHts9WBQZGBcfw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"410\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">3.\u4e0b\u8f7d\u5408\u9002\u7684\u6570\u636e\u96c6<\/span><\/em><\/strong><strong style=\"letter-spacing: 0.034em;\"><\/strong><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e00\u4e9b\u5df2\u7ecf\u9884\u5b9a\u4e49\u7684\u529f\u80fd\u57fa\u56e0\u96c6\u53ef\u4ee5\u5728http:\/\/www.gsea-msigdb.org\/gsea\/msigdb\/index.jsp\u4e2d\u4e0b\u8f7d\uff0c\u81ea\u5b9a\u4e49\u57fa\u56e0\u96c6\u9700\u8981\u6709\u8f83\u5f3a\u7684\u80cc\u666f\u77e5\u8bc6\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6839\u636e\u81ea\u5df1\u7684\u9700\u6c42\u8fdb\u884c\u4e0b\u8f7d\uff5e<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6719653179190751\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_DgVrv312icWmD1NYpmAb5yNpN2mZPg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAztctFDciaTgXQTByLub6rkEFzcSJa7iclick63C2ruqTKVv86JDgVrv312icWmD1NYpmAb5yNpN2mZPg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"\"><o:p><br \/><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u70b9\u51fb\u8fdb\u53bb\u540e\u4f1a\u51fa\u73b0\u4e0b\u9762\u7684\u9875\u9762\uff5e<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u8fd9\u91cc\u6709\u4e24\u4e2a\u7248\u672c\uff0c\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u9700\u6c42\u8fdb\u884c\u9009\u62e9\u6027\u7684\u4e0b\u8f7d\uff0c\u8fd9\u91cc\u7684genename\u4e3asymbols\u5f62\u5f0f\uff0c\u6240\u4ee5\u5c0f\u679c\u4e0b\u8f7d\u7684\u4e3ac2\u7684symbols\u7684\u683c\u5f0f\u7684\u54e6\uff5e<\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.1553398058252427\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_ISRzaSdmic1u6O6CavsKrtF0DZ55xw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAztctFDciaTgXQTByLub6rkErpRtXa0Nvf7b3u3z446HwcKGaISRzaSdmic1u6O6CavsKrtF0DZ55xw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"618\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p><br \/><\/p>\n<p style=\"text-align: center;\"><span style=\"color: rgb(51, 51, 51);font-family: "Open Sans";font-size: 12pt;\"><strong style=\"font-size: 16px;text-align: center;text-wrap: wrap;\"><em style=\"\"><span style=\"font-size: 20px;\"><span style=\"letter-spacing: 0.578px;\">4. <\/span><span style=\"letter-spacing: 0.544px;\">\u5bfc\u5165\u5206\u6790<\/span><\/span><\/em><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cpp\"><code><span class=\"code-snippet_outer\">gmtfile <- \"\/Users\/sansan\/Downloads\/c2.all.v2023.1.Hs.symbols.gmt.txt\"<\/span><\/code><code><span class=\"code-snippet_outer\">hallmark <- read.gmt(gmtfile)<\/span><\/code><code><span class=\"code-snippet_outer\">gsea.re1<-clusterProfiler::GSEA(id,TERM2GENE=hallmark,verbose = T)<\/span><\/code><code><span class=\"code-snippet_outer\">#clusterProfiler::GSEA()\u8fd9\u4e2a\u51fd\u6570\u53ef\u4ee5?clusterProfiler::GSEA\u67e5\u770b\u4e00\u4e0b\u5e2e\u52a9\uff0c\u4f1a\u83b7\u5f97\u66f4\u591a\u7684\u53c2\u6570\uff0c\u4f8b\u5982\u53ef\u4ee5\u8c03\u63a7\u7684\u53c2\u6570\uff0c\u8be6\u7ec6\u7684\u89e3\u91ca\u89c1\u9644\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8fd9\u4e00\u6b65\u662f\u5206\u6790\u7684\u4e3b\u8981\u6b65\u9aa4\uff0c\u5206\u6790\u7ed3\u675f\u540e\uff0c\u4f1a\u51fa\u73b0\u4e0b\u9762\u7684\u5b57\u6837<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.17052023121387283\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_G1UQZYWdbVkUFQJvldXSgnBADCVrpw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAztctFDciaTgXQTByLub6rkEfpYHVwvDAiaSYtMYpC5W7vFeLG1UQZYWdbVkUFQJvldXSgnBADCVrpw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><br \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code><span class=\"code-snippet_outer\">g1<-as.data.frame(gsea.re1)<\/span><\/code><code><span class=\"code-snippet_outer\">g1<-g1[order(g1$NES,decreasing = T),]<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p style=\"text-align: center;\"><strong style=\"color: rgb(51, 51, 51);font-family: "Open Sans";font-size: 16px;letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\"><span style=\"letter-spacing: 0.578px;\">5. <\/span><span style=\"letter-spacing: 0.544px;\">\u51fa\u56fe<\/span><\/span><\/em><\/strong><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/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=\"cs\"><code><span class=\"code-snippet_outer\">gseaplot2(gsea.re1,geneSetID = rownames(g1)[1],<\/span><\/code><code><span class=\"code-snippet_outer\"> title = \"sample\",#\u6807\u9898<\/span><\/code><code><span class=\"code-snippet_outer\"> base_size = 9.5,#\u5927\u5c0f\u5c3a\u5bf8<\/span><\/code><code><span class=\"code-snippet_outer\"> rel_heights = c(1, 0.2, 0.4),#\u5c0f\u56fe\u76f8\u5bf9\u9ad8\u5ea6<\/span><\/code><code><span class=\"code-snippet_outer\"> subplots = 1:3,#\u5c55\u793a\u5c0f\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalue_table = FALSE,#p\u503c\u8868\u683c<\/span><\/code><code><span class=\"code-snippet_outer\"> ES_geom = \"line\"#line or dot<\/span><\/code><code><span class=\"code-snippet_outer\">)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8f93\u51fa\u5355\u4e2a\u7684<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7384393063583815\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_u1rdZJWTlmQqRNQMDN4EFibJ9O5iaA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAztctFDciaTgXQTByLub6rkENbFHjPtBLTX4epC3uPCic5UWS9Ju1rdZJWTlmQqRNQMDN4EFibJ9O5iaA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><br \/><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><br \/><\/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<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code><span class=\"code-snippet_outer\">#\u5c55\u793a\u591a\u4e2a\u57fa\u56e0\u96c6<\/span><\/code><code><span class=\"code-snippet_outer\">num=3<\/span><\/code><code><span class=\"code-snippet_outer\">gseaplot2(gsea.re1,geneSetID = rownames(g1)[1:num],<\/span><\/code><code><span class=\"code-snippet_outer\"> title = \"sample\",#\u6807\u9898<\/span><\/code><code><span class=\"code-snippet_outer\"> color = col_gsea1[1:num2],#\u989c\u8272<\/span><\/code><code><span class=\"code-snippet_outer\"> base_size = 9.5,#\u5927\u5c0f\u5c3a\u5bf8<\/span><\/code><code><span class=\"code-snippet_outer\"> rel_heights = c(1, 0.2, 0.4),#\u5c0f\u56fe\u76f8\u5bf9\u9ad8\u5ea6<\/span><\/code><code><span class=\"code-snippet_outer\"> subplots = 1:3,#\u5c55\u793a\u5c0f\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalue_table = FALSE,#p\u503c\u8868\u683c<\/span><\/code><code><span class=\"code-snippet_outer\"> ES_geom = \"line\"#line or dot<\/span><\/code><code><span class=\"code-snippet_outer\">)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.622286541244573\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_6sqKqbYlqf4TT1t1fiaJicJOVibMlA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAztctFDciaTgXQTByLub6rkEEgrYcFhOR5JBP9cKRbDQEY5Kc176sqKqbYlqf4TT1t1fiaJicJOVibMlA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"691\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><br \/><\/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<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\">\u7ed8\u56fe\u51fd\u6570\u7684\u53c2\u6570\uff1a<\/span><\/code><code><span class=\"code-snippet_outer\">gseaplot2(<\/span><\/code><code><span class=\"code-snippet_outer\"> x,<\/span><\/code><code><span class=\"code-snippet_outer\"> geneSetID,<\/span><\/code><code><span class=\"code-snippet_outer\"> title = \"\",<\/span><\/code><code><span class=\"code-snippet_outer\"> color = \"green\",<\/span><\/code><code><span class=\"code-snippet_outer\"> base_size = 11,<\/span><\/code><code><span class=\"code-snippet_outer\"> rel_heights = c(1.5, 0.5, 1),<\/span><\/code><code><span class=\"code-snippet_outer\"> subplots = 1:3,<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalue_table = FALSE,<\/span><\/code><code><span class=\"code-snippet_outer\"> ES_geom = \"line\"<\/span><\/code><code><span class=\"code-snippet_outer\">)<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 10.5pt;\">\u9644\u4ef6<\/span><span style=\"font-size: 10.5pt;\">\uff1a<o:p><\/o:p><\/span><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;\">\u5728R\u4e2d\uff0cclusterProfiler\u5305\u4e2d\u7684GSEA()\u51fd\u6570\u7528\u4e8e\u8fdb\u884c\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u3002\u8be5\u51fd\u6570\u63d0\u4f9b\u4e86\u4e00\u4e9b\u53c2\u6570\uff0c\u53ef\u4ee5\u7528\u6765\u8c03\u6574\u7b5b\u9009\u6761\u4ef6\u548c\u6269\u5927\u7b5b\u9009\u8303\u56f4\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;\">\u4e0b\u9762\u662f\u4e00\u4e9b\u5e38\u7528\u7684\u53c2\u6570\u548c\u9009\u9879\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;\"><br \/><\/span><\/p>\n<p><span style=\"text-decoration: underline;\"><strong><span style=\"text-decoration: underline;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;color: rgb(0, 122, 170);\">minGSSize<\/span><\/strong><\/span><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;\">\uff1a\u8bbe\u7f6e\u6700\u5c0f\u57fa\u56e0\u96c6\u5927\u5c0f\u3002\u9ed8\u8ba4\u503c\u4e3a 10\u3002\u4f60\u53ef\u4ee5\u589e\u52a0\u8be5\u503c\u6765\u7b5b\u9009\u66f4\u5927\u7684\u57fa\u56e0\u96c6\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"text-decoration: underline;\"><strong><span style=\"text-decoration: underline;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;color: rgb(0, 122, 170);\">maxGSSize<\/span><\/strong><\/span><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;\">\uff1a\u8bbe\u7f6e\u6700\u5927\u57fa\u56e0\u96c6\u5927\u5c0f\u3002\u9ed8\u8ba4\u503c\u4e3a Inf\uff08\u65e0\u7a77\u5927\uff09\u3002\u4f60\u53ef\u4ee5\u51cf\u5c0f\u8be5\u503c\u6765\u7b5b\u9009\u66f4\u5c0f\u7684\u57fa\u56e0\u96c6\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"text-decoration: underline;\"><strong><span style=\"text-decoration: underline;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 10.5pt;color: rgb(0, 122, 170);\">pvalueCutoff<\/span><\/strong><\/span><span style=\"font-family: "Helvetica Neue", Helvetica, 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