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2em;\">Venn\u56fe\u53ef\u4ee5\u76f4\u89c2\u5730\u663e\u793a\u4e0d\u540c\u6761\u4ef6\u4e0b\u7684\u5dee\u5f02\u57fa\u56e0\u4e4b\u95f4\u7684\u91cd\u53e0\u60c5\u51b5\u3002\u901a\u8fc7\u4ea4\u53c9\u533a\u57df\u7684\u5927\u5c0f\u548c\u91cd\u53e0\u533a\u57df\u7684\u6570\u91cf\uff0c\u53ef\u4ee5\u4e86\u89e3\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u5177\u6709\u5171\u540c\u8868\u8fbe\u53d8\u5316\u7684\u57fa\u56e0\u6570\u91cf\u548c\u5171\u6709\u7684\u57fa\u56e0\u96c6\u5408\u3002\u7b5b\u9009\u51fa\u5177\u6709\u5171\u540c\u8c03\u8282\u7684\u57fa\u56e0\uff1a\u901a\u8fc7\u89c2\u5bdfVenn\u56fe\u4e2d\u7684\u4ea4\u53c9\u533a\u57df\uff0c\u53ef\u4ee5\u7b5b\u9009\u51fa\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u5177\u6709\u5171\u540c\u8c03\u8282\u7684\u57fa\u56e0\u3002\u4ea4\u53c9\u533a\u57df\u4e2d\u7684\u57fa\u56e0\u8868\u793a\u5728\u591a\u4e2a\u6761\u4ef6\u4e0b\u5747\u53d1\u751f\u8868\u8fbe\u53d8\u5316\uff0c\u8fd9\u4e9b\u57fa\u56e0\u53ef\u80fd\u5728\u76f8\u4f3c\u7684\u751f\u7269\u8fc7\u7a0b\u6216\u4fe1\u53f7\u901a\u8def\u4e2d\u8d77\u7740\u91cd\u8981\u7684\u8c03\u8282\u4f5c\u7528\u3002\u53ef\u89c6\u5316\u548c\u62a5\u544a\u7ed3\u679c\uff1aVenn\u56fe\u4f5c\u4e3a\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7684\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u5448\u73b0\u57fa\u56e0\u7684\u91cd\u53e0\u60c5\u51b5\u548c\u5171\u540c\u8c03\u8282\u7684\u6a21\u5f0f\u3002Venn\u56fe\u53ef\u4ee5\u5e2e\u52a9\u786e\u5b9a\u5728\u7279\u5b9a\u6761\u4ef6\u4e0b\u7279\u5f02\u6027\u7684\u5dee\u5f02\u57fa\u56e0\u3002\u901a\u8fc7\u89c2\u5bdfVenn\u56fe\u4e2d\u5355\u72ec\u7684\u533a\u57df\uff0c\u53ef\u4ee5\u8bc6\u522b\u5728\u67d0\u4e2a\u6761\u4ef6\u4e0b\u5177\u6709\u7279\u5b9a\u8868\u8fbe\u53d8\u5316\u7684\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u53ef\u80fd\u4e0e\u8be5\u6761\u4ef6\u4e0b\u7684\u751f\u7269\u8fc7\u7a0b\u6216\u75be\u75c5\u673a\u5236\u5bc6\u5207\u76f8\u5173\u3002<\/span><br \/><\/p>\n<p style=\"text-indent: 2em;text-wrap: wrap;\"><span style=\"text-indent: 2em;\"><br \/><\/span><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u786e\u5b9a\u7279\u5b9a\u6761\u4ef6\u4e0b\u7684\u5dee\u5f02\u57fa\u56e0\uff1aVenn\u56fe\u53ef\u4ee5\u5e2e\u52a9\u786e\u5b9a\u5728\u7279\u5b9a\u6761\u4ef6\u4e0b\u7279\u5f02\u6027\u7684\u5dee\u5f02\u57fa\u56e0\u3002\u901a\u8fc7\u89c2\u5bdfVenn\u56fe\u4e2d\u5355\u72ec\u7684\u533a\u57df\uff0c\u53ef\u4ee5\u8bc6\u522b\u5728\u67d0\u4e2a\u6761\u4ef6\u4e0b\u5177\u6709\u7279\u5b9a\u8868\u8fbe\u53d8\u5316\u7684\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u53ef\u80fd\u4e0e\u8be5\u6761\u4ef6\u4e0b\u7684\u751f\u7269\u8fc7\u7a0b\u6216\u75be\u75c5\u673a\u5236\u5bc6\u5207\u76f8\u5173\u3002\u901a\u8fc7\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7ed3\u679c\u6587\u4ef6\uff0c\u751f\u6210\u57fa\u8d28\u7ec6\u80de\u548c\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u57fa\u56e0\u7684Venn\u56fe\uff0c\u5e76\u8f93\u51fa\u4ea4\u96c6\u57fa\u56e0\u7684\u5e73\u5747logFC\u503c\u3002<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"limma\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"pheatmap\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">fdrFilter=<span class=\"code-snippet__number\">0.05<\/span> <span class=\"code-snippet__comment\">#fdr\u4e34\u754c\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">logFCfilter=<span class=\"code-snippet__number\">1<\/span> <span class=\"code-snippet__comment\">#logFC\u4e34\u754c\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scoreType=<span class=\"code-snippet__string\">\"ImmuneScore\"<\/span> <span class=\"code-snippet__comment\">#\u6309ImmuneScore\u5206\u7ec4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">inputFile=<span class=\"code-snippet__string\">\"symbol.txt\"<\/span> <span class=\"code-snippet__comment\">#\u8f93\u5165\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scoreFile=<span class=\"code-snippet__string\">\"scores.txt\"<\/span> <span class=\"code-snippet__comment\">#score\u6587\u4ef6<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.20136518771331058\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_6JrtZvZlu7h3dcSw4J94Fy38L7q25g-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjejHZRqSlZLmCU6a2iaLNPqu6Y6JrtZvZlu7h3dcSw4J94Fy38L7q25g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"293\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u8868\u8fbe\u8f93\u5165\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=read.table(inputFile,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,header=<span class=\"code-snippet__built_in\">T<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">rt=as.matrix(rt)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7419724770642202\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_qWLicVTSaskuZXYv7bFhIWEL0lS4pQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjPtP4cibw5zwvtl5fkic8w1ndUPFqWLicVTSaskuZXYv7bFhIWEL0lS4pQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"872\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<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=\"r\"><code><span class=\"code-snippet_outer\">rownames(rt)=rt[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">exp<\/span>=rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">list<\/span>(rownames(<span class=\"code-snippet__built_in\">exp<\/span>),colnames(<span class=\"code-snippet__built_in\">exp<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">data=matrix(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.matrix(<span class=\"code-snippet__built_in\">exp<\/span>)),nrow=nrow(<span class=\"code-snippet__built_in\">exp<\/span>),<span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">dimnames<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data=avereps(data)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[rowMeans(data)><span class=\"code-snippet__number\">0.1<\/span>,]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5220\u9664\u6b63\u5e38\u6837\u54c1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(colnames(data),<span class=\"code-snippet__string\">\"\\-\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">4<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(group,<span class=\"code-snippet__string\">\"\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=gsub(<span class=\"code-snippet__string\">\"2\"<\/span>,<span class=\"code-snippet__string\">\"1\"<\/span>,group)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[,group==<span class=\"code-snippet__number\">0<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6score\u6587\u4ef6,\u6839\u636escore\u4e2d\u4f4d\u503c\u5bf9\u6837\u54c1\u5206\u7ec4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">score=read.table(scoreFile,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,header=<span class=\"code-snippet__built_in\">T<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6515323496027242\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_qc7QRhJ4dJhicP7R1PyfEUX29dKJng-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjVPWzv2icoStPwyON0FycXgWe8Eqc7QRhJ4dJhicP7R1PyfEUX29dKJng\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"881\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<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<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<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=\"r\"><code><span class=\"code-snippet_outer\">med=median(score[,scoreType])<\/span><\/code><code><span class=\"code-snippet_outer\">conTab=score[score[,scoreType]<=med,]<\/span><\/code><code><span class=\"code-snippet_outer\">treatTab=score[score[,scoreType]>med,]<\/span><\/code><code><span class=\"code-snippet_outer\">con=as.vector(conTab[,<span class=\"code-snippet__number\">1<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">treat=as.vector(treatTab[,<span class=\"code-snippet__number\">1<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">conNum=<span class=\"code-snippet__built_in\">length<\/span>(con)<\/span><\/code><code><span class=\"code-snippet_outer\">treatNum=<span class=\"code-snippet__built_in\">length<\/span>(treat)<\/span><\/code><code><span class=\"code-snippet_outer\">data=cbind(data[,con],data[,treat])<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">outTab=data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\">Type=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__built_in\">rep<\/span>(<span class=\"code-snippet__number\">1<\/span>,conNum),<span class=\"code-snippet__built_in\">rep<\/span>(<span class=\"code-snippet__number\">2<\/span>,treatNum))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(i <span class=\"code-snippet__keyword\">in<\/span> row.names(data)){<\/span><\/code><code><span class=\"code-snippet_outer\">geneName=unlist(strsplit(i,<span class=\"code-snippet__string\">\"\\|\"<\/span>,))[<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">geneName=gsub(<span class=\"code-snippet__string\">\"\\\/\"<\/span>, <span class=\"code-snippet__string\">\"_\"<\/span>, geneName)<\/span><\/code><code><span class=\"code-snippet_outer\">rt=rbind(<span class=\"code-snippet__built_in\">expression<\/span>=data[i,],Type=Type)<\/span><\/code><code><span class=\"code-snippet_outer\">rt=as.matrix(t(rt))<\/span><\/code><code><span class=\"code-snippet_outer\">wilcoxTest<-wilcox.test(<span class=\"code-snippet__built_in\">expression<\/span> ~ Type, data=rt)<\/span><\/code><code><span class=\"code-snippet_outer\">conGeneMeans=mean(data[i,<span class=\"code-snippet__number\">1<\/span>:conNum])<\/span><\/code><code><span class=\"code-snippet_outer\">treatGeneMeans=mean(data[i,(conNum+<span class=\"code-snippet__number\">1<\/span>):ncol(data)])<\/span><\/code><code><span class=\"code-snippet_outer\">logFC=log2(treatGeneMeans)-log2(conGeneMeans)<\/span><\/code><code><span class=\"code-snippet_outer\">pvalue=wilcoxTest$p.value<\/span><\/code><code><span class=\"code-snippet_outer\">conMed=median(data[i,<span class=\"code-snippet__number\">1<\/span>:conNum])<\/span><\/code><code><span class=\"code-snippet_outer\">treatMed=median(data[i,(conNum+<span class=\"code-snippet__number\">1<\/span>):ncol(data)])<\/span><\/code><code><span class=\"code-snippet_outer\">diffMed=treatMed-conMed<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span>( ((logFC><span class=\"code-snippet__number\">0<\/span>) & (diffMed><span class=\"code-snippet__number\">0<\/span>)) | ((logFC<<span class=\"code-snippet__number\">0<\/span>) & (diffMed<<span class=\"code-snippet__number\">0<\/span>)) ){<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=rbind(outTab,cbind(gene=i,conMean=conGeneMeans,treatMean=treatGeneMeans,logFC=logFC,pValue=pvalue))<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">pValue=outTab[,<span class=\"code-snippet__string\">\"pValue\"<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">fdr=p.adjust(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.vector(pValue)),method=<span class=\"code-snippet__string\">\"fdr\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=cbind(outTab,fdr=fdr)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u6240\u6709\u57fa\u56e0\u7684\u5dee\u5f02\u60c5\u51b5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.table(outTab,file=<span class=\"code-snippet__string\">\"Immune.all.xls\"<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,row.names=<span class=\"code-snippet__built_in\">F<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u5dee\u5f02\u8868\u683c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">diffSig=outTab[(<span class=\"code-snippet__built_in\">abs<\/span>(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.vector(outTab$logFC)))>logFCfilter& <span class=\"code-snippet__built_in\">as.numeric<\/span>(as.vector(outTab$fdr))<\/span><\/code><code><span class=\"code-snippet_outer\">write.table(diffSig,file=<span class=\"code-snippet__string\">\"Immune.Diff.txt\"<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,row.names=<span class=\"code-snippet__built_in\">F<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><span style=\"text-indent: 2em;\">\u8fd9\u6837\u5c31\u5f97\u5230\u4e86\u6211\u4eec\u540e\u7eed\u5206\u6790\u4ea4\u96c6\u57fa\u56e0\u7684Immune.Diff.txt\u6587\u4ef6\uff0c\u5bf9Stromal\u57fa\u8d28\u7ec6\u80de\u64cd\u4f5c\u5b8c\u5168\u4e00\u6837,\u4e0b\u9762\u662f\u5728\u5bfb\u627e\u7b5b\u9009\u5173\u952e\u57fa\u56e0\u7684\u4ee3\u7801\uff0c\u6211\u4eec\u7ed8\u5236venn\u56fe\u7b80\u5355\u6e05\u6670\u7684\u5c55\u793a\u3002<\/span><br \/><\/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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"VennDiagram\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u7528\u4e8e\u5b89\u88c5\u6240\u9700\u7684R\u5305VennDiagram\uff0c\u5982\u679c\u5df2\u7ecf\u5b89\u88c5\u4e86\u5219\u53ef\u4ee5\u8df3\u8fc7\u5b89\u88c5\u6b65\u9aa4\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">library(VennDiagram) <span class=\"code-snippet__comment\">#\u5f15\u7528\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">StromalFile=<span class=\"code-snippet__string\">\"Stromal.Diff.txt\"<\/span> <span class=\"code-snippet__comment\">#\u57fa\u8d28\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7172330097087378\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_AWR28jLbjhKgP2MiaCALwyic4zLnIQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjhTFs4zYEibtkuvWVRWP7tHHVsZcAWR28jLbjhKgP2MiaCALwyic4zLnIQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"824\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">ImmuneFile=<span class=\"code-snippet__string\">\"Immune.Diff.txt\"<\/span> <span class=\"code-snippet__comment\">#\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.763681592039801\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_7Kt3lqALeqIQDoubYevcLDoLahXOTQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjeLdLebZM38xDLjvMa6KhDkD97Kt3lqALeqIQDoubYevcLDoLahXOTQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"804\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">upList=<span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\">downList=<span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8fd9\u4e9b\u4ee3\u7801\u6307\u5b9a\u4e86\u57fa\u8d28\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\u548c\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\u7684\u6587\u4ef6\u540d\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5e76\u521b\u5efa\u4e86\u4e24\u4e2a\u7a7a\u7684\u5217\u8868upList\u548cdownList\uff0c\u7528\u4e8e\u5b58\u50a8\u4e0a\u8c03\u548c\u4e0b\u8c03\u57fa\u56e0\u7684\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6Stromal\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Stromal=read.table(StromalFile,header=<span class=\"code-snippet__built_in\">T<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>,row.names=<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">upList[[<span class=\"code-snippet__string\">\"Stromal\"<\/span>]]=row.names(Stromal[Stromal[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]><span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><code><span class=\"code-snippet_outer\">downList[[<span class=\"code-snippet__string\">\"Stromal\"<\/span>]]=row.names(Stromal[Stromal[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]<<span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.1482758620689655\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_xCyiagN9yEpOrq8LicbLBCpLiaWpfw-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrj4GWEW0hF2rMQFLpmibPR5mcQB5pExCyiagN9yEpOrq8LicbLBCpLiaWpfw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"580\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.15357766143106458\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_9LSj14XgJs9P8akKs6dZlUNUp3Ibkw-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjggQJfJtXqAhulhibGSgIhCicyN9LSj14XgJs9P8akKs6dZlUNUp3Ibkw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"573\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u57fa\u8d28\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\uff0c\u5e76\u6839\u636elogFC\u7684\u6b63\u8d1f\u5c06\u4e0a\u8c03\u548c\u4e0b\u8c03\u7684\u57fa\u56e0\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5206\u522b\u5b58\u50a8\u5728upList[[\"Stromal\"]]\u548cdownList[[\"Stromal\"]]\u4e2d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6Immune\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Immune=read.table(ImmuneFile,header=<span class=\"code-snippet__built_in\">T<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>,row.names=<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">upList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]=row.names(Immune[Immune[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]><span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><code><span class=\"code-snippet_outer\">downList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]=row.names(Immune[Immune[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]<<span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.1804635761589404\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_Bryn5fDmr7UXoD24mvn2BcEUn0eGTQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjFG7fCZpjvcicQqiaA9da4apAL5Bryn5fDmr7UXoD24mvn2BcEUn0eGTQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"604\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<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<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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\u6839\u636elogFC\u7684\u6b63\u8d1f\u5c06\u4e0a\u8c03\u548c\u4e0b\u8c03\u7684\u57fa\u56e0\u540d\u79f0\u5206\u522b\u5b58\u50a8<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u5728upList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]\u548cdownList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0a\u8c03venn\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">upVenn=venn.diagram(upList,filename=<span class=\"code-snippet__literal\">NULL<\/span>,main=<span class=\"code-snippet__string\">\"Up\"<\/span>,main.cex = <span class=\"code-snippet__number\">2<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">fill=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"darkblue\"<\/span>, <span class=\"code-snippet__string\">\"darkgreen\"<\/span>),cat.cex=<span class=\"code-snippet__number\">1.2<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=<span class=\"code-snippet__string\">\"UP.venn.pdf\"<\/span>,width=<span class=\"code-snippet__number\">7<\/span>,height=<span class=\"code-snippet__number\">7<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">grid.draw(upVenn)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">upGenes=Reduce(intersect,upList)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u751f\u6210\u4e0a\u8c03\u57fa\u56e0\u7684Venn\u56fe\u3002\u4f7f\u7528venn.diagram\u51fd\u6570\u6839\u636e\u4e0a\u8c03\u57fa\u56e0\u7684\u5217\u8868upList<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236Venn\u56fe\uff0c\u5e76\u8bbe\u7f6e\u56fe\u7684\u6807\u9898\u3001\u4e3b\u6807\u9898\u5b57\u4f53\u5927\u5c0f\u3001\u586b\u5145\u989c\u8272\u7b49\u3002\u7136\u540e\u4f7f\u7528pdf #\u51fd\u6570\u521b\u5efa\u4e00\u4e2a\u8f93\u51fa\u6587\u4ef6\uff0c\u5c06Venn\u56fe\u4fdd\u5b58\u4e3aPDF\u683c\u5f0f\u3002\u63a5\u4e0b\u6765\u4f7f\u7528grid.draw\u51fd<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6570\u7ed8\u5236Venn\u56fe\uff0c\u5e76\u4f7f\u7528dev.off\u51fd\u6570\u5173\u95edPDF\u8bbe\u5907\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6700\u540e\uff0c\u4f7f\u7528Reduce\u51fd\u6570\u8ba1\u7b97\u4e0a\u8c03\u57fa\u56e0\u5217\u8868\u7684\u4ea4\u96c6\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728upGenes\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0b\u8c03venn\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">downVenn=venn.diagram(downList,filename=<span class=\"code-snippet__literal\">NULL<\/span>,main=<span class=\"code-snippet__string\">\"Down\"<\/span>,main.cex = <span class=\"code-snippet__number\">2<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">fill=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"darkblue\"<\/span>, <span class=\"code-snippet__string\">\"darkgreen\"<\/span>),cat.cex=<span class=\"code-snippet__number\">1.2<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=<span class=\"code-snippet__string\">\"DOWN.venn.pdf\"<\/span>,width=<span class=\"code-snippet__number\">7<\/span>,height=<span class=\"code-snippet__number\">7<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">grid.draw(downVenn)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">downGenes=Reduce(intersect,downList)<\/span><\/code><code><span class=\"code-snippet_outer\">\u751f\u6210\u4e0b\u8c03\u57fa\u56e0\u7684Venn\u56fe\uff0c\u8fc7\u7a0b\u4e0e\u4e0a\u8c03\u57fa\u56e0\u7684Venn\u56fe\u7c7b\u4f3c\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">\u53ea\u662f\u6807\u9898\u548c\u8f93\u51fa\u6587\u4ef6\u540d\u4e0d\u540c\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728downGenes\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u4ea4\u96c6\u57fa\u56e0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">upLogFC=(as.matrix(Stromal)[upGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>]+as.matrix(Immune)[upGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>])\/<span class=\"code-snippet__number\">2<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">downLogFC=(as.matrix(Stromal)[downGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>]+as.matrix(Immune)[downGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>])\/<span class=\"code-snippet__number\">2<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">logFC=<span class=\"code-snippet__built_in\">c<\/span>(upLogFC,downLogFC)<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=as.data.frame(logFC)<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=cbind(ID=row.names(outTab),outTab)<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(outTab)=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Gene\"<\/span>,<span class=\"code-snippet__string\">\"logFC\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">write.table(file=<span class=\"code-snippet__string\">\"intersectGenes.txt\"<\/span>,outTab,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>,row.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.5959079283887467\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_NXib8mesETPRkgsRvthTAXvoA6aOxQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjJSibUUYeqiccHaafRjUdxecAxAjNXib8mesETPRkgsRvthTAXvoA6aOxQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"391\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8ba1\u7b97\u4ea4\u96c6\u57fa\u56e0\u7684\u5e73\u5747logFC\u503c\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728logFC\u53d8\u91cf\u4e2d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\uff0c\u5c06\u4ea4\u96c6\u57fa\u56e0\u7684ID\u548clogFC\u503c\u7ec4\u5408\u6210\u4e00\u4e2a\u6570\u636e\u6846outTab\uff0c\u5e76\u4e3a\u5217\u547d\u540d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6700\u540e\uff0c\u4f7f\u7528write.table\u51fd\u6570\u5c06\u7ed3\u679c\u5199\u5165\u540d\u4e3a\"intersectGenes.txt\"\u7684\u6587\u4ef6\u4e2d<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8217562254259502\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_TticKlpyE0icHOgsyz9wWRibibSMBA-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjs9HibGsyYQp9FfICZq0dycnfxUqdKTticKlpyE0icHOgsyz9wWRibibSMBA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"763\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.91701244813278\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_BJ6rZ0H7Hy03rJKCicVffpsEDibKjg-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjf2OKTbcJVRkSHWeTze9x4BgAGMBJ6rZ0H7Hy03rJKCicVffpsEDibKjg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"723\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 98%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;border-style: solid;border-width: 2px;border-color: rgb(160, 160, 160);padding: 27px;\">\n<section style=\"text-align: justify;line-height: 1.6;letter-spacing: 0px;padding-right: 6px;padding-left: 6px;\" powered-by=\"xiumi.us\">\n<p>\u7efc\u4e0a\u6240\u8ff0\uff0c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7684Venn\u56fe\u5177\u6709\u663e\u793a\u5dee\u5f02\u57fa\u56e0\u7684\u91cd\u53e0\u60c5\u51b5\u3001\u7b5b\u9009\u5171\u540c\u8c03\u8282\u7684\u57fa\u56e0\u3001\u786e\u5b9a\u7279\u5b9a\u6761\u4ef6\u4e0b\u7684\u5dee\u5f02\u57fa\u56e0\u3001\u8f85\u52a9\u751f\u7269\u5b66\u89e3\u91ca\u548c\u5b9e\u9a8c\u8bbe\u8ba1\uff0c\u4ee5\u53ca\u53ef\u89c6\u5316\u548c\u62a5\u544a\u7ed3\u679c\u7684\u529f\u80fd\u548c\u610f\u4e49\u3002\u5b83\u5728\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u548c\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u53d1\u6325\u91cd\u8981\u4f5c\u7528\uff0c\u5e2e\u52a9\u63ed\u793a\u57fa\u56e0\u8c03\u63a7\u548c\u751f\u7269\u8fc7\u7a0b\u7684\u5dee\u5f02\uff0c\u4e3a\u75be\u75c5\u673a\u5236\u548c\u6cbb\u7597\u9776\u70b9\u7684\u7814\u7a76\u63d0\u4f9b\u91cd\u8981\u7ebf\u7d22\u3002\u4e0b\u671f\u5c06\u4e3a\u4f60\u5e26\u6765\u66f4\u591aR\u8bed\u8a00\u7684\u9a9a\u64cd\u4f5c\u6280\u5de7\uff0c\u4ee5\u4e0b\u63a8\u8350\u7684\u662f\u4e00\u4e2a\u591a\u529f\u80fd\u7684\u751f\u4fe1\u5e73\u53f0\u3002<\/p>\n<p><br 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id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-08-19 19:00:39<\/em><\/div>\n<p><content><\/p>\n<div class=\"reprint\">\n<p>\u8f6c\u81ea\u516c\u4f17\u53f7\uff1a\u751f\u4fe1\u82b1<br \/><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=MzkzODUxNjcwMA==&mid=2247484187&idx=1&sn=93b2523faf04b1da1d69b087fb8d441a\" target=\"_blank\" title=\"\u9605\u8bfb\u539f\u6587\" rel=\"noopener\">http:\/\/mp.weixin.qq.com\/s?__biz=MzkzODUxNjcwMA==&mid=2247484187&idx=1&sn=93b2523faf04b1da1d69b087fb8d441a<\/a><\/p>\n<\/div>\n<section style=\"font-size: 14px;margin-bottom: 24px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(65, 128, 216);\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;padding-left: 12px;\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);\" powered-by=\"xiumi.us\">\n<p><strong>\u70b9\u51fb\u84dd\u5b57 \u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: 34px;align-self: flex-start;flex: 0 0 auto;height: auto;overflow: hidden;margin-right: -17px;\">\n<section style=\"transform: rotateZ(60deg);\" powered-by=\"xiumi.us\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;text-align: center;\">\n<section style=\"width: 100%;height: 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10px;text-align: center;\">\n<section style=\"width: 100%;height: 5px;background-color: rgb(255, 255, 255);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><span style=\"text-indent: 2em;\">Venn\u56fe\u53ef\u4ee5\u76f4\u89c2\u5730\u663e\u793a\u4e0d\u540c\u6761\u4ef6\u4e0b\u7684\u5dee\u5f02\u57fa\u56e0\u4e4b\u95f4\u7684\u91cd\u53e0\u60c5\u51b5\u3002\u901a\u8fc7\u4ea4\u53c9\u533a\u57df\u7684\u5927\u5c0f\u548c\u91cd\u53e0\u533a\u57df\u7684\u6570\u91cf\uff0c\u53ef\u4ee5\u4e86\u89e3\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u5177\u6709\u5171\u540c\u8868\u8fbe\u53d8\u5316\u7684\u57fa\u56e0\u6570\u91cf\u548c\u5171\u6709\u7684\u57fa\u56e0\u96c6\u5408\u3002\u7b5b\u9009\u51fa\u5177\u6709\u5171\u540c\u8c03\u8282\u7684\u57fa\u56e0\uff1a\u901a\u8fc7\u89c2\u5bdfVenn\u56fe\u4e2d\u7684\u4ea4\u53c9\u533a\u57df\uff0c\u53ef\u4ee5\u7b5b\u9009\u51fa\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u5177\u6709\u5171\u540c\u8c03\u8282\u7684\u57fa\u56e0\u3002\u4ea4\u53c9\u533a\u57df\u4e2d\u7684\u57fa\u56e0\u8868\u793a\u5728\u591a\u4e2a\u6761\u4ef6\u4e0b\u5747\u53d1\u751f\u8868\u8fbe\u53d8\u5316\uff0c\u8fd9\u4e9b\u57fa\u56e0\u53ef\u80fd\u5728\u76f8\u4f3c\u7684\u751f\u7269\u8fc7\u7a0b\u6216\u4fe1\u53f7\u901a\u8def\u4e2d\u8d77\u7740\u91cd\u8981\u7684\u8c03\u8282\u4f5c\u7528\u3002\u53ef\u89c6\u5316\u548c\u62a5\u544a\u7ed3\u679c\uff1aVenn\u56fe\u4f5c\u4e3a\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7684\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u5448\u73b0\u57fa\u56e0\u7684\u91cd\u53e0\u60c5\u51b5\u548c\u5171\u540c\u8c03\u8282\u7684\u6a21\u5f0f\u3002Venn\u56fe\u53ef\u4ee5\u5e2e\u52a9\u786e\u5b9a\u5728\u7279\u5b9a\u6761\u4ef6\u4e0b\u7279\u5f02\u6027\u7684\u5dee\u5f02\u57fa\u56e0\u3002\u901a\u8fc7\u89c2\u5bdfVenn\u56fe\u4e2d\u5355\u72ec\u7684\u533a\u57df\uff0c\u53ef\u4ee5\u8bc6\u522b\u5728\u67d0\u4e2a\u6761\u4ef6\u4e0b\u5177\u6709\u7279\u5b9a\u8868\u8fbe\u53d8\u5316\u7684\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u53ef\u80fd\u4e0e\u8be5\u6761\u4ef6\u4e0b\u7684\u751f\u7269\u8fc7\u7a0b\u6216\u75be\u75c5\u673a\u5236\u5bc6\u5207\u76f8\u5173\u3002<\/span><br \/><\/p>\n<p style=\"text-indent: 2em;text-wrap: wrap;\"><span style=\"text-indent: 2em;\"><br \/><\/span><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u786e\u5b9a\u7279\u5b9a\u6761\u4ef6\u4e0b\u7684\u5dee\u5f02\u57fa\u56e0\uff1aVenn\u56fe\u53ef\u4ee5\u5e2e\u52a9\u786e\u5b9a\u5728\u7279\u5b9a\u6761\u4ef6\u4e0b\u7279\u5f02\u6027\u7684\u5dee\u5f02\u57fa\u56e0\u3002\u901a\u8fc7\u89c2\u5bdfVenn\u56fe\u4e2d\u5355\u72ec\u7684\u533a\u57df\uff0c\u53ef\u4ee5\u8bc6\u522b\u5728\u67d0\u4e2a\u6761\u4ef6\u4e0b\u5177\u6709\u7279\u5b9a\u8868\u8fbe\u53d8\u5316\u7684\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u53ef\u80fd\u4e0e\u8be5\u6761\u4ef6\u4e0b\u7684\u751f\u7269\u8fc7\u7a0b\u6216\u75be\u75c5\u673a\u5236\u5bc6\u5207\u76f8\u5173\u3002\u901a\u8fc7\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7ed3\u679c\u6587\u4ef6\uff0c\u751f\u6210\u57fa\u8d28\u7ec6\u80de\u548c\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u57fa\u56e0\u7684Venn\u56fe\uff0c\u5e76\u8f93\u51fa\u4ea4\u96c6\u57fa\u56e0\u7684\u5e73\u5747logFC\u503c\u3002<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"limma\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"pheatmap\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">fdrFilter=<span class=\"code-snippet__number\">0.05<\/span> <span class=\"code-snippet__comment\">#fdr\u4e34\u754c\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">logFCfilter=<span class=\"code-snippet__number\">1<\/span> <span class=\"code-snippet__comment\">#logFC\u4e34\u754c\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scoreType=<span class=\"code-snippet__string\">\"ImmuneScore\"<\/span> <span class=\"code-snippet__comment\">#\u6309ImmuneScore\u5206\u7ec4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">inputFile=<span class=\"code-snippet__string\">\"symbol.txt\"<\/span> <span class=\"code-snippet__comment\">#\u8f93\u5165\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scoreFile=<span class=\"code-snippet__string\">\"scores.txt\"<\/span> <span class=\"code-snippet__comment\">#score\u6587\u4ef6<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.20136518771331058\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_6JrtZvZlu7h3dcSw4J94Fy38L7q25g-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjejHZRqSlZLmCU6a2iaLNPqu6Y6JrtZvZlu7h3dcSw4J94Fy38L7q25g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"293\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u8868\u8fbe\u8f93\u5165\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=read.table(inputFile,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,header=<span class=\"code-snippet__built_in\">T<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">rt=as.matrix(rt)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7419724770642202\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_qWLicVTSaskuZXYv7bFhIWEL0lS4pQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjPtP4cibw5zwvtl5fkic8w1ndUPFqWLicVTSaskuZXYv7bFhIWEL0lS4pQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"872\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<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=\"r\"><code><span class=\"code-snippet_outer\">rownames(rt)=rt[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">exp<\/span>=rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">list<\/span>(rownames(<span class=\"code-snippet__built_in\">exp<\/span>),colnames(<span class=\"code-snippet__built_in\">exp<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">data=matrix(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.matrix(<span class=\"code-snippet__built_in\">exp<\/span>)),nrow=nrow(<span class=\"code-snippet__built_in\">exp<\/span>),<span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">dimnames<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data=avereps(data)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[rowMeans(data)><span class=\"code-snippet__number\">0.1<\/span>,]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5220\u9664\u6b63\u5e38\u6837\u54c1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(colnames(data),<span class=\"code-snippet__string\">\"\\-\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">4<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(group,<span class=\"code-snippet__string\">\"\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=gsub(<span class=\"code-snippet__string\">\"2\"<\/span>,<span class=\"code-snippet__string\">\"1\"<\/span>,group)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[,group==<span class=\"code-snippet__number\">0<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6score\u6587\u4ef6,\u6839\u636escore\u4e2d\u4f4d\u503c\u5bf9\u6837\u54c1\u5206\u7ec4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">score=read.table(scoreFile,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,header=<span class=\"code-snippet__built_in\">T<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6515323496027242\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_qc7QRhJ4dJhicP7R1PyfEUX29dKJng-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjVPWzv2icoStPwyON0FycXgWe8Eqc7QRhJ4dJhicP7R1PyfEUX29dKJng\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"881\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<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<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<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=\"r\"><code><span class=\"code-snippet_outer\">med=median(score[,scoreType])<\/span><\/code><code><span class=\"code-snippet_outer\">conTab=score[score[,scoreType]<=med,]<\/span><\/code><code><span class=\"code-snippet_outer\">treatTab=score[score[,scoreType]>med,]<\/span><\/code><code><span class=\"code-snippet_outer\">con=as.vector(conTab[,<span class=\"code-snippet__number\">1<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">treat=as.vector(treatTab[,<span class=\"code-snippet__number\">1<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">conNum=<span class=\"code-snippet__built_in\">length<\/span>(con)<\/span><\/code><code><span class=\"code-snippet_outer\">treatNum=<span class=\"code-snippet__built_in\">length<\/span>(treat)<\/span><\/code><code><span class=\"code-snippet_outer\">data=cbind(data[,con],data[,treat])<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">outTab=data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\">Type=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__built_in\">rep<\/span>(<span class=\"code-snippet__number\">1<\/span>,conNum),<span class=\"code-snippet__built_in\">rep<\/span>(<span class=\"code-snippet__number\">2<\/span>,treatNum))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(i <span class=\"code-snippet__keyword\">in<\/span> row.names(data)){<\/span><\/code><code><span class=\"code-snippet_outer\">geneName=unlist(strsplit(i,<span class=\"code-snippet__string\">\"\\|\"<\/span>,))[<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">geneName=gsub(<span class=\"code-snippet__string\">\"\\\/\"<\/span>, <span class=\"code-snippet__string\">\"_\"<\/span>, geneName)<\/span><\/code><code><span class=\"code-snippet_outer\">rt=rbind(<span class=\"code-snippet__built_in\">expression<\/span>=data[i,],Type=Type)<\/span><\/code><code><span class=\"code-snippet_outer\">rt=as.matrix(t(rt))<\/span><\/code><code><span class=\"code-snippet_outer\">wilcoxTest<-wilcox.test(<span class=\"code-snippet__built_in\">expression<\/span> ~ Type, data=rt)<\/span><\/code><code><span class=\"code-snippet_outer\">conGeneMeans=mean(data[i,<span class=\"code-snippet__number\">1<\/span>:conNum])<\/span><\/code><code><span class=\"code-snippet_outer\">treatGeneMeans=mean(data[i,(conNum+<span class=\"code-snippet__number\">1<\/span>):ncol(data)])<\/span><\/code><code><span class=\"code-snippet_outer\">logFC=log2(treatGeneMeans)-log2(conGeneMeans)<\/span><\/code><code><span class=\"code-snippet_outer\">pvalue=wilcoxTest$p.value<\/span><\/code><code><span class=\"code-snippet_outer\">conMed=median(data[i,<span class=\"code-snippet__number\">1<\/span>:conNum])<\/span><\/code><code><span class=\"code-snippet_outer\">treatMed=median(data[i,(conNum+<span class=\"code-snippet__number\">1<\/span>):ncol(data)])<\/span><\/code><code><span class=\"code-snippet_outer\">diffMed=treatMed-conMed<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span>( ((logFC><span class=\"code-snippet__number\">0<\/span>) & (diffMed><span class=\"code-snippet__number\">0<\/span>)) | ((logFC<<span class=\"code-snippet__number\">0<\/span>) & (diffMed<<span class=\"code-snippet__number\">0<\/span>)) ){<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=rbind(outTab,cbind(gene=i,conMean=conGeneMeans,treatMean=treatGeneMeans,logFC=logFC,pValue=pvalue))<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">pValue=outTab[,<span class=\"code-snippet__string\">\"pValue\"<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">fdr=p.adjust(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.vector(pValue)),method=<span class=\"code-snippet__string\">\"fdr\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=cbind(outTab,fdr=fdr)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u6240\u6709\u57fa\u56e0\u7684\u5dee\u5f02\u60c5\u51b5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.table(outTab,file=<span class=\"code-snippet__string\">\"Immune.all.xls\"<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,row.names=<span class=\"code-snippet__built_in\">F<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u5dee\u5f02\u8868\u683c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">diffSig=outTab[(<span class=\"code-snippet__built_in\">abs<\/span>(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.vector(outTab$logFC)))>logFCfilter& <span class=\"code-snippet__built_in\">as.numeric<\/span>(as.vector(outTab$fdr))<\/span><\/code><code><span class=\"code-snippet_outer\">write.table(diffSig,file=<span class=\"code-snippet__string\">\"Immune.Diff.txt\"<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,row.names=<span class=\"code-snippet__built_in\">F<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><span style=\"text-indent: 2em;\">\u8fd9\u6837\u5c31\u5f97\u5230\u4e86\u6211\u4eec\u540e\u7eed\u5206\u6790\u4ea4\u96c6\u57fa\u56e0\u7684Immune.Diff.txt\u6587\u4ef6\uff0c\u5bf9Stromal\u57fa\u8d28\u7ec6\u80de\u64cd\u4f5c\u5b8c\u5168\u4e00\u6837,\u4e0b\u9762\u662f\u5728\u5bfb\u627e\u7b5b\u9009\u5173\u952e\u57fa\u56e0\u7684\u4ee3\u7801\uff0c\u6211\u4eec\u7ed8\u5236venn\u56fe\u7b80\u5355\u6e05\u6670\u7684\u5c55\u793a\u3002<\/span><br \/><\/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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"VennDiagram\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u7528\u4e8e\u5b89\u88c5\u6240\u9700\u7684R\u5305VennDiagram\uff0c\u5982\u679c\u5df2\u7ecf\u5b89\u88c5\u4e86\u5219\u53ef\u4ee5\u8df3\u8fc7\u5b89\u88c5\u6b65\u9aa4\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">library(VennDiagram) <span class=\"code-snippet__comment\">#\u5f15\u7528\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">StromalFile=<span class=\"code-snippet__string\">\"Stromal.Diff.txt\"<\/span> <span class=\"code-snippet__comment\">#\u57fa\u8d28\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7172330097087378\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_AWR28jLbjhKgP2MiaCALwyic4zLnIQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjhTFs4zYEibtkuvWVRWP7tHHVsZcAWR28jLbjhKgP2MiaCALwyic4zLnIQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"824\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">ImmuneFile=<span class=\"code-snippet__string\">\"Immune.Diff.txt\"<\/span> <span class=\"code-snippet__comment\">#\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.763681592039801\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_7Kt3lqALeqIQDoubYevcLDoLahXOTQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjeLdLebZM38xDLjvMa6KhDkD97Kt3lqALeqIQDoubYevcLDoLahXOTQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"804\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">upList=<span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\">downList=<span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8fd9\u4e9b\u4ee3\u7801\u6307\u5b9a\u4e86\u57fa\u8d28\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\u548c\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\u7684\u6587\u4ef6\u540d\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5e76\u521b\u5efa\u4e86\u4e24\u4e2a\u7a7a\u7684\u5217\u8868upList\u548cdownList\uff0c\u7528\u4e8e\u5b58\u50a8\u4e0a\u8c03\u548c\u4e0b\u8c03\u57fa\u56e0\u7684\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6Stromal\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Stromal=read.table(StromalFile,header=<span class=\"code-snippet__built_in\">T<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>,row.names=<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">upList[[<span class=\"code-snippet__string\">\"Stromal\"<\/span>]]=row.names(Stromal[Stromal[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]><span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><code><span class=\"code-snippet_outer\">downList[[<span class=\"code-snippet__string\">\"Stromal\"<\/span>]]=row.names(Stromal[Stromal[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]<<span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.1482758620689655\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_xCyiagN9yEpOrq8LicbLBCpLiaWpfw-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrj4GWEW0hF2rMQFLpmibPR5mcQB5pExCyiagN9yEpOrq8LicbLBCpLiaWpfw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"580\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.15357766143106458\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_9LSj14XgJs9P8akKs6dZlUNUp3Ibkw-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjggQJfJtXqAhulhibGSgIhCicyN9LSj14XgJs9P8akKs6dZlUNUp3Ibkw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"573\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u57fa\u8d28\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\uff0c\u5e76\u6839\u636elogFC\u7684\u6b63\u8d1f\u5c06\u4e0a\u8c03\u548c\u4e0b\u8c03\u7684\u57fa\u56e0\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5206\u522b\u5b58\u50a8\u5728upList[[\"Stromal\"]]\u548cdownList[[\"Stromal\"]]\u4e2d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6Immune\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Immune=read.table(ImmuneFile,header=<span class=\"code-snippet__built_in\">T<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>,row.names=<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">upList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]=row.names(Immune[Immune[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]><span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><code><span class=\"code-snippet_outer\">downList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]=row.names(Immune[Immune[,<span class=\"code-snippet__string\">\"logFC\"<\/span>]<<span class=\"code-snippet__number\">0<\/span>,])<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.1804635761589404\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_Bryn5fDmr7UXoD24mvn2BcEUn0eGTQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjFG7fCZpjvcicQqiaA9da4apAL5Bryn5fDmr7UXoD24mvn2BcEUn0eGTQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"604\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<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<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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u514d\u75ab\u7ec6\u80de\u5dee\u5f02\u7ed3\u679c\u6587\u4ef6\u6839\u636elogFC\u7684\u6b63\u8d1f\u5c06\u4e0a\u8c03\u548c\u4e0b\u8c03\u7684\u57fa\u56e0\u540d\u79f0\u5206\u522b\u5b58\u50a8<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u5728upList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]\u548cdownList[[<span class=\"code-snippet__string\">\"Immune\"<\/span>]]\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0a\u8c03venn\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">upVenn=venn.diagram(upList,filename=<span class=\"code-snippet__literal\">NULL<\/span>,main=<span class=\"code-snippet__string\">\"Up\"<\/span>,main.cex = <span class=\"code-snippet__number\">2<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">fill=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"darkblue\"<\/span>, <span class=\"code-snippet__string\">\"darkgreen\"<\/span>),cat.cex=<span class=\"code-snippet__number\">1.2<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=<span class=\"code-snippet__string\">\"UP.venn.pdf\"<\/span>,width=<span class=\"code-snippet__number\">7<\/span>,height=<span class=\"code-snippet__number\">7<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">grid.draw(upVenn)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">upGenes=Reduce(intersect,upList)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u751f\u6210\u4e0a\u8c03\u57fa\u56e0\u7684Venn\u56fe\u3002\u4f7f\u7528venn.diagram\u51fd\u6570\u6839\u636e\u4e0a\u8c03\u57fa\u56e0\u7684\u5217\u8868upList<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236Venn\u56fe\uff0c\u5e76\u8bbe\u7f6e\u56fe\u7684\u6807\u9898\u3001\u4e3b\u6807\u9898\u5b57\u4f53\u5927\u5c0f\u3001\u586b\u5145\u989c\u8272\u7b49\u3002\u7136\u540e\u4f7f\u7528pdf #\u51fd\u6570\u521b\u5efa\u4e00\u4e2a\u8f93\u51fa\u6587\u4ef6\uff0c\u5c06Venn\u56fe\u4fdd\u5b58\u4e3aPDF\u683c\u5f0f\u3002\u63a5\u4e0b\u6765\u4f7f\u7528grid.draw\u51fd<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6570\u7ed8\u5236Venn\u56fe\uff0c\u5e76\u4f7f\u7528dev.off\u51fd\u6570\u5173\u95edPDF\u8bbe\u5907\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6700\u540e\uff0c\u4f7f\u7528Reduce\u51fd\u6570\u8ba1\u7b97\u4e0a\u8c03\u57fa\u56e0\u5217\u8868\u7684\u4ea4\u96c6\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728upGenes\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0b\u8c03venn\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">downVenn=venn.diagram(downList,filename=<span class=\"code-snippet__literal\">NULL<\/span>,main=<span class=\"code-snippet__string\">\"Down\"<\/span>,main.cex = <span class=\"code-snippet__number\">2<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">fill=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"darkblue\"<\/span>, <span class=\"code-snippet__string\">\"darkgreen\"<\/span>),cat.cex=<span class=\"code-snippet__number\">1.2<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=<span class=\"code-snippet__string\">\"DOWN.venn.pdf\"<\/span>,width=<span class=\"code-snippet__number\">7<\/span>,height=<span class=\"code-snippet__number\">7<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">grid.draw(downVenn)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">downGenes=Reduce(intersect,downList)<\/span><\/code><code><span class=\"code-snippet_outer\">\u751f\u6210\u4e0b\u8c03\u57fa\u56e0\u7684Venn\u56fe\uff0c\u8fc7\u7a0b\u4e0e\u4e0a\u8c03\u57fa\u56e0\u7684Venn\u56fe\u7c7b\u4f3c\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">\u53ea\u662f\u6807\u9898\u548c\u8f93\u51fa\u6587\u4ef6\u540d\u4e0d\u540c\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728downGenes\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u4ea4\u96c6\u57fa\u56e0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">upLogFC=(as.matrix(Stromal)[upGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>]+as.matrix(Immune)[upGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>])\/<span class=\"code-snippet__number\">2<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">downLogFC=(as.matrix(Stromal)[downGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>]+as.matrix(Immune)[downGenes,<span class=\"code-snippet__string\">\"logFC\"<\/span>])\/<span class=\"code-snippet__number\">2<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">logFC=<span class=\"code-snippet__built_in\">c<\/span>(upLogFC,downLogFC)<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=as.data.frame(logFC)<\/span><\/code><code><span class=\"code-snippet_outer\">outTab=cbind(ID=row.names(outTab),outTab)<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(outTab)=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Gene\"<\/span>,<span class=\"code-snippet__string\">\"logFC\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">write.table(file=<span class=\"code-snippet__string\">\"intersectGenes.txt\"<\/span>,outTab,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>,row.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.5959079283887467\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_NXib8mesETPRkgsRvthTAXvoA6aOxQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjJSibUUYeqiccHaafRjUdxecAxAjNXib8mesETPRkgsRvthTAXvoA6aOxQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"391\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8ba1\u7b97\u4ea4\u96c6\u57fa\u56e0\u7684\u5e73\u5747logFC\u503c\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728logFC\u53d8\u91cf\u4e2d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\uff0c\u5c06\u4ea4\u96c6\u57fa\u56e0\u7684ID\u548clogFC\u503c\u7ec4\u5408\u6210\u4e00\u4e2a\u6570\u636e\u6846outTab\uff0c\u5e76\u4e3a\u5217\u547d\u540d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6700\u540e\uff0c\u4f7f\u7528write.table\u51fd\u6570\u5c06\u7ed3\u679c\u5199\u5165\u540d\u4e3a\"intersectGenes.txt\"\u7684\u6587\u4ef6\u4e2d<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8217562254259502\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_TticKlpyE0icHOgsyz9wWRibibSMBA-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjs9HibGsyYQp9FfICZq0dycnfxUqdKTticKlpyE0icHOgsyz9wWRibibSMBA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"763\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.91701244813278\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_BJ6rZ0H7Hy03rJKCicVffpsEDibKjg-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjf2OKTbcJVRkSHWeTze9x4BgAGMBJ6rZ0H7Hy03rJKCicVffpsEDibKjg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"723\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 98%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;border-style: solid;border-width: 2px;border-color: rgb(160, 160, 160);padding: 27px;\">\n<section style=\"text-align: justify;line-height: 1.6;letter-spacing: 0px;padding-right: 6px;padding-left: 6px;\" powered-by=\"xiumi.us\">\n<p>\u7efc\u4e0a\u6240\u8ff0\uff0c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7684Venn\u56fe\u5177\u6709\u663e\u793a\u5dee\u5f02\u57fa\u56e0\u7684\u91cd\u53e0\u60c5\u51b5\u3001\u7b5b\u9009\u5171\u540c\u8c03\u8282\u7684\u57fa\u56e0\u3001\u786e\u5b9a\u7279\u5b9a\u6761\u4ef6\u4e0b\u7684\u5dee\u5f02\u57fa\u56e0\u3001\u8f85\u52a9\u751f\u7269\u5b66\u89e3\u91ca\u548c\u5b9e\u9a8c\u8bbe\u8ba1\uff0c\u4ee5\u53ca\u53ef\u89c6\u5316\u548c\u62a5\u544a\u7ed3\u679c\u7684\u529f\u80fd\u548c\u610f\u4e49\u3002\u5b83\u5728\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u548c\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u53d1\u6325\u91cd\u8981\u4f5c\u7528\uff0c\u5e2e\u52a9\u63ed\u793a\u57fa\u56e0\u8c03\u63a7\u548c\u751f\u7269\u8fc7\u7a0b\u7684\u5dee\u5f02\uff0c\u4e3a\u75be\u75c5\u673a\u5236\u548c\u6cbb\u7597\u9776\u70b9\u7684\u7814\u7a76\u63d0\u4f9b\u91cd\u8981\u7ebf\u7d22\u3002\u4e0b\u671f\u5c06\u4e3a\u4f60\u5e26\u6765\u66f4\u591aR\u8bed\u8a00\u7684\u9a9a\u64cd\u4f5c\u6280\u5de7\uff0c\u4ee5\u4e0b\u63a8\u8350\u7684\u662f\u4e00\u4e2a\u591a\u529f\u80fd\u7684\u751f\u4fe1\u5e73\u53f0\u3002<\/p>\n<p><br \/><\/p>\n<p>\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/p>\n<p><br \/><\/p>\n<p>\u5982\u679c\u60f3\u7528\u670d\u52a1\u5668\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490\uff08\u5feb\u6765\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u5427\uff01\uff09<\/p>\n<\/section>\n<section style=\"text-align: right;justify-content: flex-end;display: flex;flex-flow: row;transform: translate3d(40px, 0px, 0px);margin-bottom: -40px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 26px;height: 26px;vertical-align: top;overflow: hidden;background-color: rgb(255, 255, 255);border-left: 1px solid rgb(160, 160, 160);border-bottom-left-radius: 0px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><a target=\"_blank\" href=\"https:\/\/mp.weixin.qq.com\/s?__biz=MzAwNjE0MDY3MQ==&mid=2650761303&idx=2&sn=6f73471d1e82c56c0b2160d0fcd32d53&scene=21#wechat_redirect\" textvalue=\"\" linktype=\"image\" imgurl=\"https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSYCoxhZfqr5L0fxy3C9eSFdt72DV7zqsmrNaiaaoOhic3sHzUpBN4r4MaBCk9p9v16yZwvMvS5nM7sQ\/0?wx_fmt=jpeg\" imgdata=\"[object Object]\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.35083798882681566\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_pBN4r4MaBCk9p9v16yZwvMvS5nM7sQ-5.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSYCoxhZfqr5L0fxy3C9eSFdt72DV7zqsmrNaiaaoOhic3sHzUpBN4r4MaBCk9p9v16yZwvMvS5nM7sQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"895\" style=\"\" data-recalc-dims=\"1\" \/><\/span><\/a><br \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3488888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_uKaqczIP6EMQhkT9sW7c1bKv6z9AAg-5.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSYCoxhZfqr5L0fxy3C9eSFdD9CpdQZl2iaySUTmNepgg2BpMuKaqczIP6EMQhkT9sW7c1bKv6z9AAg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<section style=\"text-align: left;margin: 10px 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\u70b9\u4e00\u4e0b\u9605\u8bfb\u539f\u6587\u4e86\u89e3\u66f4\u591a\u8d44\u8baf<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 50px;height: 40px;vertical-align: top;overflow: hidden;\">\n<section style=\"text-align: center;margin-right: 0%;margin-left: 0%;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7709090909090909\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_7GMZEQNVhupP8hwk9YH2lKurEibn4A-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSbXqic9nKCfibQy6cuFlGacrjCqhdABAXkv6UMaxtMylTfETTZ7GMZEQNVhupP8hwk9YH2lKurEibn4A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"275\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" 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