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normal;\"><strong>\u70ed\u56fe\u7ed8\u5236\uff1a<\/strong>\u4ee3\u7801\u4f7f\u7528ComplexHeatmap\u5305\u7ed8\u5236\u70ed\u56fe\uff0c\u5c06\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6027\u72b6\u7684\u5173\u8054\u53ef\u89c6\u5316\u3002\u70ed\u56fe\u4e2d\uff0c\u884c\u8868\u793a\u6837\u672c\uff0c\u5217\u8868\u793a\u57fa\u56e0\u548c\u4e34\u5e8a\u6027\u72b6\uff0c\u989c\u8272\u8868\u793a\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u548c\u4e34\u5e8a\u6027\u72b6\u7684\u4e0d\u540c\u7c7b\u522b\u3002\u7ed3\u679c\u5c55\u793a\uff1a\u6700\u7ec8\u751f\u6210\u7684\u70ed\u56fe\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u76f4\u89c2\u5730\u4e86\u89e3\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u548c\u4e34\u5e8a\u6027\u72b6\u4e4b\u95f4\u7684\u5173\u7cfb\u3002\u70ed\u56fe\u4e2d\u7684\u6a21\u5f0f\u548c\u989c\u8272\u7f16\u7801\u53ef\u4ee5\u63ed\u793a\u57fa\u56e0\u8868\u8fbe\u7684\u5dee\u5f02\u4ee5\u53ca\u57fa\u56e0\u4e0e\u4e34\u5e8a\u6027\u72b6\u4e4b\u95f4\u7684\u76f8\u5173\u6027\u3002<\/p>\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=\"1.2702702702702702\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_bXMiaoriaMXAv3dMVUIcgJ6IbldwgA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXOC7kNS99NupMQcbQm69DHnWOo3CRmqg6a7YPR8tVOada3vqbXMiaoriaMXAv3dMVUIcgJ6IbldwgA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"629\" style=\"vertical-align: middle;width: 100%;\" \/><\/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\">#if (!requireNamespace(\"BiocManager\", quietly = TRUE))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># install.packages(\"BiocManager\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"ComplexHeatmap\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"limma\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5f15\u7528\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ComplexHeatmap)<\/span><\/code><code><span class=\"code-snippet_outer\">expFile=<span class=\"code-snippet__string\">\"geneExp.txt\"<\/span> <span class=\"code-snippet__comment\">#\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cliFile=<span class=\"code-snippet__string\">\"clinical.txt\"<\/span> <span class=\"code-snippet__comment\">#\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">setwd(<span class=\"code-snippet__string\">\"C:\\biowolf\\Gene\\14.cliHeatmap\"<\/span>) <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u5de5\u4f5c\u76ee\u5f55<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u901a\u8fc7library()\u51fd\u6570\u5f15\u7528\u4e86limma\u548cComplexHeatmap\u4e24\u4e2a\u5305\u3002\u6307\u5b9a\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u8def\u5f84expFile\u548c\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\u8def\u5f84cliFile\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f7f\u7528setwd()\u51fd\u6570\u8bbe\u7f6e\u5de5\u4f5c\u76ee\u5f55\u4e3a\"C:\\biowolf\\Gene\\14.cliHeatmap\"\u3002\u901a\u8fc7read.table()\u51fd\u6570\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u548c\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\u3002\u63d0\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u4e2d\u7684\u57fa\u56e0\u540d\u79f0\u548c\u7b2c\u4e00\u4e2a\u57fa\u56e0\u7684\u5217\u6570\u636e\u3002\u5220\u9664\u6b63\u5e38\u6837\u672c\uff0c\u53ea\u4fdd\u7559\u80bf\u7624\u6837\u672c\u7684\u6570\u636e\uff0c\u5e76\u5bf9\u91cd\u590d\u6837\u672c\u6c42\u5747\u503c\u3002\u6839\u636e\u76ee\u6807\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\u5c06\u6837\u672c\u8fdb\u884c\u5206\u7ec4\uff0c\u5e76\u5728\u6570\u636e\u6846\u4e2d\u6dfb\u52a0\u4e00\u4e2a\u540d\u4e3a\"Type\"\u7684\u5217\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=read.table(expFile, 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\">gene=colnames(rt)[<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5220\u6389\u6b63\u5e38\u6837\u54c1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tumorData=rt[rt$Type==<span class=\"code-snippet__string\">\"Tumor\"<\/span>,<span class=\"code-snippet__number\">1<\/span>,drop=<span class=\"code-snippet__built_in\">F<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">tumorData=as.matrix(tumorData)<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(tumorData)=gsub(<span class=\"code-snippet__string\">\"(.*?)\\-(.*?)\\-(.*?)\\-(.*?)\\-.*\"<\/span>, <span class=\"code-snippet__string\">\"\\1\\-\\2\\-\\3\"<\/span>, rownames(tumorData))<\/span><\/code><code><span class=\"code-snippet_outer\">data=avereps(tumorData)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6839\u636e\u76ee\u6807\u57fa\u56e0\u8868\u8fbe\u91cf\u5bf9\u6837\u54c1\u8fdb\u884c\u5206\u7ec4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Type=ifelse(data[,gene]>median(data[,gene]), <span class=\"code-snippet__string\">\"High\"<\/span>, <span class=\"code-snippet__string\">\"Low\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">Type=factor(Type, levels=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Low\"<\/span>,<span class=\"code-snippet__string\">\"High\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">data=cbind(as.data.frame(data), Type)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[order(data[,gene]),]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\uff0c\u5e76\u5bf9\u5176\u4e2d\u7684\"Age\"\u5217\u8fdb\u884c\u5206\u7c7b\uff0c\u6839\u636e\u5e74\u9f84\u5206\u4e3a\">65\"\u548c\"<=65\"\u4e24\u7ec4\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cli=read.table(cliFile, 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\">cli[,<span class=\"code-snippet__string\">\"Age\"<\/span>]=ifelse(cli[,<span class=\"code-snippet__string\">\"Age\"<\/span>]==<span class=\"code-snippet__string\">\"unknow\"<\/span>, <span class=\"code-snippet__string\">\"unknow\"<\/span>, ifelse(cli[,<span class=\"code-snippet__string\">\"Age\"<\/span>]><span class=\"code-snippet__number\">65<\/span>,<span class=\"code-snippet__string\">\">65\"<\/span>,<span class=\"code-snippet__string\">\"<=65\"<\/span>))<\/span><\/code><\/pre>\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=\"1.3006535947712419\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ot26CqrtaxgaWdOlwyD770wic6haoQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXOC7kNS99NupMQcbQm69DH6Ar5w0dN1CrFdzhdvVsEbsRJFot26CqrtaxgaWdOlwyD770wic6haoQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"612\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u5bf9\u4e34\u5e8a\u6027\u72b6\u8fdb\u884c\u5faa\u73af\uff0c\u5bf9\u6bcf\u4e2a\u4e34\u5e8a\u6027\u72b6\u4e0e\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u4e4b\u95f4\u7684\u5173\u8054\u8fdb\u884c\u5361\u65b9\u68c0\u9a8c\uff0c\u5f97\u5230\u663e\u8457\u6027\u6807\u8bb0\u3002\u5c06\u663e\u8457\u6027\u6807\u8bb0\u6dfb\u52a0\u5230\u70ed\u56fe\u6570\u636e\u6846rt\u7684\u5217\u540d\u4e2d\u3002<\/p>\n<p style=\"white-space: normal;\"><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<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<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\">#\u5408\u5e76\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">samSample=intersect(row.names(data), row.names(cli))<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[samSample,<span class=\"code-snippet__string\">\"Type\"<\/span>,drop=<span class=\"code-snippet__built_in\">F<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">cli=cli[samSample,,drop=<span class=\"code-snippet__built_in\">F<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">rt=cbind(data, cli)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bf9\u4e34\u5e8a\u6027\u72b6\u8fdb\u884c\u5faa\u73af\uff0c\u89c2\u5bdf\u4e34\u5e8a\u6027\u72b6\u5728\u9ad8\u4f4e\u8868\u8fbe\u7ec4\u4e4b\u95f4\u662f\u5426\u5177\u6709\u5dee\u5f02\uff0c\u5f97\u5230\u663e\u8457\u6027\u6807\u8bb0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sigVec=<span class=\"code-snippet__built_in\">c<\/span>(gene)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(clinical <span class=\"code-snippet__keyword\">in<\/span> colnames(rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)])){<\/span><\/code><code><span class=\"code-snippet_outer\">data=rt[<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Type\"<\/span>, clinical)]<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(data)=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Type\"<\/span>, <span class=\"code-snippet__string\">\"clinical\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[(data[,<span class=\"code-snippet__string\">\"clinical\"<\/span>]!=<span class=\"code-snippet__string\">\"unknow\"<\/span>),]<\/span><\/code><code><span class=\"code-snippet_outer\">tableStat=table(data)<\/span><\/code><code><span class=\"code-snippet_outer\">stat=chisq.test(tableStat)<\/span><\/code><code><span class=\"code-snippet_outer\">pvalue=stat$p.value<\/span><\/code><code><span class=\"code-snippet_outer\">Sig=ifelse(pvalue<<span class=\"code-snippet__number\">0.001<\/span>,<span class=\"code-snippet__string\">\"***\"<\/span>,ifelse(pvalue<<span class=\"code-snippet__number\">0.01<\/span>,<span class=\"code-snippet__string\">\"**\"<\/span>,ifelse(pvalue<<span class=\"code-snippet__number\">0.05<\/span>,<span class=\"code-snippet__string\">\"*\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>)))<\/span><\/code><code><span class=\"code-snippet_outer\">sigVec=<span class=\"code-snippet__built_in\">c<\/span>(sigVec, paste0(clinical, Sig))<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(rt)=sigVec<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5b9a\u4e49\u4e86\u70ed\u56fe\u6ce8\u91ca\u7684\u989c\u8272\u3002\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u4f7f\u7528\u84dd\u8272\u548c\u7ea2\u8272\u8868\u793a\u4f4e\u548c\u9ad8\uff0c\u4e34\u5e8a\u6027\u72b6\u4f7f\u7528\u81ea\u5b9a\u4e49\u7684\u989c\u8272\u5411\u91cf\u8868\u793a\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#rt=rt[apply(rt,1,function(x)any(is.na(match('unknow',x)))),,drop=F]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">bioCol=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"#0066FF\"<\/span>,<span class=\"code-snippet__string\">\"#FF9900\"<\/span>,<span class=\"code-snippet__string\">\"#FF0000\"<\/span>,<span class=\"code-snippet__string\">\"#ed1299\"<\/span>, <span class=\"code-snippet__string\">\"#0dbc21\"<\/span>, <span class=\"code-snippet__string\">\"#246b93\"<\/span>, <span class=\"code-snippet__string\">\"#cc8e12\"<\/span>, <span class=\"code-snippet__string\">\"#d561dd\"<\/span>, <span class=\"code-snippet__string\">\"#c93f00\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#ce2523\"<\/span>, <span class=\"code-snippet__string\">\"#f7aa5d\"<\/span>, <span class=\"code-snippet__string\">\"#9ed84e\"<\/span>, <span class=\"code-snippet__string\">\"#39ba30\"<\/span>, <span class=\"code-snippet__string\">\"#6ad157\"<\/span>, <span class=\"code-snippet__string\">\"#373bbf\"<\/span>, <span class=\"code-snippet__string\">\"#a1ce4c\"<\/span>, <span class=\"code-snippet__string\">\"#ef3bb6\"<\/span>, <span class=\"code-snippet__string\">\"#d66551\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#1a918f\"<\/span>, <span class=\"code-snippet__string\">\"#7149af\"<\/span>, <span class=\"code-snippet__string\">\"#ff66fc\"<\/span>, <span class=\"code-snippet__string\">\"#2927c4\"<\/span>, <span class=\"code-snippet__string\">\"#57e559\"<\/span> ,<span class=\"code-snippet__string\">\"#8e3af4\"<\/span> ,<span class=\"code-snippet__string\">\"#f9a270\"<\/span> ,<span class=\"code-snippet__string\">\"#22547f\"<\/span>, <span class=\"code-snippet__string\">\"#db5e92\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#4aef7b\"<\/span>, <span class=\"code-snippet__string\">\"#e86502\"<\/span>, <span class=\"code-snippet__string\">\"#99db27\"<\/span>, <span class=\"code-snippet__string\">\"#e07233\"<\/span>, <span class=\"code-snippet__string\">\"#8249aa\"<\/span>,<span class=\"code-snippet__string\">\"#cebb10\"<\/span>, <span class=\"code-snippet__string\">\"#03827f\"<\/span>, <span class=\"code-snippet__string\">\"#931635\"<\/span>, <span class=\"code-snippet__string\">\"#ff523f\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#edd05e\"<\/span>, <span class=\"code-snippet__string\">\"#6f25e8\"<\/span>, <span class=\"code-snippet__string\">\"#0dbc21\"<\/span>, <span class=\"code-snippet__string\">\"#167275\"<\/span>, <span class=\"code-snippet__string\">\"#280f7a\"<\/span>, <span class=\"code-snippet__string\">\"#6373ed\"<\/span>, <span class=\"code-snippet__string\">\"#5b910f\"<\/span> ,<span class=\"code-snippet__string\">\"#7b34c1\"<\/span> ,<span class=\"code-snippet__string\">\"#0cf29a\"<\/span> ,<span class=\"code-snippet__string\">\"#d80fc1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#dd27ce\"<\/span>, <span class=\"code-snippet__string\">\"#07a301\"<\/span>, <span class=\"code-snippet__string\">\"#ddd53e\"<\/span>, <span class=\"code-snippet__string\">\"#391c82\"<\/span>, <span class=\"code-snippet__string\">\"#2baeb5\"<\/span>,<span class=\"code-snippet__string\">\"#925bea\"<\/span>, <span class=\"code-snippet__string\">\"#09f9f5\"<\/span>, <span class=\"code-snippet__string\">\"#63ff4f\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">colorList=<span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\">colorList[[gene]]=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Low\"<\/span>=<span class=\"code-snippet__string\">\"blue\"<\/span>, <span class=\"code-snippet__string\">\"High\"<\/span>=<span class=\"code-snippet__string\">\"red\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">j=<span class=\"code-snippet__number\">0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(cli <span class=\"code-snippet__keyword\">in<\/span> colnames(rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)])){<\/span><\/code><code><span class=\"code-snippet_outer\">cliLength=<span class=\"code-snippet__built_in\">length<\/span>(levels(factor(rt[,cli])))<\/span><\/code><code><span class=\"code-snippet_outer\">cliCol=bioCol[(j+<span class=\"code-snippet__number\">1<\/span>):(j+cliLength)]<\/span><\/code><code><span class=\"code-snippet_outer\">j=j+cliLength<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">names<\/span>(cliCol)=levels(factor(rt[,cli]))<\/span><\/code><code><span class=\"code-snippet_outer\">cliCol[<span class=\"code-snippet__string\">\"unknow\"<\/span>]=<span class=\"code-snippet__string\">\"grey75\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">colorList[[cli]]=cliCol<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236\u70ed\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ha=HeatmapAnnotation(df=rt, col=colorList)<\/span><\/code><code><span class=\"code-snippet_outer\">zero_row_mat=matrix(nrow=<span class=\"code-snippet__number\">0<\/span>, ncol=nrow(rt))<\/span><\/code><code><span class=\"code-snippet_outer\">Hm=Heatmap(zero_row_mat, top_annotation=ha)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u521b\u5efaHeatmapAnnotation\u5bf9\u8c61ha\uff0c\u7528\u4e8e\u5b9a\u4e49\u70ed\u56fe\u7684\u6ce8\u91ca\u3002\u7a7a\u7684\u77e9zero_row_mat\u4f5c\u4e3a\u70ed\u56fe\u7684\u4e3b\u4f53\u6570\u636e\u3002\u4f7f\u7528Heatmap()\u51fd\u6570\u521b\u5efa\u70ed\u56fe\u5bf9\u8c61Hm\uff0c\u5c06\u6ce8\u91ca\u5bf9\u8c61ha\u4f5c\u4e3a\u9876\u90e8\u6ce8\u91ca\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u70ed\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=<span class=\"code-snippet__string\">\"heatmap.pdf\"<\/span>, width=<span class=\"code-snippet__number\">7<\/span>, height=<span class=\"code-snippet__number\">5<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">draw(Hm, merge_legend = <span class=\"code-snippet__literal\">TRUE<\/span>, heatmap_legend_side = <span class=\"code-snippet__string\">\"bottom\"<\/span>, annotation_legend_side = <span class=\"code-snippet__string\">\"bottom\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f7f\u7528pdf()\u51fd\u6570\u521b\u5efa\u4e00\u4e2aPDF\u6587\u4ef6\uff0c\u6587\u4ef6\u540d\u4e3a\"heatmap.pdf\"\uff0c\u6307\u5b9a\u5bbd\u5ea6\u548c\u9ad8\u5ea6\u3002\u4f7f\u7528draw()\u51fd\u6570\u5c06\u70ed\u56fe\u5bf9\u8c61Hm\u7ed8\u5236\u5230PDF\u6587\u4ef6\u4e2d\u3002<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\">\u6765\u7ed9\u5927\u5bb6\u5c55\u793a\u5c55\u793a\u7ed3\u679c\u56fe\u5427\uff0c\u4f7f\u7528firefox\u547d\u4ee4\u3002<\/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=\"0.43796296296296294\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_trQq1IbE6DoVn7sYhaq0yM5YtEZ90A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXOC7kNS99NupMQcbQm69DHOEpPWcYGAQ1S4EnN3gBGkfMMtrQq1IbE6DoVn7sYhaq0yM5YtEZ90A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u603b\u4e4b\uff0c\u7efc\u5408\u5206\u6790\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\uff0c\u5e76\u901a\u8fc7\u70ed\u56fe\u5c55\u793a\u5b83\u4eec\u4e4b\u95f4\u7684\u5173\u8054\u3002\u901a\u8fc7\u8fd9\u79cd\u7efc\u5408\u5206\u6790\u548c\u53ef\u89c6\u5316\uff0c\u53ef\u4ee5\u66f4\u5168\u9762\u5730\u7406\u89e3\u57fa\u56e0\u8868\u8fbe\u548c\u4e34\u5e8a\u6027\u72b6\u4e4b\u95f4\u7684\u5173\u7cfb\uff0c\u63ed\u793a\u6f5c\u5728\u7684\u751f\u7269\u5b66\u673a\u5236\u548c\u6307\u5bfc\u8fdb\u4e00\u6b65\u7684\u7814\u7a76\u3002<br \/><\/p>\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\">\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 style=\"white-space: normal;\">\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/p>\n<p style=\"white-space: normal;\">http:\/\/www.biocloudservice.com\/home.html\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 33.33%;align-self: center;flex: 0 0 auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;\" powered-by=\"xiumi.us\">\n<section style=\"border-top: 1px dashed rgb(249, 172, 172);\"><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 style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;margin-right: 20px;margin-left: 20px;\">\n<section style=\"margin-top: -3px;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;color: rgb(246, 207, 63);font-size: 20px;\">\n<p style=\"text-align: center;white-space: normal;\">\u2605<\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 33.3333%;align-self: center;flex: 0 0 auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;\" powered-by=\"xiumi.us\">\n<section style=\"border-top: 1px dashed rgb(249, 172, 172);\"><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<p style=\"margin-bottom: 24px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_akXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ-1.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXjjmsEC5aXz0RE4be2ib1fJPnBD8yX0Z6OF2zocd2ngHpLOakXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"900\" style=\"\" \/><\/p>\n<p style=\"margin-bottom: 24px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3488888888888889\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_orUJ7Wt6jfKhJga1B94BNRow1TXKfA-1.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/oCSOtP61aEXpV0iaewm4NOiaklxrhaox2keStd5BM9n21jcvEovKia3icPZrorUJ7Wt6jfKhJga1B94BNRow1TXKfA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"\" \/><\/p>\n<p style=\"display: none;margin-bottom: 24px;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br 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[…]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/56661"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=56661"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/56661\/revisions"}],"predecessor-version":[{"id":56667,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/56661\/revisions\/56667"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=56661"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=56661"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=56661"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":56661,"date":"2024-06-16T18:13:35","date_gmt":"2024-06-16T10:13:35","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56661"},"modified":"2024-06-16T18:13:35","modified_gmt":"2024-06-16T10:13:35","slug":"%e5%b8%88%e5%a6%b9%e5%b8%a6%e4%bd%a0%e7%bb%98%e5%88%b6%e4%b8%8d%e4%b8%80%e6%a0%b7%e7%9a%84%e4%b8%b4%e5%ba%8a%e7%9b%b8%e5%85%b3%e5%88%86%e6%9e%90%e7%83%ad%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56661","title":{"rendered":"\u5e08\u59b9\u5e26\u4f60\u7ed8\u5236\u4e0d\u4e00\u6837\u7684\u4e34\u5e8a\u76f8\u5173\u5206\u6790\u70ed\u56fe"},"content":{"rendered":"

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1.8em;border-radius: 100%;margin-left: auto;margin-right: auto;font-size: 17px;color: rgb(255, 255, 255);\">\n<p>\u5b57<\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 10%;flex: 0 0 auto;height: auto;align-self: center;\">\n<section style=\"color: rgb(255, 226, 93);font-size: 12px;\" powered-by=\"xiumi.us\">\n<p>\u2605<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 10%;flex: 0 0 auto;height: auto;align-self: center;\">\n<section style=\"font-size: 19px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;border-width: 1px;border-style: solid;border-color: rgb(249, 172, 172);background-color: rgb(249, 172, 172);width: 1.8em;height: 1.8em;line-height: 1.8em;border-radius: 100%;margin-left: auto;margin-right: auto;font-size: 17px;color: rgb(255, 255, 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2em;\">\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\u751f\u6210\u70ed\u56fe\uff0c\u5e76\u53ef\u89c6\u5316\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u548c\u4e34\u5e8a\u6027\u72b6\u4e4b\u95f4\u7684\u5173\u8054\u3002\u5176\u4e3b\u8981\u610f\u4e49\u5982\u4e0b\uff1a<\/span><br \/><\/p>\n<p style=\"text-indent: 0em;white-space: normal;\"><strong>\u6570\u636e\u6574\u5408\uff1a<\/strong>\u4ee3\u7801\u5c06\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\u8fdb\u884c\u6574\u5408\uff0c\u4ee5\u4fbf\u5728\u540e\u7eed\u5206\u6790\u4e2d\u540c\u65f6\u8003\u8651\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u548c\u4e34\u5e8a\u6027\u72b6\u3002<\/p>\n<section><br \/><\/section>\n<p style=\"text-indent: 0em;white-space: normal;\"><strong>\u5206\u7ec4\u548c\u6392\u5e8f\uff1a<\/strong>\u6839\u636e\u76ee\u6807\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\uff0c\u5c06\u6837\u672c\u5206\u4e3a\u9ad8\u8868\u8fbe\u7ec4\u548c\u4f4e\u8868\u8fbe\u7ec4\uff0c\u5e76\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u5bf9\u6837\u672c\u8fdb\u884c\u6392\u5e8f\uff0c\u4ee5\u4fbf\u540e\u7eed\u53ef\u89c6\u5316\u65f6\u80fd\u591f\u5448\u73b0\u57fa\u56e0\u8868\u8fbe\u7684\u6a21\u5f0f\u3002\u7edf\u8ba1\u5206\u6790\uff1a\u4ee3\u7801\u4f7f\u7528\u5361\u65b9\u68c0\u9a8c\uff08chisq.test\uff09\u6765\u8bc4\u4f30\u4e34\u5e8a\u6027\u72b6\u4e0e\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u4e4b\u95f4\u7684\u5173\u8054\u6027\uff0c\u5e76\u6839\u636e\u68c0\u9a8c\u7ed3\u679c\u7ed9\u51fa\u663e\u8457\u6027\u6807\u8bb0\u3002\u8fd9\u6709\u52a9\u4e8e\u7814\u7a76\u4eba\u5458\u8bc6\u522b\u54ea\u4e9b\u4e34\u5e8a\u6027\u72b6\u4e0e\u57fa\u56e0\u8868\u8fbe\u5b58\u5728\u663e\u8457\u5173\u8054\u3002<\/p>\n<p style=\"text-indent: 0em;white-space: normal;\"><br \/><\/p>\n<p style=\"text-indent: 0em;white-space: normal;\"><strong>\u70ed\u56fe\u7ed8\u5236\uff1a<\/strong>\u4ee3\u7801\u4f7f\u7528ComplexHeatmap\u5305\u7ed8\u5236\u70ed\u56fe\uff0c\u5c06\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6027\u72b6\u7684\u5173\u8054\u53ef\u89c6\u5316\u3002\u70ed\u56fe\u4e2d\uff0c\u884c\u8868\u793a\u6837\u672c\uff0c\u5217\u8868\u793a\u57fa\u56e0\u548c\u4e34\u5e8a\u6027\u72b6\uff0c\u989c\u8272\u8868\u793a\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u548c\u4e34\u5e8a\u6027\u72b6\u7684\u4e0d\u540c\u7c7b\u522b\u3002\u7ed3\u679c\u5c55\u793a\uff1a\u6700\u7ec8\u751f\u6210\u7684\u70ed\u56fe\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u76f4\u89c2\u5730\u4e86\u89e3\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u548c\u4e34\u5e8a\u6027\u72b6\u4e4b\u95f4\u7684\u5173\u7cfb\u3002\u70ed\u56fe\u4e2d\u7684\u6a21\u5f0f\u548c\u989c\u8272\u7f16\u7801\u53ef\u4ee5\u63ed\u793a\u57fa\u56e0\u8868\u8fbe\u7684\u5dee\u5f02\u4ee5\u53ca\u57fa\u56e0\u4e0e\u4e34\u5e8a\u6027\u72b6\u4e4b\u95f4\u7684\u76f8\u5173\u6027\u3002<\/p>\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=\"1.2702702702702702\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_bXMiaoriaMXAv3dMVUIcgJ6IbldwgA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXOC7kNS99NupMQcbQm69DHnWOo3CRmqg6a7YPR8tVOada3vqbXMiaoriaMXAv3dMVUIcgJ6IbldwgA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"629\" style=\"vertical-align: middle;width: 100%;\" \/><\/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\">#if (!requireNamespace(\"BiocManager\", quietly = TRUE))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># install.packages(\"BiocManager\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"ComplexHeatmap\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"limma\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5f15\u7528\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ComplexHeatmap)<\/span><\/code><code><span class=\"code-snippet_outer\">expFile=<span class=\"code-snippet__string\">\"geneExp.txt\"<\/span> <span class=\"code-snippet__comment\">#\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cliFile=<span class=\"code-snippet__string\">\"clinical.txt\"<\/span> <span class=\"code-snippet__comment\">#\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">setwd(<span class=\"code-snippet__string\">\"C:\\biowolf\\Gene\\14.cliHeatmap\"<\/span>) <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u5de5\u4f5c\u76ee\u5f55<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u901a\u8fc7library()\u51fd\u6570\u5f15\u7528\u4e86limma\u548cComplexHeatmap\u4e24\u4e2a\u5305\u3002\u6307\u5b9a\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u8def\u5f84expFile\u548c\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\u8def\u5f84cliFile\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f7f\u7528setwd()\u51fd\u6570\u8bbe\u7f6e\u5de5\u4f5c\u76ee\u5f55\u4e3a\"C:\\biowolf\\Gene\\14.cliHeatmap\"\u3002\u901a\u8fc7read.table()\u51fd\u6570\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u548c\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\u3002\u63d0\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u4e2d\u7684\u57fa\u56e0\u540d\u79f0\u548c\u7b2c\u4e00\u4e2a\u57fa\u56e0\u7684\u5217\u6570\u636e\u3002\u5220\u9664\u6b63\u5e38\u6837\u672c\uff0c\u53ea\u4fdd\u7559\u80bf\u7624\u6837\u672c\u7684\u6570\u636e\uff0c\u5e76\u5bf9\u91cd\u590d\u6837\u672c\u6c42\u5747\u503c\u3002\u6839\u636e\u76ee\u6807\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\u5c06\u6837\u672c\u8fdb\u884c\u5206\u7ec4\uff0c\u5e76\u5728\u6570\u636e\u6846\u4e2d\u6dfb\u52a0\u4e00\u4e2a\u540d\u4e3a\"Type\"\u7684\u5217\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=read.table(expFile, 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\">gene=colnames(rt)[<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5220\u6389\u6b63\u5e38\u6837\u54c1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tumorData=rt[rt$Type==<span class=\"code-snippet__string\">\"Tumor\"<\/span>,<span class=\"code-snippet__number\">1<\/span>,drop=<span class=\"code-snippet__built_in\">F<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">tumorData=as.matrix(tumorData)<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(tumorData)=gsub(<span class=\"code-snippet__string\">\"(.*?)\\-(.*?)\\-(.*?)\\-(.*?)\\-.*\"<\/span>, <span class=\"code-snippet__string\">\"\\1\\-\\2\\-\\3\"<\/span>, rownames(tumorData))<\/span><\/code><code><span class=\"code-snippet_outer\">data=avereps(tumorData)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6839\u636e\u76ee\u6807\u57fa\u56e0\u8868\u8fbe\u91cf\u5bf9\u6837\u54c1\u8fdb\u884c\u5206\u7ec4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Type=ifelse(data[,gene]>median(data[,gene]), <span class=\"code-snippet__string\">\"High\"<\/span>, <span class=\"code-snippet__string\">\"Low\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">Type=factor(Type, levels=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Low\"<\/span>,<span class=\"code-snippet__string\">\"High\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">data=cbind(as.data.frame(data), Type)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[order(data[,gene]),]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\uff0c\u5e76\u5bf9\u5176\u4e2d\u7684\"Age\"\u5217\u8fdb\u884c\u5206\u7c7b\uff0c\u6839\u636e\u5e74\u9f84\u5206\u4e3a\">65\"\u548c\"<=65\"\u4e24\u7ec4\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cli=read.table(cliFile, 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\">cli[,<span class=\"code-snippet__string\">\"Age\"<\/span>]=ifelse(cli[,<span class=\"code-snippet__string\">\"Age\"<\/span>]==<span class=\"code-snippet__string\">\"unknow\"<\/span>, <span class=\"code-snippet__string\">\"unknow\"<\/span>, ifelse(cli[,<span class=\"code-snippet__string\">\"Age\"<\/span>]><span class=\"code-snippet__number\">65<\/span>,<span class=\"code-snippet__string\">\">65\"<\/span>,<span class=\"code-snippet__string\">\"<=65\"<\/span>))<\/span><\/code><\/pre>\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=\"1.3006535947712419\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ot26CqrtaxgaWdOlwyD770wic6haoQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXOC7kNS99NupMQcbQm69DH6Ar5w0dN1CrFdzhdvVsEbsRJFot26CqrtaxgaWdOlwyD770wic6haoQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"612\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u5bf9\u4e34\u5e8a\u6027\u72b6\u8fdb\u884c\u5faa\u73af\uff0c\u5bf9\u6bcf\u4e2a\u4e34\u5e8a\u6027\u72b6\u4e0e\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u4e4b\u95f4\u7684\u5173\u8054\u8fdb\u884c\u5361\u65b9\u68c0\u9a8c\uff0c\u5f97\u5230\u663e\u8457\u6027\u6807\u8bb0\u3002\u5c06\u663e\u8457\u6027\u6807\u8bb0\u6dfb\u52a0\u5230\u70ed\u56fe\u6570\u636e\u6846rt\u7684\u5217\u540d\u4e2d\u3002<\/p>\n<p style=\"white-space: normal;\"><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<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<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\">#\u5408\u5e76\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">samSample=intersect(row.names(data), row.names(cli))<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[samSample,<span class=\"code-snippet__string\">\"Type\"<\/span>,drop=<span class=\"code-snippet__built_in\">F<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">cli=cli[samSample,,drop=<span class=\"code-snippet__built_in\">F<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">rt=cbind(data, cli)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bf9\u4e34\u5e8a\u6027\u72b6\u8fdb\u884c\u5faa\u73af\uff0c\u89c2\u5bdf\u4e34\u5e8a\u6027\u72b6\u5728\u9ad8\u4f4e\u8868\u8fbe\u7ec4\u4e4b\u95f4\u662f\u5426\u5177\u6709\u5dee\u5f02\uff0c\u5f97\u5230\u663e\u8457\u6027\u6807\u8bb0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sigVec=<span class=\"code-snippet__built_in\">c<\/span>(gene)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(clinical <span class=\"code-snippet__keyword\">in<\/span> colnames(rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)])){<\/span><\/code><code><span class=\"code-snippet_outer\">data=rt[<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Type\"<\/span>, clinical)]<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(data)=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Type\"<\/span>, <span class=\"code-snippet__string\">\"clinical\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[(data[,<span class=\"code-snippet__string\">\"clinical\"<\/span>]!=<span class=\"code-snippet__string\">\"unknow\"<\/span>),]<\/span><\/code><code><span class=\"code-snippet_outer\">tableStat=table(data)<\/span><\/code><code><span class=\"code-snippet_outer\">stat=chisq.test(tableStat)<\/span><\/code><code><span class=\"code-snippet_outer\">pvalue=stat$p.value<\/span><\/code><code><span class=\"code-snippet_outer\">Sig=ifelse(pvalue<<span class=\"code-snippet__number\">0.001<\/span>,<span class=\"code-snippet__string\">\"***\"<\/span>,ifelse(pvalue<<span class=\"code-snippet__number\">0.01<\/span>,<span class=\"code-snippet__string\">\"**\"<\/span>,ifelse(pvalue<<span class=\"code-snippet__number\">0.05<\/span>,<span class=\"code-snippet__string\">\"*\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>)))<\/span><\/code><code><span class=\"code-snippet_outer\">sigVec=<span class=\"code-snippet__built_in\">c<\/span>(sigVec, paste0(clinical, Sig))<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(rt)=sigVec<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5b9a\u4e49\u4e86\u70ed\u56fe\u6ce8\u91ca\u7684\u989c\u8272\u3002\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u4f7f\u7528\u84dd\u8272\u548c\u7ea2\u8272\u8868\u793a\u4f4e\u548c\u9ad8\uff0c\u4e34\u5e8a\u6027\u72b6\u4f7f\u7528\u81ea\u5b9a\u4e49\u7684\u989c\u8272\u5411\u91cf\u8868\u793a\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#rt=rt[apply(rt,1,function(x)any(is.na(match('unknow',x)))),,drop=F]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">bioCol=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"#0066FF\"<\/span>,<span class=\"code-snippet__string\">\"#FF9900\"<\/span>,<span class=\"code-snippet__string\">\"#FF0000\"<\/span>,<span class=\"code-snippet__string\">\"#ed1299\"<\/span>, <span class=\"code-snippet__string\">\"#0dbc21\"<\/span>, <span class=\"code-snippet__string\">\"#246b93\"<\/span>, <span class=\"code-snippet__string\">\"#cc8e12\"<\/span>, <span class=\"code-snippet__string\">\"#d561dd\"<\/span>, <span class=\"code-snippet__string\">\"#c93f00\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#ce2523\"<\/span>, <span class=\"code-snippet__string\">\"#f7aa5d\"<\/span>, <span class=\"code-snippet__string\">\"#9ed84e\"<\/span>, <span class=\"code-snippet__string\">\"#39ba30\"<\/span>, <span class=\"code-snippet__string\">\"#6ad157\"<\/span>, <span class=\"code-snippet__string\">\"#373bbf\"<\/span>, <span class=\"code-snippet__string\">\"#a1ce4c\"<\/span>, <span class=\"code-snippet__string\">\"#ef3bb6\"<\/span>, <span class=\"code-snippet__string\">\"#d66551\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#1a918f\"<\/span>, <span class=\"code-snippet__string\">\"#7149af\"<\/span>, <span class=\"code-snippet__string\">\"#ff66fc\"<\/span>, <span class=\"code-snippet__string\">\"#2927c4\"<\/span>, <span class=\"code-snippet__string\">\"#57e559\"<\/span> ,<span class=\"code-snippet__string\">\"#8e3af4\"<\/span> ,<span class=\"code-snippet__string\">\"#f9a270\"<\/span> ,<span class=\"code-snippet__string\">\"#22547f\"<\/span>, <span class=\"code-snippet__string\">\"#db5e92\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#4aef7b\"<\/span>, <span class=\"code-snippet__string\">\"#e86502\"<\/span>, <span class=\"code-snippet__string\">\"#99db27\"<\/span>, <span class=\"code-snippet__string\">\"#e07233\"<\/span>, <span class=\"code-snippet__string\">\"#8249aa\"<\/span>,<span class=\"code-snippet__string\">\"#cebb10\"<\/span>, <span class=\"code-snippet__string\">\"#03827f\"<\/span>, <span class=\"code-snippet__string\">\"#931635\"<\/span>, <span class=\"code-snippet__string\">\"#ff523f\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#edd05e\"<\/span>, <span class=\"code-snippet__string\">\"#6f25e8\"<\/span>, <span class=\"code-snippet__string\">\"#0dbc21\"<\/span>, <span class=\"code-snippet__string\">\"#167275\"<\/span>, <span class=\"code-snippet__string\">\"#280f7a\"<\/span>, <span class=\"code-snippet__string\">\"#6373ed\"<\/span>, <span class=\"code-snippet__string\">\"#5b910f\"<\/span> ,<span class=\"code-snippet__string\">\"#7b34c1\"<\/span> ,<span class=\"code-snippet__string\">\"#0cf29a\"<\/span> ,<span class=\"code-snippet__string\">\"#d80fc1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"#dd27ce\"<\/span>, <span class=\"code-snippet__string\">\"#07a301\"<\/span>, <span class=\"code-snippet__string\">\"#ddd53e\"<\/span>, <span class=\"code-snippet__string\">\"#391c82\"<\/span>, <span class=\"code-snippet__string\">\"#2baeb5\"<\/span>,<span class=\"code-snippet__string\">\"#925bea\"<\/span>, <span class=\"code-snippet__string\">\"#09f9f5\"<\/span>, <span class=\"code-snippet__string\">\"#63ff4f\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">colorList=<span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\">colorList[[gene]]=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Low\"<\/span>=<span class=\"code-snippet__string\">\"blue\"<\/span>, <span class=\"code-snippet__string\">\"High\"<\/span>=<span class=\"code-snippet__string\">\"red\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">j=<span class=\"code-snippet__number\">0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(cli <span class=\"code-snippet__keyword\">in<\/span> colnames(rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)])){<\/span><\/code><code><span class=\"code-snippet_outer\">cliLength=<span class=\"code-snippet__built_in\">length<\/span>(levels(factor(rt[,cli])))<\/span><\/code><code><span class=\"code-snippet_outer\">cliCol=bioCol[(j+<span class=\"code-snippet__number\">1<\/span>):(j+cliLength)]<\/span><\/code><code><span class=\"code-snippet_outer\">j=j+cliLength<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">names<\/span>(cliCol)=levels(factor(rt[,cli]))<\/span><\/code><code><span class=\"code-snippet_outer\">cliCol[<span class=\"code-snippet__string\">\"unknow\"<\/span>]=<span class=\"code-snippet__string\">\"grey75\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">colorList[[cli]]=cliCol<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236\u70ed\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ha=HeatmapAnnotation(df=rt, col=colorList)<\/span><\/code><code><span class=\"code-snippet_outer\">zero_row_mat=matrix(nrow=<span class=\"code-snippet__number\">0<\/span>, ncol=nrow(rt))<\/span><\/code><code><span class=\"code-snippet_outer\">Hm=Heatmap(zero_row_mat, top_annotation=ha)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u521b\u5efaHeatmapAnnotation\u5bf9\u8c61ha\uff0c\u7528\u4e8e\u5b9a\u4e49\u70ed\u56fe\u7684\u6ce8\u91ca\u3002\u7a7a\u7684\u77e9zero_row_mat\u4f5c\u4e3a\u70ed\u56fe\u7684\u4e3b\u4f53\u6570\u636e\u3002\u4f7f\u7528Heatmap()\u51fd\u6570\u521b\u5efa\u70ed\u56fe\u5bf9\u8c61Hm\uff0c\u5c06\u6ce8\u91ca\u5bf9\u8c61ha\u4f5c\u4e3a\u9876\u90e8\u6ce8\u91ca\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u70ed\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=<span class=\"code-snippet__string\">\"heatmap.pdf\"<\/span>, width=<span class=\"code-snippet__number\">7<\/span>, height=<span class=\"code-snippet__number\">5<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">draw(Hm, merge_legend = <span class=\"code-snippet__literal\">TRUE<\/span>, heatmap_legend_side = <span class=\"code-snippet__string\">\"bottom\"<\/span>, annotation_legend_side = <span class=\"code-snippet__string\">\"bottom\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f7f\u7528pdf()\u51fd\u6570\u521b\u5efa\u4e00\u4e2aPDF\u6587\u4ef6\uff0c\u6587\u4ef6\u540d\u4e3a\"heatmap.pdf\"\uff0c\u6307\u5b9a\u5bbd\u5ea6\u548c\u9ad8\u5ea6\u3002\u4f7f\u7528draw()\u51fd\u6570\u5c06\u70ed\u56fe\u5bf9\u8c61Hm\u7ed8\u5236\u5230PDF\u6587\u4ef6\u4e2d\u3002<\/span><\/span><\/code><\/pre>\n<\/section>\n<p 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