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data-type=\"jpeg\" data-w=\"1080\" style=\"\"><\/p>\n <\/p>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n\u4e00\u81f4\u6cd5\u65e0\u76d1\u7763\u805a\u7c7b\u5e7f\u6cdb\u5e94\u7528\u4e8e\u764c\u75c7\u5206\u5b50\u4e9a\u578b\u5206\u578b\u4e2d\uff0c\u6211\u4eec\u5728\u67e5\u770b\u6587\u732e\u8fd9\u90e8\u5206\u5206\u6790\u4e2d\u7ecf\u5e38\u770b\u5230\u4ee5\u4e0b\u51e0\u4e2a\u56fe<\/p>\n <\/p>\nTracking plot \uff0c\u53ef\u4ee5\u770b\u5230\u4e0d\u540cK\u4e4b\u4e0b\u5404\u4e2a\u6837\u672c\u7684\u4e9a\u578b\u5206\u7ec4\u60c5\u51b5\uff0c\u5982\u679c\u8be5\u6837\u672c\u5728\u4e0d\u540c\u7684k\u503c\u4e0b\u4e9a\u578b\u5206\u7ec4\u4e0d\u53d8\uff0c\u5c31\u8bf4\u660e\u8be5\u6837\u672c\u6bd4\u8f83\u7a33\u5b9a\uff0c\u53cd\u4e4b\u5219\u4e0d\u7a33\u5b9a\uff0c\u5982\u679c\u4e00\u79cd\u4e9a\u578b\u542b\u6709\u5f88\u591a\u4e0d\u7a33\u5b9a\u6837\u672c\uff0c\u5219\u8bf4\u660e\u8be5\u4e9a\u578b\u4e0d\u7a33\u5b9a\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9755201958384333\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/2_bRwszMSC5Tt11y3V1JPibB5CibYfsw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCL2fXj9HOzXHmldficibUPrGJKjX0MibRwszMSC5Tt11y3V1JPibB5CibYfsw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"817\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\"><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n\u5c0f\u679c\u4e4b\u524d\u7ed9\u5927\u5bb6\u5206\u4eab\u8fc7\u591a\u7bc7\u53cc\u75be\u75c5\u7684\u7814\u7a76\u601d\u8def\u6587\u7ae0<\/p>\n <\/p>\nDelta 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auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.003680981595092\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/3_1TzngmlNj3ZpXARFgvgSbpJVxliahw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCLyibC3VvFB2rRdOqpGzB6RxgaEU1TzngmlNj3ZpXARFgvgSbpJVxliahw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"815\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\"><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\nCDF\u56fe\uff0c\u5c55\u793a\u5404\u4e2aK\u503c\u4e0b\u7684\u66f2\u7ebf\u4e0b\u9762\u79ef<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.915702479338843\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/4_WADmeGmNNJ6KRy33UNZiabUUobx3AA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCLMpGUyuCv6PGmNqlZfQeFgjCBWWADmeGmNNJ6KRy33UNZiabUUobx3AA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"605\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n\u4e00\u81f4\u6027\u77e9\u9635\u70ed\u56fe\uff0c\u805a\u7c7b\u6548\u679c\u597d\u7684\u8bdd\uff0c\u4e0b\u56fe\u4e2d\u7684\u84dd\u8272\u548c\u767d\u8272\u4e5f\u5c31\u662f\u77e9\u9635\u5bf9\u5e94\u76840\u548c1\u4f1a\u5206\u5272\u7684\u5f88\u6e05\u695a\uff0c\u770b\u8d77\u6765\u6bd4\u8f83\u5e72\u51c0\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0045180722891567\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/5_Im9MAtrcPHD9KclDHPXib4NgshH0HA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCL9bt0Xia7Z2mN8VOSDcBibLzib0FeIm9MAtrcPHD9KclDHPXib4NgshH0HA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"664\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\"><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"white-space: normal;box-sizing: border-box;font-size: 16px;\" powered-by=\"xiumi.us\">\n\u4e0b\u9762\u5c0f\u679c\u5c31\u628a\u5bf9\u5e94\u7684\u4ee3\u7801\u8d34\u51fa\u6765<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index 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class=\"code-snippet__js\" data-lang=\"sql\"><code>rm(list=ls());gc();<\/span><\/code><code>BiocManager::install<\/span>(\"ConsensusClusterPlus\"<\/span>)<\/span><\/code><code>#\u51c6\u5907\u8f93\u5165\u6570\u636e<\/span><\/span><\/code><code>library<\/span>(data.table)<\/span><\/code><code> <\/span><\/code><code>express<-fread(\"express.CSV\"<\/span>)<\/span><\/code><code>express<-as.data.frame(express)<\/span><\/code><code>rownames(express)<-express[,1<\/span>]<\/span><\/code><code>express<-express[,-1<\/span>]<\/span><\/code><code>class<\/span>(express)<\/span><\/code><code>colname<-colnames(express)#\u4fdd\u5b58\u884c\u540d<\/span><\/span><\/code><code>rowname<-rownames(express)#\u4fdd\u5b58\u5217\u540d<\/span><\/span><\/code><code>express<-as.data.frame(lapply(express,as.numeric))#\u6570\u636e\u6846\u8f6c\u6362\u4e3a\u6570\u503c\u578b<\/span><\/span><\/code><code>colnames(express)<-colname<\/span><\/code><code>rownames(express)<-rowname<\/span><\/code><code>#\u5f52\u4e00\u5316<\/span><\/span><\/code><code>express = sweep(express,1<\/span>, apply<\/span>(express,1<\/span>,median<\/span>,na.rm=T))<\/span><\/code><code>express<-as.matrix(express)<\/span><\/code><code> <\/span><\/code><code>#\u8fd0\u884cConsensusClusterPlus<\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>library<\/span>(ConsensusClusterPlus)<\/span><\/code><code>title=\"untitled_consensus_cluster\"<\/span><\/span><\/code><code>results = ConsensusClusterPlus(express,maxK=10<\/span>,reps=1000<\/span>,pItem=0.8<\/span>,pFeature=1<\/span>, <\/span><\/code><code> title=title,clusterAlg=\"hc\"<\/span>,distance=\"pearson\"<\/span>,<\/span><\/code><code> seed<\/span>=1262118388.71279<\/span>,plot=\"pdf\"<\/span>, writeTable = TRUE<\/span>)<\/span><\/code><code> <\/span><\/code><code>#1. pItem, \u9009\u62e980%\u7684\u6837\u672c\u8fdb\u884c\u91cd\u590d\u62bd\u6837<\/span><\/span><\/code><code> <\/span><\/code><code>#2. pfeature, \u9009\u62e980%\u7684\u57fa\u56e0\u8fdb\u884c\u91cd\u590d\u62bd\u6837<\/span><\/span><\/code><code> <\/span><\/code><code>#3. maxK, \u6700\u5927\u7684K\u503c\uff0c\u5f62\u6210\u4e00\u7cfb\u5217\u68af\u5ea6<\/span><\/span><\/code><code> <\/span><\/code><code>#4. reps, \u91cd\u590d\u62bd\u6837\u7684\u6570\u76ee<\/span><\/span><\/code><code> <\/span><\/code><code>#5. clusterAlg, \u5c42\u6b21\u805a\u7c7b\u7684\u7b97\u6cd5<\/span><\/span><\/code><code> <\/span><\/code><code>#6. distanc, \u8ddd\u79bb\u77e9\u9635\u7684\u7b97\u6cd5<\/span><\/span><\/code><code> <\/span><\/code><code>#7. title, \u8f93\u51fa\u7ed3\u679c\u7684\u6587\u4ef6\u5939\u540d\u5b57\uff0c\u5305\u542b\u4e86\u8f93\u51fa\u7684\u56fe\u7247<\/span><\/span><\/code><code> <\/span><\/code><code>#8. seed, \u968f\u673a\u79cd\u5b50\uff0c\u7528\u4e8e\u91cd\u590d\u7ed3\u679c<\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>str<\/span>(results[[2<\/span>]])<\/span><\/code><code> <\/span><\/code><code># \u4e00\u81f4\u6027\u77e9\u9635\uff0c\u6837\u672c\u7684\u90bb\u63a5\u77e9\u9635<\/span><\/span><\/code><code>dim(d)<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>dim(results[[2<\/span>]][[\"consensusMatrix\"<\/span>]])<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>results[[2<\/span>]][[\"consensusMatrix\"<\/span>]][1<\/span>:5<\/span>,1<\/span>:5<\/span>]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code># \u6837\u672c\u7684\u805a\u7c7b\u6811<\/span><\/span><\/code><code>results[[2<\/span>]][[\"consensusTree\"<\/span>]]<\/span><\/code><code> <\/span><\/code><code># ml, \u5c31\u662fconsensusMatrix<\/span><\/span><\/code><code>results[[2<\/span>]][[\"ml\"<\/span>]][1<\/span>:5<\/span>,1<\/span>:5<\/span>]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>results[[2<\/span>]][[\"consensusMatrix\"<\/span>]][1<\/span>:5<\/span>,1<\/span>:5<\/span>]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code># clrs, \u989c\u8272<\/span><\/span><\/code><code>results[[2<\/span>]][[\"clrs\"<\/span>]]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>#\u6536\u96c6cluster-consensus\u548citem-consensus \u77e9\u9635<\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>icl = calcICL(results,title=title,plot=\"pdf\"<\/span>,writeTable=TRUE<\/span>)<\/span><\/code><code>icl[[\"clusterConsensus\"<\/span>]]<\/span><\/code><code> <\/span><\/code><code>dim(icl[[\"itemConsensus\"<\/span>]])<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>icl[[\"itemConsensus\"<\/span>]][1<\/span>:5<\/span>,]<\/span><\/code><\/pre>\n<\/section>\n <\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u81f3\u6b64\uff0c\u7ed3\u675f<\/p>\n <\/p>\n\u5173\u6ce8\u5c0f\u679c\uff0c\u5c0f\u679c\u5c06\u4f1a\u6301\u7eed\u4e3a\u4f60\u5e26\u6765\u66f4\u591a\u751f\u4fe1\u5e72\u8d27\u54e6\u3002<\/p>\n<section><mp-common-profile class=\"js_uneditable custom_select_card mp_profile_iframe\" data-pluginname=\"mpprofile\" data-weui-theme=\"light\" data-id=\"Mzg3OTg3MjQyNg==\" data-headimg=\"http:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAwvyLLXlYq0SJu55voD1bnb7juHUdkAibE5woL3FrUvV4nmfhXjL5DgcNYqYFsyFCZrof6ibA2ibPmuw\/0?wx_fmt=png\" data-nickname=\"\u751f\u4fe1\u679c\" data-alias=\"shengxinguoer\" data-signature=\"\u751f\u4fe1\u5165\u95e8\u3001R\u8bed\u8a00\u3001\u751f\u4fe1\u56fe\u89e3\u8bfb\u4e0e\u7ed8\u5236\u3001\u8f6f\u4ef6\u64cd\u4f5c\u3001\u4ee3\u7801\u590d\u73b0\u3001\u751f\u4fe1\u786c\u6838\u77e5\u8bc6\u6280\u80fd\u3001\u670d\u52a1\u5668\u7b49\" data-from=\"0\" data-is_biz_ban=\"0\"><\/mp-common-profile><\/section>\n <\/p>\n<\/section>\n<\/section>\n<mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<\/content>\n<\/div>\n<\/body> \n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b \u539f\u521b \u5c0f\u679c &nb […]<\/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\/48677"}],"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=48677"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48677\/revisions"}],"predecessor-version":[{"id":48679,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48677\/revisions\/48679"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=48677"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=48677"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=48677"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":48677,"date":"2024-06-15T20:08:15","date_gmt":"2024-06-15T12:08:15","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48677"},"modified":"2024-06-15T20:08:15","modified_gmt":"2024-06-15T12:08:15","slug":"r%e8%af%ad%e8%a8%80consensusclusterplus%e5%8c%85%e6%97%a0%e7%9b%91%e7%9d%a3%e8%81%9a%e7%b1%bb-3","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48677","title":{"rendered":"R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b"},"content":{"rendered":"

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href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2710852131288875010#wechat_redirect\" title=\"r\u8bed\u8a00\" target=\"_blank\" rel=\"noopener\">#r\u8bed\u8a00<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2655932655410184193#wechat_redirect\" title=\"\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#\u4ee3\u7801<\/a><\/p>\n<\/div>\n<section style=\"box-sizing: border-box;font-size: 16px;\" data-mpa-powered-by=\"yiban.io\">\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.18518518518518517\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/1_qsloKfZGRth6ibO0NdBBDBJoo74Dsg.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAyutn1WKcQhrNecLmL3uYCLmJ1P8879ib8OJtHJBWJywnB3RiaqsloKfZGRth6ibO0NdBBDBJoo74Dsg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"\"><\/p>\n <\/p>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n\u4e00\u81f4\u6cd5\u65e0\u76d1\u7763\u805a\u7c7b\u5e7f\u6cdb\u5e94\u7528\u4e8e\u764c\u75c7\u5206\u5b50\u4e9a\u578b\u5206\u578b\u4e2d\uff0c\u6211\u4eec\u5728\u67e5\u770b\u6587\u732e\u8fd9\u90e8\u5206\u5206\u6790\u4e2d\u7ecf\u5e38\u770b\u5230\u4ee5\u4e0b\u51e0\u4e2a\u56fe<\/p>\n <\/p>\nTracking plot \uff0c\u53ef\u4ee5\u770b\u5230\u4e0d\u540cK\u4e4b\u4e0b\u5404\u4e2a\u6837\u672c\u7684\u4e9a\u578b\u5206\u7ec4\u60c5\u51b5\uff0c\u5982\u679c\u8be5\u6837\u672c\u5728\u4e0d\u540c\u7684k\u503c\u4e0b\u4e9a\u578b\u5206\u7ec4\u4e0d\u53d8\uff0c\u5c31\u8bf4\u660e\u8be5\u6837\u672c\u6bd4\u8f83\u7a33\u5b9a\uff0c\u53cd\u4e4b\u5219\u4e0d\u7a33\u5b9a\uff0c\u5982\u679c\u4e00\u79cd\u4e9a\u578b\u542b\u6709\u5f88\u591a\u4e0d\u7a33\u5b9a\u6837\u672c\uff0c\u5219\u8bf4\u660e\u8be5\u4e9a\u578b\u4e0d\u7a33\u5b9a\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9755201958384333\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/2_bRwszMSC5Tt11y3V1JPibB5CibYfsw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCL2fXj9HOzXHmldficibUPrGJKjX0MibRwszMSC5Tt11y3V1JPibB5CibYfsw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"817\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\"><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n\u5c0f\u679c\u4e4b\u524d\u7ed9\u5927\u5bb6\u5206\u4eab\u8fc7\u591a\u7bc7\u53cc\u75be\u75c5\u7684\u7814\u7a76\u601d\u8def\u6587\u7ae0<\/p>\n <\/p>\nDelta area\uff0c\u6839\u636e\u6b64\u56fe\u6211\u4eec\u53ef\u4ee5\u4f9d\u636e\u62d0\u70b9\u6cd5\u5224\u65ad\u6700\u4f73\u5206\u7ec4\uff0c\u62d0\u70b9\u540e\u968f\u7740\u805a\u7c7b\u6570\u7684\u589e\u52a0\uff0c\u635f\u5931\u51fd\u6570\u7684\u6536\u76ca\u8d8a\u6765\u8d8a\u5c0f\uff0c\u56e0\u6b64\u901a\u5e38\u9009\u62e9\u62d0\u70b9\u4f5c\u4e3a\u6700\u4f73K\u503c\uff0c\u8fd9\u79cd\u65b9\u6cd5\u4e5f\u88ab\u5f62\u8c61\u7684\u79f0\u4e3a\u624b\u8098\u6cd5\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.003680981595092\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/3_1TzngmlNj3ZpXARFgvgSbpJVxliahw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCLyibC3VvFB2rRdOqpGzB6RxgaEU1TzngmlNj3ZpXARFgvgSbpJVxliahw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"815\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\"><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\nCDF\u56fe\uff0c\u5c55\u793a\u5404\u4e2aK\u503c\u4e0b\u7684\u66f2\u7ebf\u4e0b\u9762\u79ef<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.915702479338843\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/4_WADmeGmNNJ6KRy33UNZiabUUobx3AA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCLMpGUyuCv6PGmNqlZfQeFgjCBWWADmeGmNNJ6KRy33UNZiabUUobx3AA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"605\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"color: rgb(0, 0, 0);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n\u4e00\u81f4\u6027\u77e9\u9635\u70ed\u56fe\uff0c\u805a\u7c7b\u6548\u679c\u597d\u7684\u8bdd\uff0c\u4e0b\u56fe\u4e2d\u7684\u84dd\u8272\u548c\u767d\u8272\u4e5f\u5c31\u662f\u77e9\u9635\u5bf9\u5e94\u76840\u548c1\u4f1a\u5206\u5272\u7684\u5f88\u6e05\u695a\uff0c\u770b\u8d77\u6765\u6bd4\u8f83\u5e72\u51c0\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0045180722891567\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2022-12-17_R\u8bed\u8a00ConsensusClusterPlus\u5305\u65e0\u76d1\u7763\u805a\u7c7b\/5_Im9MAtrcPHD9KclDHPXib4NgshH0HA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyutn1WKcQhrNecLmL3uYCL9bt0Xia7Z2mN8VOSDcBibLzib0FeIm9MAtrcPHD9KclDHPXib4NgshH0HA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"664\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\"><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"> <\/section>\n<\/section>\n<section style=\"white-space: normal;box-sizing: border-box;font-size: 16px;\" powered-by=\"xiumi.us\">\n\u4e0b\u9762\u5c0f\u679c\u5c31\u628a\u5bf9\u5e94\u7684\u4ee3\u7801\u8d34\u51fa\u6765<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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<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=\"sql\"><code>rm(list=ls());gc();<\/span><\/code><code>BiocManager::install<\/span>(\"ConsensusClusterPlus\"<\/span>)<\/span><\/code><code>#\u51c6\u5907\u8f93\u5165\u6570\u636e<\/span><\/span><\/code><code>library<\/span>(data.table)<\/span><\/code><code> <\/span><\/code><code>express<-fread(\"express.CSV\"<\/span>)<\/span><\/code><code>express<-as.data.frame(express)<\/span><\/code><code>rownames(express)<-express[,1<\/span>]<\/span><\/code><code>express<-express[,-1<\/span>]<\/span><\/code><code>class<\/span>(express)<\/span><\/code><code>colname<-colnames(express)#\u4fdd\u5b58\u884c\u540d<\/span><\/span><\/code><code>rowname<-rownames(express)#\u4fdd\u5b58\u5217\u540d<\/span><\/span><\/code><code>express<-as.data.frame(lapply(express,as.numeric))#\u6570\u636e\u6846\u8f6c\u6362\u4e3a\u6570\u503c\u578b<\/span><\/span><\/code><code>colnames(express)<-colname<\/span><\/code><code>rownames(express)<-rowname<\/span><\/code><code>#\u5f52\u4e00\u5316<\/span><\/span><\/code><code>express = sweep(express,1<\/span>, apply<\/span>(express,1<\/span>,median<\/span>,na.rm=T))<\/span><\/code><code>express<-as.matrix(express)<\/span><\/code><code> <\/span><\/code><code>#\u8fd0\u884cConsensusClusterPlus<\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>library<\/span>(ConsensusClusterPlus)<\/span><\/code><code>title=\"untitled_consensus_cluster\"<\/span><\/span><\/code><code>results = ConsensusClusterPlus(express,maxK=10<\/span>,reps=1000<\/span>,pItem=0.8<\/span>,pFeature=1<\/span>, <\/span><\/code><code> title=title,clusterAlg=\"hc\"<\/span>,distance=\"pearson\"<\/span>,<\/span><\/code><code> seed<\/span>=1262118388.71279<\/span>,plot=\"pdf\"<\/span>, writeTable = TRUE<\/span>)<\/span><\/code><code> <\/span><\/code><code>#1. pItem, \u9009\u62e980%\u7684\u6837\u672c\u8fdb\u884c\u91cd\u590d\u62bd\u6837<\/span><\/span><\/code><code> <\/span><\/code><code>#2. pfeature, \u9009\u62e980%\u7684\u57fa\u56e0\u8fdb\u884c\u91cd\u590d\u62bd\u6837<\/span><\/span><\/code><code> <\/span><\/code><code>#3. maxK, \u6700\u5927\u7684K\u503c\uff0c\u5f62\u6210\u4e00\u7cfb\u5217\u68af\u5ea6<\/span><\/span><\/code><code> <\/span><\/code><code>#4. reps, \u91cd\u590d\u62bd\u6837\u7684\u6570\u76ee<\/span><\/span><\/code><code> <\/span><\/code><code>#5. clusterAlg, \u5c42\u6b21\u805a\u7c7b\u7684\u7b97\u6cd5<\/span><\/span><\/code><code> <\/span><\/code><code>#6. distanc, \u8ddd\u79bb\u77e9\u9635\u7684\u7b97\u6cd5<\/span><\/span><\/code><code> <\/span><\/code><code>#7. title, \u8f93\u51fa\u7ed3\u679c\u7684\u6587\u4ef6\u5939\u540d\u5b57\uff0c\u5305\u542b\u4e86\u8f93\u51fa\u7684\u56fe\u7247<\/span><\/span><\/code><code> <\/span><\/code><code>#8. seed, \u968f\u673a\u79cd\u5b50\uff0c\u7528\u4e8e\u91cd\u590d\u7ed3\u679c<\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>str<\/span>(results[[2<\/span>]])<\/span><\/code><code> <\/span><\/code><code># \u4e00\u81f4\u6027\u77e9\u9635\uff0c\u6837\u672c\u7684\u90bb\u63a5\u77e9\u9635<\/span><\/span><\/code><code>dim(d)<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>dim(results[[2<\/span>]][[\"consensusMatrix\"<\/span>]])<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>results[[2<\/span>]][[\"consensusMatrix\"<\/span>]][1<\/span>:5<\/span>,1<\/span>:5<\/span>]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code># \u6837\u672c\u7684\u805a\u7c7b\u6811<\/span><\/span><\/code><code>results[[2<\/span>]][[\"consensusTree\"<\/span>]]<\/span><\/code><code> <\/span><\/code><code># ml, \u5c31\u662fconsensusMatrix<\/span><\/span><\/code><code>results[[2<\/span>]][[\"ml\"<\/span>]][1<\/span>:5<\/span>,1<\/span>:5<\/span>]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>results[[2<\/span>]][[\"consensusMatrix\"<\/span>]][1<\/span>:5<\/span>,1<\/span>:5<\/span>]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code># clrs, \u989c\u8272<\/span><\/span><\/code><code>results[[2<\/span>]][[\"clrs\"<\/span>]]<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>#\u6536\u96c6cluster-consensus\u548citem-consensus \u77e9\u9635<\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>icl = calcICL(results,title=title,plot=\"pdf\"<\/span>,writeTable=TRUE<\/span>)<\/span><\/code><code>icl[[\"clusterConsensus\"<\/span>]]<\/span><\/code><code> <\/span><\/code><code>dim(icl[[\"itemConsensus\"<\/span>]])<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>icl[[\"itemConsensus\"<\/span>]][1<\/span>:5<\/span>,]<\/span><\/code><\/pre>\n<\/section>\n <\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u81f3\u6b64\uff0c\u7ed3\u675f<\/p>\n <\/p>\n\u5173\u6ce8\u5c0f\u679c\uff0c\u5c0f\u679c\u5c06\u4f1a\u6301\u7eed\u4e3a\u4f60\u5e26\u6765\u66f4\u591a\u751f\u4fe1\u5e72\u8d27\u54e6\u3002<\/p>\n<section><mp-common-profile class=\"js_uneditable custom_select_card 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