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\u52a0\u8f7dR\u5305<\/p>\n<p>2\u3001 \u5bfc\u5165\u6570\u636e<\/p>\n<p>3\u3001 \u8fd0\u884c\u805a\u7c7b\u7684\u51fd\u6570<\/p>\n<p>\u662f\u4e0d\u662f\u548c\u5f92\u624b\u5288\u69b4\u83b2\u4e00\u6837\u7b80\u5355\uff1f\u662f\u4e0d\u662f\u4e5f\u6b63\u597d\u7b26\u5408\u4f60\u7684\u60f3\u6cd5\uff1f\u90a3\u5c31\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u9996\u5148\u5b89\u88c5R\u5305\uff0c\u9700\u8981\u4f7f\u7528BiocManager\u6765\u5b89\u88c5\u54e6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\"># if (!require(\"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(\"ConsensusClusterPlus\") <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5b89\u88c5\u8fc7\u7a0b\u4e2d\u4f1a\u5b89\u88c5\u5b98\u65b9\u4f9d\u8d56\u5305\u201cALL\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\">#\u672c\u6b21\u5206\u6790\u4f7f\u7528\u7684\u6837\u4f8b\u6570\u636e\u6765\u6e90\u4e8e\u5b98\u65b9\u63d0\u4f9b\u7684ALL\u5305\u4e2d\u7684\u63a2\u9488\u8868\u8fbe\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\">#\u5bfc\u5165R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> library(ALL)<\/span><\/code><code><span class=\"code-snippet_outer\"> library(ConsensusClusterPlus)<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\">#\u5bfc\u5165\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data(ALL)<\/span><\/code><code><span class=\"code-snippet_outer\">d=exprs(ALL)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8981\u6c42\u884c\u4e3a\u57fa\u56e0\uff0c\u5217\u4e3a\u6837\u672c\uff0c\u884c\u5217\u76f8\u53cd\u7684\u5c0f\u4f19\u4f34\u7528t()\u8fdb\u884c\u8f6c\u7f6e\u54e6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">d[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>,<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>]<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.26944444444444443\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_36tibKXEnfWZGQGPZBCdHa8QVW5Ipw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhfdHia0SIiaVQ3BAbMbibZekuzbIh36tibKXEnfWZGQGPZBCdHa8QVW5Ipw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8fd9\u91cc\u4e3a\u4e86\u8ba9\u6548\u679c\u66f4\u4f73\uff0c\u6211\u4eec\u5bf9\u6570\u636e\u8fdb\u884c\u4e00\u4e9b\u9884\u5904\u7406<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u53d6\u4e2d\u4f4d\u6570\u7edd\u5bf9\u504f\u5dee(Median Absolute Deviation)\u8f83\u5927\u7684\u524d5000\u4e2a\u63a2\u9488<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mads=apply(d,<span class=\"code-snippet__number\">1<\/span>,mad)<\/span><\/code><code><span class=\"code-snippet_outer\">df=d [rev(order(mads))[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5000<\/span>],]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># order(mads):\u4ece\u5c0f\u5230\u5927\u6392\u5e8f\uff0c\u8fd4\u56de\u7d22\u5f15<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># rev(order(mads):\u4ece\u5927\u5230\u5c0f\u6392\u5e8f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8ba1\u7b97\u6bcf\u4e2a\u503c\u51cf\u53bb\u6bcf\u884c\u7684\u4e2d\u4f4d\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">df = sweep(df,<span class=\"code-snippet__number\">1<\/span>, apply(d,<span class=\"code-snippet__number\">1<\/span>,median,na.rm=<span class=\"code-snippet__built_in\">T<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5904\u7406\u7ed3\u675f\uff0c\u770b\u4e00\u4e0b\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">df[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>,<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>]<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.23055555555555557\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_WQqImTrB0uiagDbIMcL7Ox8uOMiaZg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhib0tpxEBQUQVgH8KKqiagSEYGhwIWQqImTrB0uiagDbIMcL7Ox8uOMiaZg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u6211\u4eec\u5b9a\u4e49\u4e00\u4e0b\u8f93\u51fa\u6587\u4ef6\u5939\u7684\u540d\u5b57<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">outdir=<span class=\"code-snippet__string\">\"clusterResult\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5f00\u59cb\u805a\u7c7b\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">results = ConsensusClusterPlus(df,maxK=<span class=\"code-snippet__number\">6<\/span>,reps=<span class=\"code-snippet__number\">50<\/span>,pItem=<span class=\"code-snippet__number\">0.8<\/span>,pFeature=<span class=\"code-snippet__number\">1<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">title=outdir,clusterAlg=<span class=\"code-snippet__string\">\"hc\"<\/span>,distance=<span class=\"code-snippet__string\">\"pearson\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> seed=<span class=\"code-snippet__number\">1213<\/span>,plot=<span class=\"code-snippet__string\">\"pdf\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>#\u8fd9\u91cc\u5927\u6d77\u54e5\u7a0d\u5fae\u4ecb\u7ecd\u4e00\u4e0b\u51fd\u6570\u4e2d\u5305\u542b\u7684\u53c2\u6570<\/p>\n<p> df:\u5c31\u662f\u6211\u4eec\u7684\u6570\u636e\uff0c\u8981\u6c42\u884c\u4e3a\u57fa\u56e0\uff0c\u5217\u4e3a\u6837\u672c<\/p>\n<p> maxK:\u805a\u7c7b\u7684\u6700\u5927\u7c07\u6570\uff0c\u8981\u6c42\u4e3a\u6574\u6570<\/p>\n<p> reps:\u91cd\u91c7\u6837\u7684\u6b21\u6570<\/p>\n<p> pItem:\u62bd\u6837\u6bd4\u4f8b<\/p>\n<p> pFeature:\u6837\u672c\u7279\u5f81\u7684\u6bd4\u4f8b\uff0c\u4e00\u822c\u5c31\u662f1<\/p>\n<p> title:\u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u5939\u540d\u4ee5\u53ca\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00<\/p>\n<p> clusterAlg:\u805a\u7c7b\u91c7\u7528\u7684\u7b97\u6cd5\uff0c\u9ed8\u8ba4\u662f\u201chc\u201d\u6307\u5c42\u6b21\u805a\u7c7b\uff0c\u8fd8\u53ef\u4ee5\u9009\u62e9\u201ckm\u201d\u6307K-means\u805a\u7c7b\uff0c\u6216\u8005\u4e00\u4e2a\u8fd4\u56de\u805a\u7c7b\u7684\u51fd\u6570<\/p>\n<p> distance:\u8ba1\u7b97\u57fa\u56e0\u8ddd\u79bb\u7684\u65b9\u5f0f\uff0c\u6709pearson\u3001spearman\u3001euclidean\u3001binary\u3001maximum\u3001canberra\u3001minkowski\u7b49\uff0c\u5927\u5bb6\u81ea\u884c\u9009\u62e9<\/p>\n<p> seed:\u968f\u673a\u7684\u7a0b\u5ea6\uff0c\u5c31\u968f\u610f\u8bbe\u7f6e\u5c31\u597d\u4e86<\/p>\n<p> plot:\u53ef\u4ee5\u9009\u62e9png\u6216\u8005pdf\uff0c\u8fd8\u6709pngBMP<\/p>\n<p>#\u4e3b\u8981\u5c31\u662f\u8fd9\u4e9b\u53c2\u6570\uff0c\u66f4\u591a\u53c2\u6570\u5927\u5bb6\u53ef\u4ee5\u4e0a\u5b98\u7f51\u77a7\u77a7\u54e6\uff01<\/p>\n<p>#\u8fd0\u884c\u5b8c\u4e0a\u9762\u90a3\u884c\u4ee3\u7801\uff0c\u5c31\u53ef\u4ee5\u5f97\u5230\u57fa\u672c\u7684\u805a\u7c7b\u7ed3\u679c\u4e86\uff0c\u6211\u4eec\u6765\u770b\u770b\u5427<\/p>\n<p>#\u4e0b\u9762\u4e3a\u4e3b\u8981\u7684\u805a\u7c7b\u7ed3\u679c\u56fe<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.5703703703703704\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ASR8pUPlgr5F8nLLlf6yVLFfV3fsCw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhLsic9Lr5jibGWAicvTJONWuXMzQASR8pUPlgr5F8nLLlf6yVLFfV3fsCw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"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=\"1.0462962962962963\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_MOsNMsQxOZictnR67P4uzlpfEmzr4g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhvLYIXzibxQj3aClklILBTo4HzNMOsNMsQxOZictnR67P4uzlpfEmzr4g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0a\u56fe\u4e2dconsensus matrix\u4e3a\u6837\u672c\u805a\u7c7b\u70ed\u56fe\uff0c\u4e00\u5171\u67095\u5f20\uff0c\u5927\u6d77\u54e5\u8fd9\u91cc\u5c55\u793a\u4e863\u5f20\uff0c\u4e00\u822c\u6742\u4e71\u7ebf\u6761\u8d8a\u5c11\u8bf4\u660e\u805a\u7c7b\u7ed3\u679c\u8d8a\u597d\uff1b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#consensus CDF\u4e3a\u7d2f\u8ba1\u5206\u5e03\u56fe\uff0c\u6211\u4eec\u4e00\u822c\u770bconsensus CDF\u7684\u90a3\u4e2a\u66f2\u7ebf\u4e8eX\u8f74\u66f4\u5e73\u884c\uff0c\u5c31\u9009k\u4e3a\u51e0\uff0c\u6216\u8005\u901a\u8fc7\u624b\u8098\u6cd5\u89c2\u5bdfDelta area\u6765\u786e\u5b9a\uff0c\u7136\u540e\u9009\u62e9\u8f93\u51fa\u7ed3\u679c\u4e2d\u7684\u5bf9\u5e94k\u4e3a\u51e0\u7684\u8868\u683c\u6587\u4ef6\u5c31\u597d\u4e86<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#tracling plot\u4e2d\u884c\u4e3a\u6837\u672c\uff0c\u5217\u4e3a\u6bcf\u4e2aK\uff0c\u4e00\u822c\u7528\u4e8e\u5b9a\u6027\u8bc4\u4f30\u4e0d\u7a33\u5b9a\u7684\u805a\u7c7b\u548c\u4e0d\u7a33\u5b9a\u7684\u6837\u672c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6709\u7684\u5c0f\u4f19\u4f34\u8fd8\u60f3\u770b\u770b\u7ec4\u95f4\u4e00\u81f4\u6027\u548c\u7ec4\u7c7b\u4e00\u81f4\u6027\uff0c\u5c31\u7528\u4e0b\u9762\u7684\u4ee3\u7801<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">icl = calcICL(results,title=outdir,plot=<span class=\"code-snippet__string\">\"pdf\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u5c31\u53ef\u4ee5\u5f97\u5230\u4e0b\u9762\u7684\u56fe<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.9694444444444444\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_RHQiaaKllxEiciazhkVBFPPkK1QfxQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhDPAhjyJKb3Z9q7umYWliaOFoI7yVRHQiaaKllxEiciazhkVBFPPkK1QfxQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.3416666666666667\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_J5RcjUqtzNnWOLfnbiaTyrS9KeLdeQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhKibjZqLBDpGU35RJLay6iab24Q1J5RcjUqtzNnWOLfnbiaTyrS9KeLdeQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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\">#\u9009\u62e9\u5408\u9002\u7684k\u503c\u540e\uff0c\u53ef\u4ee5\u5f97\u5230\u5bf9\u5e94\u805a\u7c7b\u7ed3\u679c\u7684\u6570\u636e\u6846<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample_cluster <- results[[<span class=\"code-snippet__number\">6<\/span>]]$consensusClass<\/span><\/code><code><span class=\"code-snippet_outer\">sample_cluster_df <- data.frame(sample = <span class=\"code-snippet__built_in\">names<\/span>(sample_cluster), cluster = sample_cluster)<\/span><\/code><code><span class=\"code-snippet_outer\">head(sample_cluster_df)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.6103023516237402\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_qyvciayFOMt9fPz089bsFibhrdtDug.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhWVgD1hrxHpkOlv0obfM7Z1fyn0qyvciayFOMt9fPz089bsFibhrdtDug\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"893\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"display: 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115);\">\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\uff0c\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u4ef6\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2\u54df\uff0c\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/span><\/strong>\uff09<\/p>\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"border-bottom: 2px solid rgb(0, 150, 136);text-align: left;font-size: 14px;\" powered-by=\"xiumi.us\">\n<p>\u70b9\u51fb\u201c\u9605\u8bfb\u539f\u6587\u201d\u8fdb\u5165\u7f51\u5740<\/p>\n<\/section>\n<section style=\"margin-left: 8%;margin-right: 8%;line-height: 1.1em;\" powered-by=\"xiumi.us\">\n<section style=\"width: 0px;display: inline-block;vertical-align: top;border-top: 1em solid rgb(0, 150, 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{"id":59136,"date":"2024-06-17T07:42:46","date_gmt":"2024-06-16T23:42:46","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59136"},"modified":"2024-06-17T07:42:46","modified_gmt":"2024-06-16T23:42:46","slug":"%e6%83%b3%e7%94%a8%e6%97%a0%e7%9b%91%e7%9d%a3%e8%81%9a%e7%b1%bb%e9%a2%84%e6%b5%8b%e5%88%86%e5%ad%90%e4%ba%9a%e5%9e%8b%ef%bc%9f%e7%a1%ae%e5%ae%9a%e4%b8%8d%e8%80%83%e8%99%91consensusclusterplus%e5%8c%85","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59136","title":{"rendered":"\u60f3\u7528\u65e0\u76d1\u7763\u805a\u7c7b\u9884\u6d4b\u5206\u5b50\u4e9a\u578b\uff1f\u786e\u5b9a\u4e0d\u8003\u8651ConsensusClusterPlus\u5305\u5417\uff1f"},"content":{"rendered":"

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auto;height: auto;align-self: flex-start;\">\n<section style=\"display: flex;flex-flow: row;margin: -9px 0% 5px;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;line-height: 0;align-self: flex-start;border-width: 0px;margin-top: 5px;margin-left: 7px;\">\n<section style=\"text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 2px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(59, 149, 115);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;margin: -6px 0% 4px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 10px;height: 2px;vertical-align: top;overflow: hidden;background-color: rgb(59, 149, 115);\"><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: top;width: auto;flex: 0 0 0%;height: auto;line-height: 0;border-width: 0px;margin-left: 4px;\">\n<section style=\"text-align: center;margin-top: -4px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 9px;height: 9px;vertical-align: top;overflow: hidden;border-width: 2px;border-radius: 47px;border-style: solid;border-color: rgb(59, 149, 115);\"><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: top;width: auto;min-width: 10%;flex: 0 0 auto;height: auto;\">\n<section style=\"margin-right: 0%;margin-left: 0%;text-align: center;transform: translate3d(-1px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"color: rgb(59, 149, 115);font-size: 19px;padding-right: 11px;padding-left: 11px;line-height: 1;text-align: justify;\">\n<p style=\"text-align: left;text-wrap: wrap;\"><strong>\u70b9\u51fb\u84dd\u5b57 \u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;line-height: 0;flex: 0 0 0%;height: auto;\">\n<section style=\"text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 16px;height: 12px;vertical-align: top;overflow: hidden;background-color: rgb(59, 149, 115);padding-right: 2px;padding-left: 2px;\">\n<section style=\"justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: 50%;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"margin-top: 4px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 3px;height: 3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);\"><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: top;width: 50%;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"margin-top: 4px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 3px;height: 3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);\"><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 style=\"text-align: center;transform: translate3d(3px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 0px 0px 4px 4px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(59, 149, 115);\"><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 style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u6700\u8fd1\u5927\u6d77\u54e5\u53d1\u73b0\u5f88\u591a\u5c0f\u4f19\u4f34\u90fd\u901a\u8fc7\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u6765\u5bf9\u6837\u672c\u8fdb\u884c\u805a\u7c7b\uff0c\u5212\u5206\u4e3a\u591a\u4e2a\u5206\u5b50\u4e9a\u578b\u6765\u5c55\u5f00\u5206\u6790\uff0c\u5e76\u4e14\u90fd\u53d1\u4e86\u9ad8\u5206SCI\uff0c\u8fd9\u8ba9\u5176\u4ed6\u7684\u5c0f\u4f19\u4f34\u7eb7\u7eb7\u8868\u793a\uff0c\u6211\u4e5f\u8981\u8bd5\u4e00\u4e0b\u8fd9\u4e2a\u65b9\u6cd5\uff0c\u4f46\u662f\u8981\u600e\u4e48\u64cd\u4f5c\u5462\uff1f\u522b\u62c5\u5fc3\uff0c\u5927\u6d77\u54e5\u6765\u66ff\u4f60\u6392\u5fe7\u89e3\u96be\uff01\u4eca\u5929\u5927\u6d77\u54e5\u5c06\u4ecb\u7ecd\u4e00\u4e2aR\u5305\uff0c\u53eb\u505aConsensusClusterPlus,\u540d\u5b57\u771f\u957f\uff0c\u597d\u7528\u4e5f\u662f\u771f\u597d\u7528\u3002\u8fd9\u4e2aR\u5305\u662f\u4e13\u95e8\u7528\u4e8e\u65e0\u76d1\u7763\u4e00\u81f4\u6027\u805a\u7c7b\uff0c\u5176\u53ef\u6839\u636e\u4e0d\u540c\u7ec4\u5b66\u6570\u636e\u96c6\u5c06\u6837\u672c\u533a\u5206\u6210\u51e0\u4e2a\u4e9a\u578b\uff0c\u4ece\u800c\u53d1\u73b0\u65b0\u7684\u75be\u75c5\u4e9a\u578b\u6216\u8005\u5bf9\u4e0d\u540c\u4e9a\u578b\u8fdb\u884c\u6bd4\u8f83\u5206\u6790\uff0c\u4e3a\u4e86\u7b80\u5316\u8fc7\u7a0b\uff0c\u8fd9\u4e2aR\u5305\u628a\u6240\u6709\u7684\u6b65\u9aa4\u90fd\u5c01\u88c5\u5230\u4e86\u4e00\u4e2a\u51fd\u6570\u91cc\uff0c\u6240\u4ee5\u4f7f\u7528\u8d77\u6765\u975e\u5e38\u7b80\u5355\uff0c\u53ea\u9700\u8981\u4e09\u6b65<\/p>\n<p>1\u3001 \u52a0\u8f7dR\u5305<\/p>\n<p>2\u3001 \u5bfc\u5165\u6570\u636e<\/p>\n<p>3\u3001 \u8fd0\u884c\u805a\u7c7b\u7684\u51fd\u6570<\/p>\n<p>\u662f\u4e0d\u662f\u548c\u5f92\u624b\u5288\u69b4\u83b2\u4e00\u6837\u7b80\u5355\uff1f\u662f\u4e0d\u662f\u4e5f\u6b63\u597d\u7b26\u5408\u4f60\u7684\u60f3\u6cd5\uff1f\u90a3\u5c31\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u9996\u5148\u5b89\u88c5R\u5305\uff0c\u9700\u8981\u4f7f\u7528BiocManager\u6765\u5b89\u88c5\u54e6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\"># if (!require(\"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(\"ConsensusClusterPlus\") <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5b89\u88c5\u8fc7\u7a0b\u4e2d\u4f1a\u5b89\u88c5\u5b98\u65b9\u4f9d\u8d56\u5305\u201cALL\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\">#\u672c\u6b21\u5206\u6790\u4f7f\u7528\u7684\u6837\u4f8b\u6570\u636e\u6765\u6e90\u4e8e\u5b98\u65b9\u63d0\u4f9b\u7684ALL\u5305\u4e2d\u7684\u63a2\u9488\u8868\u8fbe\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\">#\u5bfc\u5165R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> library(ALL)<\/span><\/code><code><span class=\"code-snippet_outer\"> library(ConsensusClusterPlus)<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\">#\u5bfc\u5165\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data(ALL)<\/span><\/code><code><span class=\"code-snippet_outer\">d=exprs(ALL)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8981\u6c42\u884c\u4e3a\u57fa\u56e0\uff0c\u5217\u4e3a\u6837\u672c\uff0c\u884c\u5217\u76f8\u53cd\u7684\u5c0f\u4f19\u4f34\u7528t()\u8fdb\u884c\u8f6c\u7f6e\u54e6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">d[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>,<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>]<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.26944444444444443\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_36tibKXEnfWZGQGPZBCdHa8QVW5Ipw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhfdHia0SIiaVQ3BAbMbibZekuzbIh36tibKXEnfWZGQGPZBCdHa8QVW5Ipw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8fd9\u91cc\u4e3a\u4e86\u8ba9\u6548\u679c\u66f4\u4f73\uff0c\u6211\u4eec\u5bf9\u6570\u636e\u8fdb\u884c\u4e00\u4e9b\u9884\u5904\u7406<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u53d6\u4e2d\u4f4d\u6570\u7edd\u5bf9\u504f\u5dee(Median Absolute Deviation)\u8f83\u5927\u7684\u524d5000\u4e2a\u63a2\u9488<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mads=apply(d,<span class=\"code-snippet__number\">1<\/span>,mad)<\/span><\/code><code><span class=\"code-snippet_outer\">df=d [rev(order(mads))[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5000<\/span>],]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># order(mads):\u4ece\u5c0f\u5230\u5927\u6392\u5e8f\uff0c\u8fd4\u56de\u7d22\u5f15<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># rev(order(mads):\u4ece\u5927\u5230\u5c0f\u6392\u5e8f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8ba1\u7b97\u6bcf\u4e2a\u503c\u51cf\u53bb\u6bcf\u884c\u7684\u4e2d\u4f4d\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">df = sweep(df,<span class=\"code-snippet__number\">1<\/span>, apply(d,<span class=\"code-snippet__number\">1<\/span>,median,na.rm=<span class=\"code-snippet__built_in\">T<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5904\u7406\u7ed3\u675f\uff0c\u770b\u4e00\u4e0b\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">df[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>,<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>]<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.23055555555555557\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_WQqImTrB0uiagDbIMcL7Ox8uOMiaZg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhib0tpxEBQUQVgH8KKqiagSEYGhwIWQqImTrB0uiagDbIMcL7Ox8uOMiaZg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u6211\u4eec\u5b9a\u4e49\u4e00\u4e0b\u8f93\u51fa\u6587\u4ef6\u5939\u7684\u540d\u5b57<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">outdir=<span class=\"code-snippet__string\">\"clusterResult\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5f00\u59cb\u805a\u7c7b\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">results = ConsensusClusterPlus(df,maxK=<span class=\"code-snippet__number\">6<\/span>,reps=<span class=\"code-snippet__number\">50<\/span>,pItem=<span class=\"code-snippet__number\">0.8<\/span>,pFeature=<span class=\"code-snippet__number\">1<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">title=outdir,clusterAlg=<span class=\"code-snippet__string\">\"hc\"<\/span>,distance=<span class=\"code-snippet__string\">\"pearson\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> seed=<span class=\"code-snippet__number\">1213<\/span>,plot=<span class=\"code-snippet__string\">\"pdf\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>#\u8fd9\u91cc\u5927\u6d77\u54e5\u7a0d\u5fae\u4ecb\u7ecd\u4e00\u4e0b\u51fd\u6570\u4e2d\u5305\u542b\u7684\u53c2\u6570<\/p>\n<p> df:\u5c31\u662f\u6211\u4eec\u7684\u6570\u636e\uff0c\u8981\u6c42\u884c\u4e3a\u57fa\u56e0\uff0c\u5217\u4e3a\u6837\u672c<\/p>\n<p> maxK:\u805a\u7c7b\u7684\u6700\u5927\u7c07\u6570\uff0c\u8981\u6c42\u4e3a\u6574\u6570<\/p>\n<p> reps:\u91cd\u91c7\u6837\u7684\u6b21\u6570<\/p>\n<p> pItem:\u62bd\u6837\u6bd4\u4f8b<\/p>\n<p> pFeature:\u6837\u672c\u7279\u5f81\u7684\u6bd4\u4f8b\uff0c\u4e00\u822c\u5c31\u662f1<\/p>\n<p> title:\u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u5939\u540d\u4ee5\u53ca\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00<\/p>\n<p> clusterAlg:\u805a\u7c7b\u91c7\u7528\u7684\u7b97\u6cd5\uff0c\u9ed8\u8ba4\u662f\u201chc\u201d\u6307\u5c42\u6b21\u805a\u7c7b\uff0c\u8fd8\u53ef\u4ee5\u9009\u62e9\u201ckm\u201d\u6307K-means\u805a\u7c7b\uff0c\u6216\u8005\u4e00\u4e2a\u8fd4\u56de\u805a\u7c7b\u7684\u51fd\u6570<\/p>\n<p> distance:\u8ba1\u7b97\u57fa\u56e0\u8ddd\u79bb\u7684\u65b9\u5f0f\uff0c\u6709pearson\u3001spearman\u3001euclidean\u3001binary\u3001maximum\u3001canberra\u3001minkowski\u7b49\uff0c\u5927\u5bb6\u81ea\u884c\u9009\u62e9<\/p>\n<p> seed:\u968f\u673a\u7684\u7a0b\u5ea6\uff0c\u5c31\u968f\u610f\u8bbe\u7f6e\u5c31\u597d\u4e86<\/p>\n<p> plot:\u53ef\u4ee5\u9009\u62e9png\u6216\u8005pdf\uff0c\u8fd8\u6709pngBMP<\/p>\n<p>#\u4e3b\u8981\u5c31\u662f\u8fd9\u4e9b\u53c2\u6570\uff0c\u66f4\u591a\u53c2\u6570\u5927\u5bb6\u53ef\u4ee5\u4e0a\u5b98\u7f51\u77a7\u77a7\u54e6\uff01<\/p>\n<p>#\u8fd0\u884c\u5b8c\u4e0a\u9762\u90a3\u884c\u4ee3\u7801\uff0c\u5c31\u53ef\u4ee5\u5f97\u5230\u57fa\u672c\u7684\u805a\u7c7b\u7ed3\u679c\u4e86\uff0c\u6211\u4eec\u6765\u770b\u770b\u5427<\/p>\n<p>#\u4e0b\u9762\u4e3a\u4e3b\u8981\u7684\u805a\u7c7b\u7ed3\u679c\u56fe<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.5703703703703704\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ASR8pUPlgr5F8nLLlf6yVLFfV3fsCw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhLsic9Lr5jibGWAicvTJONWuXMzQASR8pUPlgr5F8nLLlf6yVLFfV3fsCw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"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=\"1.0462962962962963\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_MOsNMsQxOZictnR67P4uzlpfEmzr4g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhvLYIXzibxQj3aClklILBTo4HzNMOsNMsQxOZictnR67P4uzlpfEmzr4g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0a\u56fe\u4e2dconsensus matrix\u4e3a\u6837\u672c\u805a\u7c7b\u70ed\u56fe\uff0c\u4e00\u5171\u67095\u5f20\uff0c\u5927\u6d77\u54e5\u8fd9\u91cc\u5c55\u793a\u4e863\u5f20\uff0c\u4e00\u822c\u6742\u4e71\u7ebf\u6761\u8d8a\u5c11\u8bf4\u660e\u805a\u7c7b\u7ed3\u679c\u8d8a\u597d\uff1b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#consensus CDF\u4e3a\u7d2f\u8ba1\u5206\u5e03\u56fe\uff0c\u6211\u4eec\u4e00\u822c\u770bconsensus CDF\u7684\u90a3\u4e2a\u66f2\u7ebf\u4e8eX\u8f74\u66f4\u5e73\u884c\uff0c\u5c31\u9009k\u4e3a\u51e0\uff0c\u6216\u8005\u901a\u8fc7\u624b\u8098\u6cd5\u89c2\u5bdfDelta area\u6765\u786e\u5b9a\uff0c\u7136\u540e\u9009\u62e9\u8f93\u51fa\u7ed3\u679c\u4e2d\u7684\u5bf9\u5e94k\u4e3a\u51e0\u7684\u8868\u683c\u6587\u4ef6\u5c31\u597d\u4e86<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#tracling plot\u4e2d\u884c\u4e3a\u6837\u672c\uff0c\u5217\u4e3a\u6bcf\u4e2aK\uff0c\u4e00\u822c\u7528\u4e8e\u5b9a\u6027\u8bc4\u4f30\u4e0d\u7a33\u5b9a\u7684\u805a\u7c7b\u548c\u4e0d\u7a33\u5b9a\u7684\u6837\u672c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6709\u7684\u5c0f\u4f19\u4f34\u8fd8\u60f3\u770b\u770b\u7ec4\u95f4\u4e00\u81f4\u6027\u548c\u7ec4\u7c7b\u4e00\u81f4\u6027\uff0c\u5c31\u7528\u4e0b\u9762\u7684\u4ee3\u7801<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">icl = calcICL(results,title=outdir,plot=<span class=\"code-snippet__string\">\"pdf\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u5c31\u53ef\u4ee5\u5f97\u5230\u4e0b\u9762\u7684\u56fe<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.9694444444444444\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_RHQiaaKllxEiciazhkVBFPPkK1QfxQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhDPAhjyJKb3Z9q7umYWliaOFoI7yVRHQiaaKllxEiciazhkVBFPPkK1QfxQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.3416666666666667\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_J5RcjUqtzNnWOLfnbiaTyrS9KeLdeQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhKibjZqLBDpGU35RJLay6iab24Q1J5RcjUqtzNnWOLfnbiaTyrS9KeLdeQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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\">#\u9009\u62e9\u5408\u9002\u7684k\u503c\u540e\uff0c\u53ef\u4ee5\u5f97\u5230\u5bf9\u5e94\u805a\u7c7b\u7ed3\u679c\u7684\u6570\u636e\u6846<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample_cluster <- results[[<span class=\"code-snippet__number\">6<\/span>]]$consensusClass<\/span><\/code><code><span class=\"code-snippet_outer\">sample_cluster_df <- data.frame(sample = <span class=\"code-snippet__built_in\">names<\/span>(sample_cluster), cluster = sample_cluster)<\/span><\/code><code><span class=\"code-snippet_outer\">head(sample_cluster_df)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.6103023516237402\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_qyvciayFOMt9fPz089bsFibhrdtDug.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjST9ArwBXiaXNPp8Aa6WEib2jhWVgD1hrxHpkOlv0obfM7Z1fyn0qyvciayFOMt9fPz089bsFibhrdtDug\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"893\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"display: flex;flex-flow: row;margin: 10px 0% 20px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;align-self: flex-start;line-height: 0;\">\n<section style=\"text-align: right;margin-right: 0%;margin-bottom: -20px;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 8px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 241, 224);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 16px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 21px 21px 0px 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(231, 215, 173);\"><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: top;width: auto;background-color: rgb(245, 241, 224);flex: 100 100 0%;align-self: flex-start;height: auto;border-right: 0px none rgb(62, 62, 62);border-top-right-radius: 12px;overflow: hidden;box-shadow: rgb(231, 215, 173) 0px 6px 0px;\">\n<section style=\"margin: 20px 0% 30px;\" powered-by=\"xiumi.us\">\n<section style=\"padding-right: 23px;padding-left: 23px;text-align: justify;font-size: 14px;line-height: 1.8;letter-spacing: 2px;\">\n<p>\u597d\u4e86\uff0c\u65e0\u76d1\u7763\u4e00\u81f4\u6027\u805a\u7c7b\u7684\u64cd\u4f5c\u6d41\u7a0b\u5230\u8fd9\u91cc\u5c31\u7ed3\u675f\u4e86\uff0c\u4ee3\u7801\u53ef\u4ee5\u8bf4\u662f\u975e\u5e38\u7b80\u6d01\uff0c\u4f46\u662f\u8f93\u51fa\u7ed3\u679c\u4ee5\u53ca\u4ee3\u7801\u4e2d\u7684\u53c2\u6570\u5176\u5b9e\u6709\u5f88\u591a\u5730\u65b9\u9700\u8981\u6ce8\u610f\uff0c\u6240\u4ee5\u5927\u5bb6\u4e00\u5b9a\u8981\u591a\u8bd5\u51e0\u904d\u624d\u597d\uff0c\u4e0d\u7136\u7b49\u771f\u6b63\u7528\u5b83\u6765\u505a\u5206\u6790\u7684\u65f6\u5019\uff0c\u4e00\u4e0b\u5b50\u53d1\u73b0\u81ea\u5df1\u597d\u50cf\u770b\u4e0d\u61c2\uff0c\u6240\u4ee5\u5c0f\u4f19\u4f34\u4eec\u5982\u679c\u624b\u5934\u6709\u6570\u636e\u7684\u8bdd\uff0c\u5c31\u52a8\u624b\u8bd5\u8bd5\u5427\uff01\uff08<strong><span style=\"color: rgb(59, 149, 115);\">\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\uff0c\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u4ef6\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2\u54df\uff0c\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/span><\/strong>\uff09<\/p>\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"border-bottom: 2px solid rgb(0, 150, 136);text-align: left;font-size: 14px;\" powered-by=\"xiumi.us\">\n<p>\u70b9\u51fb\u201c\u9605\u8bfb\u539f\u6587\u201d\u8fdb\u5165\u7f51\u5740<\/p>\n<\/section>\n<section style=\"margin-left: 8%;margin-right: 8%;line-height: 1.1em;\" powered-by=\"xiumi.us\">\n<section style=\"width: 0px;display: inline-block;vertical-align: top;border-top: 1em solid rgb(0, 150, 136);border-left: 0.8em solid transparent !important;border-right: 0.8em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<p style=\"margin-bottom: 24px;\"><br \/><\/p>\n<p style=\"display: none;margin-bottom: 24px;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u60f3\u7528\u65e0\u76d1\u7763\u805a\u7c7b\u9884\u6d4b\u5206\u5b50\u4e9a\u578b\uff1f\u786e\u5b9a\u4e0d\u8003\u8651ConsensusClusterPlus\u5305\u5417\uff1f \u5927\u6d77\u54e5 &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\/59136"}],"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=59136"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59136\/revisions"}],"predecessor-version":[{"id":59144,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59136\/revisions\/59144"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59136"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59136"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59136"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}