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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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#install.packages(\"survival\")<\/span><\/span><\/code><code>#install.packages(\"regplot\")<\/span><\/span><\/code><code>#install.packages(\"rms\")<\/span><\/span><\/code><code>#\u5f15\u7528\u5305<\/span><\/span><\/code><code>library(survival)<\/span><\/code><code>library(regplot)<\/span><\/code><code>library(rms)<\/span><\/code><code> <\/span><\/code><code>expFile=\"expTime.txt\"<\/span> #\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>cliFile=\"clinical.txt\"<\/span> #\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>setwd() #\u8bbe\u7f6e\u5de5\u4f5c\u76ee\u5f55<\/span><\/span><\/code><code>#\u5b9a\u4e49\u4e86\u51e0\u4e2a\u53d8\u91cf\uff0c\u5305\u62ec\"expFile\"\u548c\"cliFile\"\uff0c\u5206\u522b\u4e3a\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u548c\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\u7684\u6587\u4ef6\u540d\u3002<\/span><\/span><\/code><code>#\u53e6\u5916\uff0c\u901a\u8fc7\"setwd\"\u51fd\u6570\u8bbe\u7f6e\u4e86\u5de5\u4f5c\u76ee\u5f55<\/span><\/span><\/code><code> <\/span><\/code><code>exp<\/span>=read.table(expFile, header=T<\/span>, sep=\"t\"<\/span>, check.names=F<\/span>, row.names=1<\/span>)<\/span><\/code><code>#\u8bfb\u53d6\u540d\u4e3a\"expFile\"\u7684\u8868\u8fbe\u6570\u636e\u6587\u4ef6\uff0c\u8be5\u6587\u4ef6\u662f\u4e00\u4e2a\u4ee5\u5236\u8868\u7b26\u5206\u9694\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5305\u542b\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002<\/span><\/span><\/code><code>#\"header=T\"\u8868\u793a\u7b2c\u4e00\u884c\u662f\u5217\u540d\uff0c\"sep=\"t\"\"\u8868\u793a\u4f7f\u7528\u5236\u8868\u7b26\u4f5c\u4e3a\u5206\u9694\u7b26\uff0c\"check.names=F\"\u8868\u793a\u4e0d\u68c0\u67e5\u5217\u540d\u7684\u5408\u6cd5\u6027\uff0c<\/span><\/span><\/code><code>#\"row.names=1\"\u8868\u793a\u4f7f\u7528\u7b2c\u4e00\u5217\u4f5c\u4e3a\u884c\u540d\u3002\u8bfb\u53d6\u540e\u7684\u6570\u636e\u88ab\u4fdd\u5b58\u5728\u53d8\u91cf\"exp\"\u4e2d\uff0c\u662f\u4e00\u4e2a\u5305\u542b\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u7684\u6570\u636e\u6846\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>cli=read.table(cliFile, header=T<\/span>, sep=\"t\"<\/span>, check.names=F<\/span>, row.names=1<\/span>)<\/span><\/code><code>cli=cli[apply(cli,1<\/span>,function<\/span>(x)any<\/span>(is.na<\/span>(match('unknow'<\/span>,x)))),,drop=F<\/span>]<\/span><\/code><code>cli$Age=as.numeric<\/span>(cli$Age)<\/span><\/code><code>#\u8bfb\u53d6\u540d\u4e3a\"cliFile\"\u7684\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\uff0c\u8be5\u6587\u4ef6\u4e5f\u662f\u4e00\u4e2a\u4ee5\u5236\u8868\u7b26\u5206\u9694\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5305\u542b\u4e0e\u6bcf\u4e2a\u6837\u672c\u76f8\u5173\u7684\u4e34\u5e8a\u4fe1\u606f\u3002<\/span><\/span><\/code><code>#\"header=T\"\u8868\u793a\u7b2c\u4e00\u884c\u662f\u5217\u540d\uff0c\"sep=\"t\"\"\u8868\u793a\u4f7f\u7528\u5236\u8868\u7b26\u4f5c\u4e3a\u5206\u9694\u7b26\uff0c\"check.names=F\"\u8868\u793a\u4e0d\u68c0\u67e5\u5217\u540d\u7684\u5408\u6cd5\u6027\uff0c<\/span><\/span><\/code><code>#\"row.names=1\"\u8868\u793a\u4f7f\u7528\u7b2c\u4e00\u5217\u4f5c\u4e3a\u884c\u540d\u3002<\/span><\/span><\/code><code>#\u7136\u540e\uff0c\u4ee3\u7801\u4f7f\u7528apply\u51fd\u6570\u8fc7\u6ee4\u51fa\u542b\u6709\"unknow\"\u7684\u884c\uff0c\u518d\u5c06\"Age\"\u5217\u8f6c\u6362\u4e3a\u6570\u503c\u7c7b\u578b\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>samSample=intersect(row.names(exp<\/span>), row.names(cli))<\/span><\/code><code>exp1=exp<\/span>[samSample,,drop=F<\/span>]<\/span><\/code><code>cli=cli[samSample,,drop=F<\/span>]<\/span><\/code><code>rt=cbind(exp1, cli)<\/span><\/code><code>#\u5408\u5e76\u8868\u8fbe\u6570\u636e\"exp\"\u548c\u4e34\u5e8a\u6570\u636e\"cli\"\u3002\u9996\u5148\uff0c\u627e\u51fa\u4e24\u4e2a\u6570\u636e\u6846\u4e2d\u5171\u540c\u5177\u6709\u7684\u6837\u672c\uff08\u884c\u540d\uff09\uff0c\u5e76\u5c06\u8fd9\u4e9b\u6837\u672c\u4f5c\u4e3a\"exp\"\u548c\"cli\"\u7684\u5b50\u96c6\u3002<\/span><\/span><\/code><code>#\u7136\u540e\u4f7f\u7528cbind\u51fd\u6570\u5c06\"exp1\"\u548c\"cli\"\u6309\u5217\u5408\u5e76\uff0c\u5f97\u5230\u540d\u4e3a\"rt\"\u7684\u65b0\u6570\u636e\u6846\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u4fe1\u606f\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>res.cox=coxph(Surv(futime, fustat) ~ . , data = rt)<\/span><\/code><code>nom1=regplot(res.cox,<\/span><\/code><code>plots = c<\/span>(\"density\"<\/span>, \"boxes\"<\/span>),<\/span><\/code><code>clickable=F<\/span>,<\/span><\/code><code>title=\"\"<\/span>,<\/span><\/code><code>points=TRUE<\/span>,<\/span><\/code><code>droplines=TRUE<\/span>,<\/span><\/code><code>observation=rt[2<\/span>,],<\/span><\/code><code>rank=\"sd\"<\/span>,<\/span><\/code><code>failtime = c<\/span>(1<\/span>,3<\/span>,5<\/span>),<\/span><\/code><code>prfail = F<\/span>)<\/span><\/code><code>#\u8fdb\u884c\u751f\u5b58\u5206\u6790\u3002\u9996\u5148\uff0c\u4f7f\u7528coxph\u51fd\u6570\u8fdb\u884cCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u62df\u5408\uff0c\u5176\u4e2d\"Surv(futime, fustat)\"\u662f\u751f\u5b58\u65f6\u95f4\u548c\u4e8b\u4ef6\uff08\u6b7b\u4ea1\u6216\u4e8b\u4ef6\uff09\u7684\u751f\u5b58\u5bf9\u8c61\u3002<\/span><\/span><\/code><code>#\u62df\u5408\u7ed3\u679c\u4fdd\u5b58\u5728\"res.cox\"\u53d8\u91cf\u4e2d\u3002<\/span><\/span><\/code><code>#\u7136\u540e\uff0c\u4f7f\u7528\"regplot\"\u51fd\u6570\u7ed8\u5236\u5217\u7ebf\u56fe\uff08Nomogram\u56fe\uff09\uff0c\u663e\u793a\u57fa\u56e0\u8868\u8fbe\u548c\u4e34\u5e8a\u56e0\u7d20\u4e0e\u751f\u5b58\u98ce\u9669\u7684\u5173\u7cfb\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>nomoRisk=predict(res.cox, data=rt, type=\"risk\"<\/span>)<\/span><\/code><code>rt=cbind(exp1, Nomogram=nomoRisk)<\/span><\/code><code>outTab=rbind(ID=colnames(rt), rt)<\/span><\/code><code>write.table(outTab, file=\"nomoRisk.txt\"<\/span>, sep=\"t\"<\/span>, col.names=F<\/span>, quote<\/span>=F<\/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=\"0.820627802690583\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_qqIwMjyTxMibhtafah7SsUKx4Gwicg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXW94AvH9euLIr2w3PTfxJJu2F3icsC5DqMzibMBrf6iaHBV7tCQqqIwMjyTxMibhtafah7SsUKx4Gwicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"669\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#\u8f93\u51fa\u5217\u7ebf\u56fe\u7684\u98ce\u9669\u6253\u5206\u6587\u4ef6\uff0c\u8ba1\u7b97\u5e76\u8f93\u51fa\u5217\u7ebf\u56fe\uff08Nomogram\u56fe\uff09\u4e2d\u7684\u98ce\u9669\u5f97\u5206\u3002<\/span><\/span><\/code><code>#\u4f7f\u7528predict\u51fd\u6570\u57fa\u4e8eCox\u6a21\u578b\u8ba1\u7b97\u6bcf\u4e2a\u6837\u672c\u7684\u98ce\u9669\u5f97\u5206\uff0c\u5e76\u5c06\u7ed3\u679c\u4fdd\u5b58\u5728\"nomoRisk\"\u53d8\u91cf\u4e2d\u3002<\/span><\/span><\/code><code>#\u63a5\u7740\uff0c\u5c06\u98ce\u9669\u5f97\u5206\u4e0e\u8868\u8fbe\u6570\u636e\u5408\u5e76\u4e3a\u65b0\u7684\u6570\u636e\u6846\"rt\"\uff0c\u518d\u5c06\u6570\u636e\u6846\u7684\u5217\u540d\u548c\u6570\u636e\u5199\u5165\u540d\u4e3a\"nomoRisk.txt\"\u7684\u6587\u672c\u6587\u4ef6\u4e2d\u3002<\/span><\/span><\/code><code>#\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>pdf(file=\"calibration.pdf\"<\/span>, width=5<\/span>, height=5<\/span>)<\/span><\/code><code>#\u7ed8\u5236\u4e86\u6821\u51c6\u66f2\u7ebf\uff08Calibration Curve\uff09\uff0c\u7528\u4e8e\u8bc4\u4f30Nomogram\u6a21\u578b\u7684\u9884\u6d4b\u6027\u80fd<\/span><\/span><\/code><code>#1\u5e74\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>f <- cph(Surv(futime, fustat) ~ Nomogram, x=T<\/span>, y=T<\/span>, surv=T<\/span>, data=rt, time.inc=1<\/span>)<\/span><\/code><code>cal <- calibrate(f, cmethod=\"KM\"<\/span>, method=\"boot\"<\/span>, u=1<\/span>, m=(nrow(rt)\/3<\/span>), B=1000<\/span>)<\/span><\/code><code>plot(cal, xlim=c<\/span>(0<\/span>,1<\/span>), ylim=c<\/span>(0<\/span>,1<\/span>),<\/span><\/code><code>xlab=\"Nomogram-predicted OS (%)\"<\/span>, ylab=\"Observed OS (%)\"<\/span>, lwd=1.5<\/span>, col=\"green\"<\/span>, sub=F<\/span>)<\/span><\/code><code>#3\u5e74\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>f <- cph(Surv(futime, fustat) ~ Nomogram, x=T<\/span>, y=T<\/span>, surv=T<\/span>, data=rt, time.inc=3<\/span>)<\/span><\/code><code>cal <- calibrate(f, cmethod=\"KM\"<\/span>, method=\"boot\"<\/span>, u=3<\/span>, m=(nrow(rt)\/3<\/span>), B=1000<\/span>)<\/span><\/code><code>plot(cal, xlim=c<\/span>(0<\/span>,1<\/span>), ylim=c<\/span>(0<\/span>,1<\/span>), xlab=\"\"<\/span>, ylab=\"\"<\/span>, lwd=1.5<\/span>, col=\"blue\"<\/span>, sub=F<\/span>, add=T<\/span>)<\/span><\/code><code>#5\u5e74\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>f <- cph(Surv(futime, fustat) ~ Nomogram, x=T<\/span>, y=T<\/span>, surv=T<\/span>, data=rt, time.inc=5<\/span>)<\/span><\/code><code>cal <- calibrate(f, cmethod=\"KM\"<\/span>, method=\"boot\"<\/span>, u=5<\/span>, m=(nrow(rt)\/3<\/span>), B=1000<\/span>)<\/span><\/code><code>plot(cal, xlim=c<\/span>(0<\/span>,1<\/span>), ylim=c<\/span>(0<\/span>,1<\/span>), xlab=\"\"<\/span>, ylab=\"\"<\/span>, lwd=1.5<\/span>, col=\"red\"<\/span>, sub=F<\/span>, add=T<\/span>)<\/span><\/code><code>legend('bottomright'<\/span>, c<\/span>('1-year'<\/span>, '3-year'<\/span>, '5-year'<\/span>),<\/span><\/code><code>col=c<\/span>(\"green\"<\/span>,\"blue\"<\/span>,\"red\"<\/span>), lwd=1.5<\/span>, bty = 'n'<\/span>)<\/span><\/code><code>dev.off()<\/span><\/code><code>#\u4f7f\u7528cph\u51fd\u6570\u5efa\u7acbCox\u6a21\u578b\uff0c\u5c06Nomogram\u4f5c\u4e3a\u89e3\u91ca\u53d8\u91cf\uff0c\u5e76\u8bbe\u5b9a\u4e0d\u540c\u7684\u65f6\u95f4\u95f4\u9694\u3002<\/span><\/span><\/code><code>#\u7136\u540e\uff0c\u4f7f\u7528calibrate\u51fd\u6570\u751f\u6210\u6821\u51c6\u66f2\u7ebf\u3002\u4ee3\u7801\u5c06\u6821\u51c6\u66f2\u7ebf\u7ed8\u5236\u5728\u4e00\u4e2aPDF\u6587\u4ef6\u4e2d\uff0c<\/span><\/span><\/code><code>#\u5206\u522b\u7ed8\u52361\u5e74\u30013\u5e74\u548c5\u5e74\u7684\u6821\u51c6\u66f2\u7ebf\uff0c\u5e76\u5728\u56fe\u4f8b\u4e2d\u663e\u793a\u4e0d\u540c\u65f6\u95f4\u95f4\u9694\u7684\u989c\u8272\u3002\u6700\u540e\uff0c\u901a\u8fc7dev.off()\u51fd\u6570\u5173\u95edPDF\u7ed8\u56fe\u8bbe\u5907\u3002<\/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=\"0.7787958115183246\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_474aW2aNzmL6CgK34kHGZWRfyB8YIQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXW94AvH9euLIr2w3PTfxJJaibBCmO7iaGObibWW5cIfFgLxicn474aW2aNzmL6CgK34kHGZWRfyB8YIQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"764\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9849785407725322\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_icwyQRnGhpUCRicTUGeSn9cjMtLfJw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXW94AvH9euLIr2w3PTfxJJe7quPltOsSge1wO6Wxu9hGZQ2yicwyQRnGhpUCRicTUGeSn9cjMtLfJw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"466\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n\u7efc\u5408\u5206\u6790\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\uff0c\u7136\u540e\u5229\u7528\u751f\u5b58\u5206\u6790\u548c\u6821\u51c6\u66f2\u7ebf\u8bc4\u4f30\u57fa\u56e0\u8868\u8fbe\u548c\u4e34\u5e8a\u4fe1\u606f\u5bf9\u80bf\u7624\u60a3\u8005\u9884\u540e\u7684\u9884\u6d4b\u80fd\u529b\uff0c\u9884\u6d4b\u60a3\u8005\u9884\u540e\u4ee5\u53ca\u53d1\u73b0\u6f5c\u5728\u7684\u751f\u7269\u6807\u5fd7\u7269\u3002\u4e0b\u671f\u5c06\u4e3a\u4f60\u5e26\u6765\u66f4\u591aR\u8bed\u8a00\u7684\u9a9a\u64cd\u4f5c\u6280\u5de7\uff0c\u4ee5\u4e0b\u63a8\u8350\u7684\u662f\u4e00\u4e2a\u591a\u529f\u80fd\u7684\u751f\u4fe1\u5e73\u53f0\u3002<\/p>\n<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;\" 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255, 255, 0);background-color: rgb(241, 203, 206);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u6211\u4eec\u7ecf\u5e38\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e0e\u4e34\u5e8a\u6570\u636e\u8fdb\u884c\u751f\u5b58\u5206\u6790\uff0c\u4eca\u5929\u5c0f\u5e08\u59b9\u7ed9\u5927\u5bb6\u5e26\u6765\u4e0d\u4e00\u6837\u7684\u5206\u6790\u9884\u6d4b\uff0c\u4ed6\u5c31\u662fNomogram\u3002\u6211\u4eec\u5148\u4e86\u89e3\u4e00\u4e0b\u6982\u5ff5\u7406\u8bba\u518d\u8fdb\u884c\u64cd\u4f5c\u3002<\/span><\/p>\n <\/span><\/p>\nNomogram\uff0c\u4e5f\u5e38\u79f0\u4e3a\u8bfa\u83ab\u56fe\u6216\u8005\u5217\u7ebf\u56fe\uff0c\u5728\u533b\u5b66\u9886\u57df\u7684\u671f\u520a\u51fa\u73b0\u9891\u7387\u8d8a\u6765\u6108\u591a\uff0c\u5e38\u7528\u4e8e\u8bc4\u4f30\u80bf\u7624\u5b66\u548c\u533b\u5b66\u7684\u9884\u540e\u60c5\u51b5\uff0c\u53ef\u5c06Logistic\u56de\u5f52\u6216Cox\u56de\u5f52\u7684\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\u5448\u73b0\u3002<\/p>\n <\/p>\n\u6821\u51c6\u66f2\u7ebf\uff08Calibration Curve\uff09\u91cf\u5ea6\u7740\u9884\u6d4b\u51c6\u786e\u6027\u3002\u6709\u52a9\u4e8e\u786e\u5b9a\u5728\u4e0d\u540c\u65f6\u95f4\u70b9\u4e0a\u6a21\u578b\u7684\u9884\u6d4b\u80fd\u529b\u5982\u4f55\u3002\u8fd9\u6837\u7684\u5206\u6790\u5bf9\u4e8e\u57fa\u56e0\u4e0e\u4e34\u5e8a\u56e0\u7d20\u5728\u80bf\u7624\u7814\u7a76\u4e2d\u7684\u5e94\u7528\u5177\u6709\u91cd\u8981\u610f\u4e49\u3002<\/p>\n <\/p>\n\u8a00\u5f52\u6b63\u4f20\uff0c\u5b9e\u64cd\u90e8\u5206\u6765\u4e86\u3002\u4e0b\u9762\u662f\u793a\u4f8b\u6837\u672c\u7684\u8868\u8fbe\u91cf\u4fe1\u606f\u548c\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\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=\"0.871031746031746\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_bgUDrRpiaETKibibBP57he83JmgEVQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXW94AvH9euLIr2w3PTfxJJpB0ABibFKRGvNCrgeyzqic3YGpdaPibgUDrRpiaETKibibBP57he83JmgEVQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"504\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.1095334685598377\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_dfhwoNwYJTmqo2Mhcr1IyReKDF7bSQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXW94AvH9euLIr2w3PTfxJJbpQicFLmMII0NTxDr12Ll9Hq0dfhwoNwYJTmqo2Mhcr1IyReKDF7bSQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"493\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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>#install.packages(\"survival\")<\/span><\/span><\/code><code>#install.packages(\"regplot\")<\/span><\/span><\/code><code>#install.packages(\"rms\")<\/span><\/span><\/code><code>#\u5f15\u7528\u5305<\/span><\/span><\/code><code>library(survival)<\/span><\/code><code>library(regplot)<\/span><\/code><code>library(rms)<\/span><\/code><code> <\/span><\/code><code>expFile=\"expTime.txt\"<\/span> #\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>cliFile=\"clinical.txt\"<\/span> #\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>setwd() #\u8bbe\u7f6e\u5de5\u4f5c\u76ee\u5f55<\/span><\/span><\/code><code>#\u5b9a\u4e49\u4e86\u51e0\u4e2a\u53d8\u91cf\uff0c\u5305\u62ec\"expFile\"\u548c\"cliFile\"\uff0c\u5206\u522b\u4e3a\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u548c\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\u7684\u6587\u4ef6\u540d\u3002<\/span><\/span><\/code><code>#\u53e6\u5916\uff0c\u901a\u8fc7\"setwd\"\u51fd\u6570\u8bbe\u7f6e\u4e86\u5de5\u4f5c\u76ee\u5f55<\/span><\/span><\/code><code> <\/span><\/code><code>exp<\/span>=read.table(expFile, header=T<\/span>, sep=\"t\"<\/span>, check.names=F<\/span>, row.names=1<\/span>)<\/span><\/code><code>#\u8bfb\u53d6\u540d\u4e3a\"expFile\"\u7684\u8868\u8fbe\u6570\u636e\u6587\u4ef6\uff0c\u8be5\u6587\u4ef6\u662f\u4e00\u4e2a\u4ee5\u5236\u8868\u7b26\u5206\u9694\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5305\u542b\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002<\/span><\/span><\/code><code>#\"header=T\"\u8868\u793a\u7b2c\u4e00\u884c\u662f\u5217\u540d\uff0c\"sep=\"t\"\"\u8868\u793a\u4f7f\u7528\u5236\u8868\u7b26\u4f5c\u4e3a\u5206\u9694\u7b26\uff0c\"check.names=F\"\u8868\u793a\u4e0d\u68c0\u67e5\u5217\u540d\u7684\u5408\u6cd5\u6027\uff0c<\/span><\/span><\/code><code>#\"row.names=1\"\u8868\u793a\u4f7f\u7528\u7b2c\u4e00\u5217\u4f5c\u4e3a\u884c\u540d\u3002\u8bfb\u53d6\u540e\u7684\u6570\u636e\u88ab\u4fdd\u5b58\u5728\u53d8\u91cf\"exp\"\u4e2d\uff0c\u662f\u4e00\u4e2a\u5305\u542b\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u7684\u6570\u636e\u6846\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>cli=read.table(cliFile, header=T<\/span>, sep=\"t\"<\/span>, check.names=F<\/span>, row.names=1<\/span>)<\/span><\/code><code>cli=cli[apply(cli,1<\/span>,function<\/span>(x)any<\/span>(is.na<\/span>(match('unknow'<\/span>,x)))),,drop=F<\/span>]<\/span><\/code><code>cli$Age=as.numeric<\/span>(cli$Age)<\/span><\/code><code>#\u8bfb\u53d6\u540d\u4e3a\"cliFile\"\u7684\u4e34\u5e8a\u6570\u636e\u6587\u4ef6\uff0c\u8be5\u6587\u4ef6\u4e5f\u662f\u4e00\u4e2a\u4ee5\u5236\u8868\u7b26\u5206\u9694\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5305\u542b\u4e0e\u6bcf\u4e2a\u6837\u672c\u76f8\u5173\u7684\u4e34\u5e8a\u4fe1\u606f\u3002<\/span><\/span><\/code><code>#\"header=T\"\u8868\u793a\u7b2c\u4e00\u884c\u662f\u5217\u540d\uff0c\"sep=\"t\"\"\u8868\u793a\u4f7f\u7528\u5236\u8868\u7b26\u4f5c\u4e3a\u5206\u9694\u7b26\uff0c\"check.names=F\"\u8868\u793a\u4e0d\u68c0\u67e5\u5217\u540d\u7684\u5408\u6cd5\u6027\uff0c<\/span><\/span><\/code><code>#\"row.names=1\"\u8868\u793a\u4f7f\u7528\u7b2c\u4e00\u5217\u4f5c\u4e3a\u884c\u540d\u3002<\/span><\/span><\/code><code>#\u7136\u540e\uff0c\u4ee3\u7801\u4f7f\u7528apply\u51fd\u6570\u8fc7\u6ee4\u51fa\u542b\u6709\"unknow\"\u7684\u884c\uff0c\u518d\u5c06\"Age\"\u5217\u8f6c\u6362\u4e3a\u6570\u503c\u7c7b\u578b\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>samSample=intersect(row.names(exp<\/span>), row.names(cli))<\/span><\/code><code>exp1=exp<\/span>[samSample,,drop=F<\/span>]<\/span><\/code><code>cli=cli[samSample,,drop=F<\/span>]<\/span><\/code><code>rt=cbind(exp1, cli)<\/span><\/code><code>#\u5408\u5e76\u8868\u8fbe\u6570\u636e\"exp\"\u548c\u4e34\u5e8a\u6570\u636e\"cli\"\u3002\u9996\u5148\uff0c\u627e\u51fa\u4e24\u4e2a\u6570\u636e\u6846\u4e2d\u5171\u540c\u5177\u6709\u7684\u6837\u672c\uff08\u884c\u540d\uff09\uff0c\u5e76\u5c06\u8fd9\u4e9b\u6837\u672c\u4f5c\u4e3a\"exp\"\u548c\"cli\"\u7684\u5b50\u96c6\u3002<\/span><\/span><\/code><code>#\u7136\u540e\u4f7f\u7528cbind\u51fd\u6570\u5c06\"exp1\"\u548c\"cli\"\u6309\u5217\u5408\u5e76\uff0c\u5f97\u5230\u540d\u4e3a\"rt\"\u7684\u65b0\u6570\u636e\u6846\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u4fe1\u606f\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>res.cox=coxph(Surv(futime, fustat) ~ . , data = rt)<\/span><\/code><code>nom1=regplot(res.cox,<\/span><\/code><code>plots = c<\/span>(\"density\"<\/span>, \"boxes\"<\/span>),<\/span><\/code><code>clickable=F<\/span>,<\/span><\/code><code>title=\"\"<\/span>,<\/span><\/code><code>points=TRUE<\/span>,<\/span><\/code><code>droplines=TRUE<\/span>,<\/span><\/code><code>observation=rt[2<\/span>,],<\/span><\/code><code>rank=\"sd\"<\/span>,<\/span><\/code><code>failtime = c<\/span>(1<\/span>,3<\/span>,5<\/span>),<\/span><\/code><code>prfail = F<\/span>)<\/span><\/code><code>#\u8fdb\u884c\u751f\u5b58\u5206\u6790\u3002\u9996\u5148\uff0c\u4f7f\u7528coxph\u51fd\u6570\u8fdb\u884cCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u62df\u5408\uff0c\u5176\u4e2d\"Surv(futime, fustat)\"\u662f\u751f\u5b58\u65f6\u95f4\u548c\u4e8b\u4ef6\uff08\u6b7b\u4ea1\u6216\u4e8b\u4ef6\uff09\u7684\u751f\u5b58\u5bf9\u8c61\u3002<\/span><\/span><\/code><code>#\u62df\u5408\u7ed3\u679c\u4fdd\u5b58\u5728\"res.cox\"\u53d8\u91cf\u4e2d\u3002<\/span><\/span><\/code><code>#\u7136\u540e\uff0c\u4f7f\u7528\"regplot\"\u51fd\u6570\u7ed8\u5236\u5217\u7ebf\u56fe\uff08Nomogram\u56fe\uff09\uff0c\u663e\u793a\u57fa\u56e0\u8868\u8fbe\u548c\u4e34\u5e8a\u56e0\u7d20\u4e0e\u751f\u5b58\u98ce\u9669\u7684\u5173\u7cfb\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>nomoRisk=predict(res.cox, data=rt, type=\"risk\"<\/span>)<\/span><\/code><code>rt=cbind(exp1, Nomogram=nomoRisk)<\/span><\/code><code>outTab=rbind(ID=colnames(rt), rt)<\/span><\/code><code>write.table(outTab, file=\"nomoRisk.txt\"<\/span>, sep=\"t\"<\/span>, col.names=F<\/span>, quote<\/span>=F<\/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=\"0.820627802690583\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_qqIwMjyTxMibhtafah7SsUKx4Gwicg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXW94AvH9euLIr2w3PTfxJJu2F3icsC5DqMzibMBrf6iaHBV7tCQqqIwMjyTxMibhtafah7SsUKx4Gwicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"669\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#\u8f93\u51fa\u5217\u7ebf\u56fe\u7684\u98ce\u9669\u6253\u5206\u6587\u4ef6\uff0c\u8ba1\u7b97\u5e76\u8f93\u51fa\u5217\u7ebf\u56fe\uff08Nomogram\u56fe\uff09\u4e2d\u7684\u98ce\u9669\u5f97\u5206\u3002<\/span><\/span><\/code><code>#\u4f7f\u7528predict\u51fd\u6570\u57fa\u4e8eCox\u6a21\u578b\u8ba1\u7b97\u6bcf\u4e2a\u6837\u672c\u7684\u98ce\u9669\u5f97\u5206\uff0c\u5e76\u5c06\u7ed3\u679c\u4fdd\u5b58\u5728\"nomoRisk\"\u53d8\u91cf\u4e2d\u3002<\/span><\/span><\/code><code>#\u63a5\u7740\uff0c\u5c06\u98ce\u9669\u5f97\u5206\u4e0e\u8868\u8fbe\u6570\u636e\u5408\u5e76\u4e3a\u65b0\u7684\u6570\u636e\u6846\"rt\"\uff0c\u518d\u5c06\u6570\u636e\u6846\u7684\u5217\u540d\u548c\u6570\u636e\u5199\u5165\u540d\u4e3a\"nomoRisk.txt\"\u7684\u6587\u672c\u6587\u4ef6\u4e2d\u3002<\/span><\/span><\/code><code>#\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>pdf(file=\"calibration.pdf\"<\/span>, width=5<\/span>, height=5<\/span>)<\/span><\/code><code>#\u7ed8\u5236\u4e86\u6821\u51c6\u66f2\u7ebf\uff08Calibration Curve\uff09\uff0c\u7528\u4e8e\u8bc4\u4f30Nomogram\u6a21\u578b\u7684\u9884\u6d4b\u6027\u80fd<\/span><\/span><\/code><code>#1\u5e74\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>f <- cph(Surv(futime, fustat) ~ Nomogram, x=T<\/span>, y=T<\/span>, surv=T<\/span>, data=rt, time.inc=1<\/span>)<\/span><\/code><code>cal <- calibrate(f, cmethod=\"KM\"<\/span>, method=\"boot\"<\/span>, u=1<\/span>, m=(nrow(rt)\/3<\/span>), B=1000<\/span>)<\/span><\/code><code>plot(cal, xlim=c<\/span>(0<\/span>,1<\/span>), ylim=c<\/span>(0<\/span>,1<\/span>),<\/span><\/code><code>xlab=\"Nomogram-predicted OS (%)\"<\/span>, ylab=\"Observed OS (%)\"<\/span>, lwd=1.5<\/span>, col=\"green\"<\/span>, sub=F<\/span>)<\/span><\/code><code>#3\u5e74\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>f <- cph(Surv(futime, fustat) ~ Nomogram, x=T<\/span>, y=T<\/span>, surv=T<\/span>, data=rt, time.inc=3<\/span>)<\/span><\/code><code>cal <- calibrate(f, cmethod=\"KM\"<\/span>, method=\"boot\"<\/span>, u=3<\/span>, m=(nrow(rt)\/3<\/span>), B=1000<\/span>)<\/span><\/code><code>plot(cal, xlim=c<\/span>(0<\/span>,1<\/span>), ylim=c<\/span>(0<\/span>,1<\/span>), xlab=\"\"<\/span>, ylab=\"\"<\/span>, lwd=1.5<\/span>, col=\"blue\"<\/span>, sub=F<\/span>, add=T<\/span>)<\/span><\/code><code>#5\u5e74\u6821\u51c6\u66f2\u7ebf<\/span><\/span><\/code><code>f <- cph(Surv(futime, fustat) ~ Nomogram, x=T<\/span>, y=T<\/span>, surv=T<\/span>, data=rt, time.inc=5<\/span>)<\/span><\/code><code>cal <- calibrate(f, cmethod=\"KM\"<\/span>, method=\"boot\"<\/span>, u=5<\/span>, m=(nrow(rt)\/3<\/span>), B=1000<\/span>)<\/span><\/code><code>plot(cal, xlim=c<\/span>(0<\/span>,1<\/span>), ylim=c<\/span>(0<\/span>,1<\/span>), xlab=\"\"<\/span>, ylab=\"\"<\/span>, lwd=1.5<\/span>, col=\"red\"<\/span>, sub=F<\/span>, add=T<\/span>)<\/span><\/code><code>legend('bottomright'<\/span>, c<\/span>('1-year'<\/span>, '3-year'<\/span>, '5-year'<\/span>),<\/span><\/code><code>col=c<\/span>(\"green\"<\/span>,\"blue\"<\/span>,\"red\"<\/span>), lwd=1.5<\/span>, bty = 'n'<\/span>)<\/span><\/code><code>dev.off()<\/span><\/code><code>#\u4f7f\u7528cph\u51fd\u6570\u5efa\u7acbCox\u6a21\u578b\uff0c\u5c06Nomogram\u4f5c\u4e3a\u89e3\u91ca\u53d8\u91cf\uff0c\u5e76\u8bbe\u5b9a\u4e0d\u540c\u7684\u65f6\u95f4\u95f4\u9694\u3002<\/span><\/span><\/code><code>#\u7136\u540e\uff0c\u4f7f\u7528calibrate\u51fd\u6570\u751f\u6210\u6821\u51c6\u66f2\u7ebf\u3002\u4ee3\u7801\u5c06\u6821\u51c6\u66f2\u7ebf\u7ed8\u5236\u5728\u4e00\u4e2aPDF\u6587\u4ef6\u4e2d\uff0c<\/span><\/span><\/code><code>#\u5206\u522b\u7ed8\u52361\u5e74\u30013\u5e74\u548c5\u5e74\u7684\u6821\u51c6\u66f2\u7ebf\uff0c\u5e76\u5728\u56fe\u4f8b\u4e2d\u663e\u793a\u4e0d\u540c\u65f6\u95f4\u95f4\u9694\u7684\u989c\u8272\u3002\u6700\u540e\uff0c\u901a\u8fc7dev.off()\u51fd\u6570\u5173\u95edPDF\u7ed8\u56fe\u8bbe\u5907\u3002<\/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: 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