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<\/p>\n\u4ee3\u7801\u4e2d\u5bf9\u9009\u5b9a\u7684\u57fa\u56e0vcan\u7684\u6837\u672c\u8868\u8fbe\u91cf\u8fdb\u884c\u5206\u6790\u3002\u4e0b\u9762\u662f\u4e0b\u8f7d\u7684\u80bf\u7624\u5fae\u73af\u5883\u8bc4\u5206\u5206\u6570\u6587\u4ef6\uff0c\u63a5\u4e0b\u6765\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.3744075829383886\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_k07ic7ibBPaETYyajyxG4EmzicRsKg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXQiaKOpVTDIszpmEiaPbbicjdicQTq0TQCueUVib7E0bKOAQPHsddNk07ic7ibBPaETYyajyxG4EmzicRsKg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"633\" style=\"vertical-align: middle;width: 100%;\" \/><\/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=\"0.7447045707915273\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_7OpQcpyvOac0pzIicI1zY1WexOy2uA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXQiaKOpVTDIszpmEiaPbbicjdibr7icvAkG4KN4rufPNzWGJ2mZT7OpQcpyvOac0pzIicI1zY1WexOy2uA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"897\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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>#if (!requireNamespace(\"BiocManager\", quietly = TRUE))<\/span><\/span><\/code><code># install.packages(\"BiocManager\")<\/span><\/span><\/code><code>#BiocManager::install(\"limma\")<\/span><\/span><\/code><code> <\/span><\/code><code>#install.packages(\"reshape2\")<\/span><\/span><\/code><code>#install.packages(\"ggpubr\")<\/span><\/span><\/code><code>#\u68c0\u67e5\u662f\u5426\u5df2\u5b89\u88c5BiocManager\u5305\uff08\u7528\u4e8e\u5b89\u88c5Bioconductor\u4e2d\u7684\u5305\uff09\uff0c<\/span><\/span><\/code><code>#\u5982\u679c\u6ca1\u6709\u5b89\u88c5\uff0c\u5219\u4f7f\u7528install.packages\u51fd\u6570\u5b89\u88c5BiocManager\u5305\u3002<\/span><\/span><\/code><code>#\u7136\u540e\u4f7f\u7528BiocManager::install\u51fd\u6570\u5b89\u88c5limma\u5305\uff0c\u8be5\u5305\u7528\u4e8e\u540e\u7eed\u7684\u6570\u636e\u5206\u6790\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>#\u5f15\u7528\u5305<\/span><\/span><\/code><code>library(limma)<\/span><\/code><code>library(reshape2)<\/span><\/code><code>library(ggpubr)<\/span><\/code><code>#\u8fd9\u4e24\u4e2a\u5305\u5206\u522b\u662freshape2\u548cggpubr\uff0c\u7528\u4e8e\u6570\u636e\u91cd\u5851\u548c\u56fe\u5f62\u7ed8\u5236<\/span><\/span><\/code><code>expFile=\"geneExp.txt\"<\/span> #\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>scoreFile=\"TMEscores.txt\"<\/span> #\u80bf\u7624\u5fae\u73af\u5883\u7684\u6253\u5206\u6587\u4ef6<\/span><\/span><\/code><code>#\u6307\u5b9a\u4e86\u8868\u8fbe\u6570\u636e\u6587\u4ef6\uff08expFile\uff09\u548c\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6587\u4ef6\uff08scoreFile\uff09<\/span><\/span><\/code><code>#\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\uff08expFile\uff09\u5e76\u8fdb\u884c\u9884\u5904\u7406\u3002<\/span><\/span><\/code><code>#\u6570\u636e\u6587\u4ef6\u4e2d\u7684\u8868\u8fbe\u91cf\u6570\u636e\u88ab\u5b58\u50a8\u5728\u540d\u4e3aexp\u7684\u6570\u636e\u6846\u4e2d\u3002<\/span><\/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>gene=colnames(exp<\/span>)[1<\/span>]<\/span><\/code><code>exp<\/span>=exp<\/span>[exp<\/span>$Type==\"Tumor\"<\/span>,1<\/span>,drop=F<\/span>]<\/span><\/code><code>exp<\/span>$Type=ifelse(exp<\/span>[,gene]>median(exp<\/span>[,gene]), \"High\"<\/span>, \"Low\"<\/span>)<\/span><\/code><code>#\u9996\u5148\uff0c\u901a\u8fc7colnames(exp)[1]\u53d6\u5f97\u7b2c\u4e00\u5217\u7684\u5217\u540d\uff08\u57fa\u56e0\u540d\uff09\uff0c\u7136\u540e\u6839\u636e\"Type\"\u5217\u7b5b\u9009\u51fa\"Tumor\"\u7c7b\u578b\u7684\u6837\u672c\u3002<\/span><\/span><\/code><code>#\u63a5\u7740\uff0c\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u4e2d\u4f4d\u6570\uff0c\u5c06\u6837\u672c\u5206\u4e3a\"High\"\u548c\"Low\"\u4e24\u7ec4\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728\u540d\u4e3a\"Type\"\u7684\u5217\u4e2d\u3002<\/span><\/span><\/code><code>score=read.table(scoreFile, header=T<\/span>, sep=\"t\"<\/span>, check.names=F<\/span>, row.names=1<\/span>)<\/span><\/code><code>score=score[,1<\/span>:3<\/span>]<\/span><\/code><code>#\u8bfb\u53d6\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6587\u4ef6\uff0c\u5e76\u5bf9\u6570\u636e\u8fdb\u884c\u6574\u7406\u8bfb\u53d6\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6587\u4ef6\uff08scoreFile\uff09\u5e76\u8fdb\u884c\u9884\u5904\u7406\u3002<\/span><\/span><\/code><code>#\u6570\u636e\u6587\u4ef6\u4e2d\u7684\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6570\u636e\u88ab\u5b58\u50a8\u5728\u540d\u4e3ascore\u7684\u6570\u636e\u6846\u4e2d\u3002\u5728\u8fd9\u91cc\uff0c\u53ea\u4fdd\u7559\u524d3\u5217\u7684\u6570\u636e\uff0c\u5373\u5305\u542b\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u7684\u5217\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>sameSample=intersect(row.names(exp<\/span>), row.names(score))<\/span><\/code><code>exp<\/span>=exp<\/span>[sameSample,\"Type\"<\/span>,drop=F<\/span>]<\/span><\/code><code>score=score[sameSample,,drop=F<\/span>]<\/span><\/code><code>rt=cbind(score, exp<\/span>)<\/span><\/code><code>rt$Type=factor(rt$Type, levels=c<\/span>(\"Low\"<\/span>, \"High\"<\/span>))<\/span><\/code><code>#\u6837\u54c1\u53d6\u4ea4\u96c6\u8868\u8fbe\u6570\u636e\uff08exp\uff09\u548c\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6570\u636e\uff08score\uff09\u7684\u6837\u672c\u53d6\u4ea4\u96c6\uff0c\u4ee5\u786e\u4fdd\u4e24\u8005\u5177\u6709\u76f8\u540c\u7684\u6837\u672c\u3002<\/span><\/span><\/code><code>#\u7136\u540e\u5c06\u4e24\u4e2a\u6570\u636e\u6846\u6309\u7167\u6837\u672c\u8fdb\u884c\u5408\u5e76\uff0c\u5408\u5e76\u540e\u7684\u6570\u636e\u5b58\u50a8\u5728\u540d\u4e3art\u7684\u6570\u636e\u6846\u4e2d\u3002<\/span><\/span><\/code><code>#\u6700\u540e\uff0c\u5c06\"Type\"\u5217\u8f6c\u6362\u4e3a\u56e0\u5b50\u53d8\u91cf\uff0c\u5e76\u6307\u5b9a\u6c34\u5e73\u987a\u5e8f\u4e3a\"Low\"\u548c\"High\"\u3002<\/span><\/span><\/code><code>data=melt(rt, id.vars=c<\/span>(\"Type\"<\/span>))<\/span><\/code><code>colnames(data)=c<\/span>(\"Type\"<\/span>, \"scoreType\"<\/span>, \"Score\"<\/span>)<\/span><\/code><code>#\u5c06\u5408\u5e76\u540e\u7684\u6570\u636e\u8f6c\u6362\u4e3aggplot2\u7684\u8f93\u5165\u6587\u4ef6\u4f7f\u7528melt\u51fd\u6570\u5c06\u5408\u5e76\u540e\u7684\u6570\u636e\uff08rt\uff09\u8f6c\u6362\u4e3aggplot2\u7ed8\u56fe\u51fd\u6570\u7684\u8f93\u5165\u683c\u5f0f\u3002<\/span><\/span><\/code><code>#melt\u51fd\u6570\u5c06\u6570\u636e\u6846\u4ece\u5bbd\u683c\u5f0f\u8f6c\u6362\u4e3a\u957f\u683c\u5f0f\uff0c\u5176\u4e2d\"Type\"\u5217\u4f5c\u4e3aid\u53d8\u91cf\uff0c\u5176\u4f59\u7684\u5217\u88ab\u8f6c\u6362\u4e3a\u4e24\u5217\uff1ascoreType\u548cScore\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>#\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe<\/span><\/span><\/code><code>p=ggviolin(data, x=\"scoreType\"<\/span>, y=\"Score\"<\/span>, fill = \"Type\"<\/span>,<\/span><\/code><code>xlab=\"\"<\/span>,<\/span><\/code><code>ylab=\"TME score\"<\/span>,<\/span><\/code><code>legend.title=gene,<\/span><\/code><code>add = \"boxplot\"<\/span>, add.params = list<\/span>(color=\"white\"<\/span>),<\/span><\/code><code>palette = c<\/span>(\"blue\"<\/span>,\"red\"<\/span>), width=1<\/span>)<\/span><\/code><code>p=p+rotate_x_text(45<\/span>)<\/span><\/code><code>p1=p+stat_compare_means(aes(group=Type),<\/span><\/code><code>method=\"wilcox.test\"<\/span>,<\/span><\/code><code>symnum.args=list<\/span>(cutpoints = c<\/span>(0<\/span>, 0.001<\/span>, 0.01<\/span>, 0.05<\/span>, 1<\/span>), symbols = c<\/span>(\"***\"<\/span>, \"**\"<\/span>, \"*\"<\/span>, \" \"<\/span>)),<\/span><\/code><code>label = \"p.signif\"<\/span>)<\/span><\/code><code>#\u7528ggviolin\u51fd\u6570\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe\u3002\u5c0f\u63d0\u7434\u56fe\u662f\u4e00\u79cd\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u7528\u4e8e\u663e\u793a\u4e0d\u540c\u7ec4\u4e4b\u95f4\u6570\u503c\u6570\u636e\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/span><\/span><\/code><code>#x\u8f74\u4e3ascoreType\uff0cy\u8f74\u4e3aScore\uff0c\u5c0f\u63d0\u7434\u56fe\u6309\u7167\"Type\"\u5217\uff08\"Low\"\u548c\"High\"\uff09\u8fdb\u884c\u586b\u5145\u3002\u540c\u65f6\uff0c\u6dfb\u52a0\u76d2\u56fe\u5728\u5c0f\u63d0\u7434\u56fe\u4e0a\uff0c<\/span><\/span><\/code><code>#\u5e76\u6307\u5b9a\u76d2\u56fe\u7684\u989c\u8272\u4e3a\u767d\u8272\u3002\u8fd9\u6837\u53ef\u4ee5\u540c\u65f6\u5c55\u793a\u6570\u636e\u7684\u5206\u5e03\u548c\u4e2d\u4f4d\u6570\u7b49\u7edf\u8ba1\u4fe1\u606f\u3002<\/span><\/span><\/code><code>#\u8f93\u51fa\u56fe\u5f62<\/span><\/span><\/code><code>pdf(file=\"vioplot.pdf\"<\/span>, width=6<\/span>, height=5<\/span>)<\/span><\/code><code>print(p1)<\/span><\/code><code>dev.off()<\/span><\/code><code>#\u4f7f\u7528pdf\u51fd\u6570\u5c06\u7ed8\u5236\u597d\u7684\u5c0f\u63d0\u7434\u56fe\u4fdd\u5b58\u4e3a\u540d\u4e3a\"vioplot.pdf\"\u7684PDF\u6587\u4ef6\u3002<\/span><\/span><\/code><code>#\u8fd9\u4e2a\u56fe\u5f62\u663e\u793a\u4e86\u4e0d\u540c\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u7ec4\uff08\"Low\"\u548c\"High\"\uff09\u4e4b\u95f4\u7684\u5dee\u5f02\uff0c<\/span><\/span><\/code><code>#\u5e76\u4f7f\u7528\u661f\u53f7\u6807\u8bb0\u4e0d\u540c\u7ec4\u4e4b\u95f4\u7684\u663e\u8457\u6027\u5dee\u5f02\uff08\u6839\u636ewilcox.test\u7684p\u503c\uff09\u3002<\/span><\/span><\/code><code>#\u901a\u8fc7\u8fd9\u4e2a\u5c0f\u63d0\u7434\u56fe\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u5c55\u793a\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u4e0e\u57fa\u56e0\u8868\u8fbe\u91cf\u4e4b\u95f4\u7684\u5173\u8054\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=\"0.8527980535279805\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gp6agB316lU2g5zoAXxtBOqCt64bmQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXQiaKOpVTDIszpmEiaPbbicjdCEPK2ibNZpibE1icgOSRbdIT9Dogp6agB316lU2g5zoAXxtBOqCt64bmQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"822\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u4e0e\u57fa\u56e0\u8868\u8fbe\u91cf\u4e4b\u95f4\u7684\u5173\u8054\u3002\u901a\u8fc7\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u89c2\u5bdf\u4e0d\u540c\u5f97\u5206\u7ec4\u4e4b\u95f4\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u5dee\u5f02\uff0c\u8fdb\u800c\u4e86\u89e3\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u5728\u4e0d\u540c\u57fa\u56e0\u8868\u8fbe\u6a21\u5f0f\u4e2d\u7684\u5206\u5e03\u60c5\u51b5\u3002\u8fd9\u79cd\u5173\u8054\u5206\u6790\u53ef\u4ee5\u4e3a\u80bf\u7624\u7814\u7a76\u63d0\u4f9b\u91cd\u8981\u7684\u7ebf\u7d22\uff0c\u5e2e\u52a9\u53d1\u73b0\u4e0e\u80bf\u7624\u5fae\u73af\u5883\u76f8\u5173\u7684\u91cd\u8981\u57fa\u56e0\u6216\u901a\u8def\uff0c\u4e3a\u6df1\u5165\u7814\u7a76\u80bf\u7624\u53d1\u751f\u548c\u53d1\u5c55\u63d0\u4f9b\u6709\u76ca\u7684\u4fe1\u606f\u3002<\/p>\n 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10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(249, 172, 172);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;border-style: solid;border-width: 1px;border-color: rgb(249, 172, 172);padding-right: 8px;padding-left: 8px;margin-right: 10px;\">\n<section style=\"text-align: justify;color: rgb(249, 172, 172);\" powered-by=\"xiumi.us\">\nE<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;border-style: solid;border-width: 1px;border-color: rgb(249, 172, 172);padding-right: 8px;padding-left: 8px;margin-right: 10px;\">\n<section style=\"text-align: justify;color: rgb(249, 172, 172);\" 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rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<\/body> \n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"\u5e08\u59b9\u5e26\u4f60\u5206\u6790\u5355\u57fa\u56e0\u4e0e\u80bf\u7624\u5fae\u73af\u5883\u8bc4\u5206\u7684\u76f8\u5173\u6027—\u5c0f\u63d0\u7434\u56fe \u5c0f\u5e08\u59b9 \u751f\u4fe1\u679c&nbs […]<\/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\/57681"}],"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=57681"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/57681\/revisions"}],"predecessor-version":[{"id":57687,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/57681\/revisions\/57687"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=57681"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=57681"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=57681"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":57681,"date":"2024-06-16T20:23:13","date_gmt":"2024-06-16T12:23:13","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=57681"},"modified":"2024-06-16T20:23:13","modified_gmt":"2024-06-16T12:23:13","slug":"%e5%b8%88%e5%a6%b9%e5%b8%a6%e4%bd%a0%e5%88%86%e6%9e%90%e5%8d%95%e5%9f%ba%e5%9b%a0%e4%b8%8e%e8%82%bf%e7%98%a4%e5%be%ae%e7%8e%af%e5%a2%83%e8%af%84%e5%88%86%e7%9a%84%e7%9b%b8%e5%85%b3%e6%80%a7","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=57681","title":{"rendered":"\u5e08\u59b9\u5e26\u4f60\u5206\u6790\u5355\u57fa\u56e0\u4e0e\u80bf\u7624\u5fae\u73af\u5883\u8bc4\u5206\u7684\u76f8\u5173\u6027—\u5c0f\u63d0\u7434\u56fe"},"content":{"rendered":"

\n
\n<\/title> \n<meta charset=\"utf-8\"> \n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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<\/p>\n\u4ee3\u7801\u4e2d\u5bf9\u9009\u5b9a\u7684\u57fa\u56e0vcan\u7684\u6837\u672c\u8868\u8fbe\u91cf\u8fdb\u884c\u5206\u6790\u3002\u4e0b\u9762\u662f\u4e0b\u8f7d\u7684\u80bf\u7624\u5fae\u73af\u5883\u8bc4\u5206\u5206\u6570\u6587\u4ef6\uff0c\u63a5\u4e0b\u6765\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.3744075829383886\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_k07ic7ibBPaETYyajyxG4EmzicRsKg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXQiaKOpVTDIszpmEiaPbbicjdicQTq0TQCueUVib7E0bKOAQPHsddNk07ic7ibBPaETYyajyxG4EmzicRsKg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"633\" style=\"vertical-align: middle;width: 100%;\" \/><\/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=\"0.7447045707915273\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_7OpQcpyvOac0pzIicI1zY1WexOy2uA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXQiaKOpVTDIszpmEiaPbbicjdibr7icvAkG4KN4rufPNzWGJ2mZT7OpQcpyvOac0pzIicI1zY1WexOy2uA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"897\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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>#if (!requireNamespace(\"BiocManager\", quietly = TRUE))<\/span><\/span><\/code><code># install.packages(\"BiocManager\")<\/span><\/span><\/code><code>#BiocManager::install(\"limma\")<\/span><\/span><\/code><code> <\/span><\/code><code>#install.packages(\"reshape2\")<\/span><\/span><\/code><code>#install.packages(\"ggpubr\")<\/span><\/span><\/code><code>#\u68c0\u67e5\u662f\u5426\u5df2\u5b89\u88c5BiocManager\u5305\uff08\u7528\u4e8e\u5b89\u88c5Bioconductor\u4e2d\u7684\u5305\uff09\uff0c<\/span><\/span><\/code><code>#\u5982\u679c\u6ca1\u6709\u5b89\u88c5\uff0c\u5219\u4f7f\u7528install.packages\u51fd\u6570\u5b89\u88c5BiocManager\u5305\u3002<\/span><\/span><\/code><code>#\u7136\u540e\u4f7f\u7528BiocManager::install\u51fd\u6570\u5b89\u88c5limma\u5305\uff0c\u8be5\u5305\u7528\u4e8e\u540e\u7eed\u7684\u6570\u636e\u5206\u6790\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>#\u5f15\u7528\u5305<\/span><\/span><\/code><code>library(limma)<\/span><\/code><code>library(reshape2)<\/span><\/code><code>library(ggpubr)<\/span><\/code><code>#\u8fd9\u4e24\u4e2a\u5305\u5206\u522b\u662freshape2\u548cggpubr\uff0c\u7528\u4e8e\u6570\u636e\u91cd\u5851\u548c\u56fe\u5f62\u7ed8\u5236<\/span><\/span><\/code><code>expFile=\"geneExp.txt\"<\/span> #\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>scoreFile=\"TMEscores.txt\"<\/span> #\u80bf\u7624\u5fae\u73af\u5883\u7684\u6253\u5206\u6587\u4ef6<\/span><\/span><\/code><code>#\u6307\u5b9a\u4e86\u8868\u8fbe\u6570\u636e\u6587\u4ef6\uff08expFile\uff09\u548c\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6587\u4ef6\uff08scoreFile\uff09<\/span><\/span><\/code><code>#\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6\uff08expFile\uff09\u5e76\u8fdb\u884c\u9884\u5904\u7406\u3002<\/span><\/span><\/code><code>#\u6570\u636e\u6587\u4ef6\u4e2d\u7684\u8868\u8fbe\u91cf\u6570\u636e\u88ab\u5b58\u50a8\u5728\u540d\u4e3aexp\u7684\u6570\u636e\u6846\u4e2d\u3002<\/span><\/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>gene=colnames(exp<\/span>)[1<\/span>]<\/span><\/code><code>exp<\/span>=exp<\/span>[exp<\/span>$Type==\"Tumor\"<\/span>,1<\/span>,drop=F<\/span>]<\/span><\/code><code>exp<\/span>$Type=ifelse(exp<\/span>[,gene]>median(exp<\/span>[,gene]), \"High\"<\/span>, \"Low\"<\/span>)<\/span><\/code><code>#\u9996\u5148\uff0c\u901a\u8fc7colnames(exp)[1]\u53d6\u5f97\u7b2c\u4e00\u5217\u7684\u5217\u540d\uff08\u57fa\u56e0\u540d\uff09\uff0c\u7136\u540e\u6839\u636e\"Type\"\u5217\u7b5b\u9009\u51fa\"Tumor\"\u7c7b\u578b\u7684\u6837\u672c\u3002<\/span><\/span><\/code><code>#\u63a5\u7740\uff0c\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u4e2d\u4f4d\u6570\uff0c\u5c06\u6837\u672c\u5206\u4e3a\"High\"\u548c\"Low\"\u4e24\u7ec4\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728\u540d\u4e3a\"Type\"\u7684\u5217\u4e2d\u3002<\/span><\/span><\/code><code>score=read.table(scoreFile, header=T<\/span>, sep=\"t\"<\/span>, check.names=F<\/span>, row.names=1<\/span>)<\/span><\/code><code>score=score[,1<\/span>:3<\/span>]<\/span><\/code><code>#\u8bfb\u53d6\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6587\u4ef6\uff0c\u5e76\u5bf9\u6570\u636e\u8fdb\u884c\u6574\u7406\u8bfb\u53d6\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6587\u4ef6\uff08scoreFile\uff09\u5e76\u8fdb\u884c\u9884\u5904\u7406\u3002<\/span><\/span><\/code><code>#\u6570\u636e\u6587\u4ef6\u4e2d\u7684\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6570\u636e\u88ab\u5b58\u50a8\u5728\u540d\u4e3ascore\u7684\u6570\u636e\u6846\u4e2d\u3002\u5728\u8fd9\u91cc\uff0c\u53ea\u4fdd\u7559\u524d3\u5217\u7684\u6570\u636e\uff0c\u5373\u5305\u542b\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u7684\u5217\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>sameSample=intersect(row.names(exp<\/span>), row.names(score))<\/span><\/code><code>exp<\/span>=exp<\/span>[sameSample,\"Type\"<\/span>,drop=F<\/span>]<\/span><\/code><code>score=score[sameSample,,drop=F<\/span>]<\/span><\/code><code>rt=cbind(score, exp<\/span>)<\/span><\/code><code>rt$Type=factor(rt$Type, levels=c<\/span>(\"Low\"<\/span>, \"High\"<\/span>))<\/span><\/code><code>#\u6837\u54c1\u53d6\u4ea4\u96c6\u8868\u8fbe\u6570\u636e\uff08exp\uff09\u548c\u80bf\u7624\u5fae\u73af\u5883\u6253\u5206\u6570\u636e\uff08score\uff09\u7684\u6837\u672c\u53d6\u4ea4\u96c6\uff0c\u4ee5\u786e\u4fdd\u4e24\u8005\u5177\u6709\u76f8\u540c\u7684\u6837\u672c\u3002<\/span><\/span><\/code><code>#\u7136\u540e\u5c06\u4e24\u4e2a\u6570\u636e\u6846\u6309\u7167\u6837\u672c\u8fdb\u884c\u5408\u5e76\uff0c\u5408\u5e76\u540e\u7684\u6570\u636e\u5b58\u50a8\u5728\u540d\u4e3art\u7684\u6570\u636e\u6846\u4e2d\u3002<\/span><\/span><\/code><code>#\u6700\u540e\uff0c\u5c06\"Type\"\u5217\u8f6c\u6362\u4e3a\u56e0\u5b50\u53d8\u91cf\uff0c\u5e76\u6307\u5b9a\u6c34\u5e73\u987a\u5e8f\u4e3a\"Low\"\u548c\"High\"\u3002<\/span><\/span><\/code><code>data=melt(rt, id.vars=c<\/span>(\"Type\"<\/span>))<\/span><\/code><code>colnames(data)=c<\/span>(\"Type\"<\/span>, \"scoreType\"<\/span>, \"Score\"<\/span>)<\/span><\/code><code>#\u5c06\u5408\u5e76\u540e\u7684\u6570\u636e\u8f6c\u6362\u4e3aggplot2\u7684\u8f93\u5165\u6587\u4ef6\u4f7f\u7528melt\u51fd\u6570\u5c06\u5408\u5e76\u540e\u7684\u6570\u636e\uff08rt\uff09\u8f6c\u6362\u4e3aggplot2\u7ed8\u56fe\u51fd\u6570\u7684\u8f93\u5165\u683c\u5f0f\u3002<\/span><\/span><\/code><code>#melt\u51fd\u6570\u5c06\u6570\u636e\u6846\u4ece\u5bbd\u683c\u5f0f\u8f6c\u6362\u4e3a\u957f\u683c\u5f0f\uff0c\u5176\u4e2d\"Type\"\u5217\u4f5c\u4e3aid\u53d8\u91cf\uff0c\u5176\u4f59\u7684\u5217\u88ab\u8f6c\u6362\u4e3a\u4e24\u5217\uff1ascoreType\u548cScore\u3002<\/span><\/span><\/code><code> <\/span><\/code><code>#\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe<\/span><\/span><\/code><code>p=ggviolin(data, x=\"scoreType\"<\/span>, y=\"Score\"<\/span>, fill = \"Type\"<\/span>,<\/span><\/code><code>xlab=\"\"<\/span>,<\/span><\/code><code>ylab=\"TME score\"<\/span>,<\/span><\/code><code>legend.title=gene,<\/span><\/code><code>add = \"boxplot\"<\/span>, add.params = list<\/span>(color=\"white\"<\/span>),<\/span><\/code><code>palette = c<\/span>(\"blue\"<\/span>,\"red\"<\/span>), width=1<\/span>)<\/span><\/code><code>p=p+rotate_x_text(45<\/span>)<\/span><\/code><code>p1=p+stat_compare_means(aes(group=Type),<\/span><\/code><code>method=\"wilcox.test\"<\/span>,<\/span><\/code><code>symnum.args=list<\/span>(cutpoints = c<\/span>(0<\/span>, 0.001<\/span>, 0.01<\/span>, 0.05<\/span>, 1<\/span>), symbols = c<\/span>(\"***\"<\/span>, \"**\"<\/span>, \"*\"<\/span>, \" \"<\/span>)),<\/span><\/code><code>label = \"p.signif\"<\/span>)<\/span><\/code><code>#\u7528ggviolin\u51fd\u6570\u7ed8\u5236\u5c0f\u63d0\u7434\u56fe\u3002\u5c0f\u63d0\u7434\u56fe\u662f\u4e00\u79cd\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u7528\u4e8e\u663e\u793a\u4e0d\u540c\u7ec4\u4e4b\u95f4\u6570\u503c\u6570\u636e\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/span><\/span><\/code><code>#x\u8f74\u4e3ascoreType\uff0cy\u8f74\u4e3aScore\uff0c\u5c0f\u63d0\u7434\u56fe\u6309\u7167\"Type\"\u5217\uff08\"Low\"\u548c\"High\"\uff09\u8fdb\u884c\u586b\u5145\u3002\u540c\u65f6\uff0c\u6dfb\u52a0\u76d2\u56fe\u5728\u5c0f\u63d0\u7434\u56fe\u4e0a\uff0c<\/span><\/span><\/code><code>#\u5e76\u6307\u5b9a\u76d2\u56fe\u7684\u989c\u8272\u4e3a\u767d\u8272\u3002\u8fd9\u6837\u53ef\u4ee5\u540c\u65f6\u5c55\u793a\u6570\u636e\u7684\u5206\u5e03\u548c\u4e2d\u4f4d\u6570\u7b49\u7edf\u8ba1\u4fe1\u606f\u3002<\/span><\/span><\/code><code>#\u8f93\u51fa\u56fe\u5f62<\/span><\/span><\/code><code>pdf(file=\"vioplot.pdf\"<\/span>, width=6<\/span>, height=5<\/span>)<\/span><\/code><code>print(p1)<\/span><\/code><code>dev.off()<\/span><\/code><code>#\u4f7f\u7528pdf\u51fd\u6570\u5c06\u7ed8\u5236\u597d\u7684\u5c0f\u63d0\u7434\u56fe\u4fdd\u5b58\u4e3a\u540d\u4e3a\"vioplot.pdf\"\u7684PDF\u6587\u4ef6\u3002<\/span><\/span><\/code><code>#\u8fd9\u4e2a\u56fe\u5f62\u663e\u793a\u4e86\u4e0d\u540c\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u7ec4\uff08\"Low\"\u548c\"High\"\uff09\u4e4b\u95f4\u7684\u5dee\u5f02\uff0c<\/span><\/span><\/code><code>#\u5e76\u4f7f\u7528\u661f\u53f7\u6807\u8bb0\u4e0d\u540c\u7ec4\u4e4b\u95f4\u7684\u663e\u8457\u6027\u5dee\u5f02\uff08\u6839\u636ewilcox.test\u7684p\u503c\uff09\u3002<\/span><\/span><\/code><code>#\u901a\u8fc7\u8fd9\u4e2a\u5c0f\u63d0\u7434\u56fe\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u5c55\u793a\u80bf\u7624\u5fae\u73af\u5883\u5f97\u5206\u4e0e\u57fa\u56e0\u8868\u8fbe\u91cf\u4e4b\u95f4\u7684\u5173\u8054\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=\"0.8527980535279805\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gp6agB316lU2g5zoAXxtBOqCt64bmQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXQiaKOpVTDIszpmEiaPbbicjdCEPK2ibNZpibE1icgOSRbdIT9Dogp6agB316lU2g5zoAXxtBOqCt64bmQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"822\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section 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[…]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/57681"}],"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=57681"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/57681\/revisions"}],"predecessor-version":[{"id":57687,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/57681\/revisions\/57687"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=57681"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=57681"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=57681"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}