{"id":50280,"date":"2024-06-16T09:50:33","date_gmt":"2024-06-16T01:50:33","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=50280"},"modified":"2024-06-16T09:50:33","modified_gmt":"2024-06-16T01:50:33","slug":"%e5%8d%95%e4%b8%aa%e6%95%b0%e6%8d%ae%e5%ba%93%e7%94%a8%e8%85%bb%e4%ba%86%ef%bc%9f%e5%a4%9a%e6%95%b0%e6%8d%ae%e5%ba%93%e7%bb%84%e5%90%88%e6%8b%b3%e5%b8%a6%e4%bd%a0%e6%89%93%e5%bc%80-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=50280","title":{"rendered":"\u5355\u4e2a\u6570\u636e\u5e93\u7528\u817b\u4e86\uff1f\u591a\u6570\u636e\u5e93\u201c\u7ec4\u5408\u62f3\u201d\u5e26\u4f60\u6253\u5f00\u514d\u75ab\u6d78\u6da6\u65b0\u601d\u8def\uff01"},"content":{"rendered":"


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normal;font-variant-position: normal;color: rgb(255, 0, 0);\">\u8003\u8651\u5230\u672c\u6b21\u590d\u73b0\u7684\u6570\u636e\u91cf\u6bd4\u8f83\u5927\uff0c\u5c0f\u679c\u63a8\u8350\u5927\u5bb6\u79df\u8d41\u6211\u4eec\u7684\u670d\u52a1\u5668\u8fdb\u884c\u672c\u6b21\u7684\u590d\u73b0\u5b66\u4e60\uff5e<\/span><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(255, 0, 0);font-size: 16px;\">    <img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015098\" data-ratio=\"0.38981481481481484\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png&wxfrom=5&wx_lazy=1&wx_co=1'\" data-w=\"1080\" data-recalc-dims=\"1\" \/>      <o:p> <\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u672c\u6b21\u6211\u4eec\u4f7f\u7528\u7684\u662f\u4e0b\u9762\u8fd9\u51e0\u4e2a\u6570\u636e\u5e93\uff1a<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">TARGET\uff1a<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">https:\/\/ocg.cancer.gov\/programs\/target<\/span><\/section>\n<section style=\"text-align: left;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">CBTN\uff1a<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">https:\/\/cbtn.org\/research\/specimendata\/<\/span><\/section>\n<section style=\"text-align: left;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">ICGC \uff1ahttps:\/\/icgc.org\/icgc\/<\/span><\/section>\n<section style=\"text-align: left;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">TCGA\uff1ahttps:\/\/www.cancer.gov\/about-nci\/organization<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5728\u8fd9\u51e0\u4e2a\u6570\u636e\u5e93\u4e2d\uff0c\u6211\u4eec\u4eca\u5929\u4e3b\u8981\u4f7f\u7528\u5176\u4e2d\u7684\u513f\u7ae5\u60a3\u8005\u6570\u636e\u4e3a\u5927\u5bb6\u8fdb\u884c\u6559\u7a0b\uff0c\u5c0f\u4f19\u4f34\u4eec\u5982\u679c\u5bf9\u5176\u4ed6\u7684\u80bf\u7624\u6570\u636e\u611f\u5174\u8da3\uff0c\u4e5f\u53ef\u4ee5\u81ea\u5df1\u8bd5\u4e00\u8bd5\u5176\u4ed6\u7684\u6570\u636e\u5466\uff0c\u6211\u4eec\u5728\u6570\u636e\u5e93\u4e2d\u83b7\u53d6\u513f\u79d1\u795e\u7ecf\u7cfb\u7edf\u80bf\u7624(pedNST)\u7684RNA-seq\u6570\u636e\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u5df2\u7ecf\u5e2e\u5927\u5bb6\u6574\u7406\u597d\u4e86\uff0c\u5927\u5bb6\u4ece\u4e0b\u9762\u7684\u94fe\u63a5\u5c31\u53ef\u4ee5\u83b7\u53d6\uff1a<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">        <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u94fe\u63a5\uff1ahttps:\/\/pan.baidu.com\/s\/135jKVqVbFB8CuAvDAGmgFw<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u63d0\u53d6\u7801\uff1a9if2<\/span><span style=\"font-size: 16px;letter-spacing: 0.034em;\">         <\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"5.3334146\" style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\"><br \/><\/td>\n<td width=\"0.0\" height=\"5.3334146\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015092\" data-ratio=\"0.5805555555555556\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_Nw5luKRp9ajZotO4AXicJpRqTRsSFQ-3.png?resize=553%2C321\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0Jv9xmHctwVGibIdOf37FWQ7y3SqvNw5luKRp9ajZotO4AXicJpRqTRsSFQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"321 .4700012207031\" width=\"553 .739990234375\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5982\u56fe\uff0c\u662f\u6211\u4eec\u672c\u6b21\u8981\u7528\u5230\u7684\u4e3b\u8981\u6570\u636e\uff08estimate_ped_pdx.RData\uff09\uff0c\u5176\u4e2d\u5305\u62ec\u4e86\u513f\u7ae5\u7684\u4e00\u4e9b\u80bf\u7624\u6570\u636e\uff0c\u4f8b\u5982StromalScore\uff0c\u662f\u4e00\u79cd\u57fa\u4e8e\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u9884\u6d4b\u80bf\u7624\u7ec4\u7ec7\u4e2d\u57fa\u8d28\u7ec6\u80de\u6d78\u6da6\u7a0b\u5ea6\u7684\u5206\u503c\uff0c\u6570\u503c\u8d8a\u9ad8\uff0c\u9884\u540e\u6d3b\u6027\u8d8a\u5dee\uff0c\u5e76\u4e14\u514d\u75ab\u6d3b\u6027\u8d8a\u4f4e\uff0c\u8fd8\u6709\u514d\u75ab\u5f97\u5206\uff0cESTIMATE\u514d\u75ab\u8bc4\u5206\u7b49\u3002<\/span><\/section>\n<section style=\"font-size: 16px;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(69, 107, 176);padding-right: 6px;padding-bottom: 6px;padding-left: 6px;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;transform: translate3d(19px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);\">\n<p style=\"text-wrap: wrap;\"><br \/><\/p>\n<\/section>\n<\/section>\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 255, 255);padding: 23px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"font-size: 16px;\">\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d<span style=\"color: rgb(255, 41, 65);\">\u201c111\u201d<\/span>\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6\uff1b<\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"text-decoration: underline;color: rgb(255, 41, 65);font-size: 16px;\"><em><strong>\u6587\u4ef6\u7f16\u53f7\uff1a240115<\/strong><\/em><\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"font-size: 16px;\"><strong><span style=\"color: rgb(255, 41, 65);\">\u679c\u7c89\u798f\u5229<\/span><\/strong><span style=\"color: rgb(0, 128, 255);\"><strong>\uff1a\u751f\u4fe1\u4eba\u5fc5\u5907\u795e\u5668\u2014\u2014\u670d\u52a1\u5668<\/strong><\/span><br \/><\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"font-size: 16px;\">\u5e73\u65f6\u751f\u4fe1\u5206\u6790\u5b66\u4e60\u4e2d\u6709\u8981\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\uff0c\u7c89\u4e1d\u798f\u5229\u90fd\u662f\u5e02\u573a\u8d85\u4f4e\u4ef7\u683c\uff0c\u8d76\u5feb\u627e\u5c0f\u679c\u9886\u53d6\u514d\u8d39\u7684\u8bd5\u7528\u8d26\u53f7\u5427\uff01<\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247495825&idx=2&sn=a22a72496a1c082ea5b827be94ce4d99&chksm=cf7f6054f808e94264e14bfed4359cab3fcaaca249952a9f761c37ece352dcd7108579788b89&scene=21#wechat_redirect\" textvalue=\"\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 16px;\" rel=\"noopener\"><span style=\"font-size: 16px;\">\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09<\/span><\/a><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\"> <\/o:p><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5728\u5206\u6790\u4e4b\u524d\uff0c\u5c0f\u679c\u5148\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e0b\u4eca\u5929\u7684\u5206\u6790\u601d\u8def\uff0c\u6211\u4eec\u5148\u5bfc\u5165\u4e0b\u8f7d\u7684\u6570\u636e\uff0c\u7136\u540e\u4f9d\u6b21\u5bf9\u6570\u636e\u8fdb\u884c\u603b\u4f53\u7684\u6982\u89c8\uff0c\u5229\u7528\u4e00\u4e9b\u8bc4\u5206\u6807\u51c6\u8fdb\u884c\u8bc4\u5206\uff0c\u5212\u5206\u514d\u75ab\u96c6\u7fa4\uff0c\u6700\u540e\u8fdb\u884c\u4e00\u4e9b\u76f8\u5173\u6027\u5206\u6790\uff0c\u8fd9\u4e2a\u601d\u8def\u540c\u6837\u53ef\u4ee5\u5e94\u7528\u5230\u5176\u4ed6\u7684\u514d\u75ab\u5206\u6790\u4e2d~<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">Step 1 \u5bf9\u5bfc\u5165\u7684\u56db\u4e2a\u6570\u636e\u5e93\u7684\u6837\u672c\u91cf\u548c\u7814\u7a76\u7684\u80bf\u7624\u7c7b\u578b\u8fdb\u884c\u6982\u89c8<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">        <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u5bfc\u5165\u6574\u5408\u597d\u7684\u6570\u636e\u5e93\u6570\u636e<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">load<\/span>(paste0(datapath,<span class=\"code-snippet__string\">\"estimate_ped_pdx.RData\"<\/span>))           <\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u53ea\u4fdd\u7559ped\uff08\u513f\u79d1\uff09\u6570\u636e<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">ped<\/span> <- estimate_ped_pdx[ estimate_ped_pdx<span class=\"code-snippet__variable\">$group<\/span> != <span class=\"code-snippet__string\">\"TCGA\"<\/span>,]tab <- as.data.frame(table(ped<span class=\"code-snippet__variable\">$cohort<\/span>), stringsAsFactors = F)tab <- tab[order(tab<span class=\"code-snippet__variable\">$Freq<\/span>, decreasing = T),]        <\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u6392\u5e8f<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">ped$cohort <- factor(ped$cohort, levels = tab$Var1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">ped$group <- factor(ped$group, levels = c(\"CBTN\", \"ICGC\", \"TARGET\", \"PDX (ITCC)\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fig1a <- ggplot(data = ped) + geom_bar(aes(y = cohort, fill = group)) + myaxis + myplot +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> theme(axis.title = element_blank(), axis.text.x = element_text(size = 25, angle = 0, hjust = 0.5), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> legend.position = c(0.8,0.9), legend.title = element_blank(), plot.margin = margin(1,1,1,1, \"cm\")) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_fill_manual(values = group_col)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(file = paste0(plotpath,\"Fig1_A.pdf\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> width = 10, height = 10, useDingbats = FALSE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fig1a <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dev.off()<\/span><\/span><\/code><\/section><\/pre>\n<\/section>\n<p><span style=\"color: rgb(0, 112, 192);font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">       <\/span><o:p style=\"color: rgb(0, 112, 192);font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><span style=\"font-size: 16px;letter-spacing: 0.034em;\">    <\/span><\/p>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"8.266792\" style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\"><br \/><\/td>\n<td width=\"0.0\" height=\"8.266792\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015089\" data-ratio=\"1.0023174971031286\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_nQQMKndqrH7JcbnuA3NK815zuemy8w-2.png?resize=377%2C377\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0JvnEYstchd3O2jIqH9xIQc0DibLnQQMKndqrH7JcbnuA3NK815zuemy8w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"863\" height=\"377 .9599914550781\" width=\"377 .20001220703125\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><br \/><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(17, 17, 17);\">\u5982\u56fe\u662f\u6982\u89c8\u7684\u7ed3\u679c\uff0c\u56fe\u4e2d\u663e\u793a\u4e86\u4e0d\u540c\u80bf\u7624\u7c7b\u578b\uff08\u5982ETMR\u3001NFB\u7b49\uff09\u5728CBTN\u3001ICGC\u548cTARGET\u4e09\u4e2a\u6570\u636e\u5e93\u4e2d\u7684\u6570\u91cf\u3002\u5176\u4e2d\uff0c<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">PDX:\u60a3\u8005\u6765\u6e90\u7684\u5f02\u79cd\u79fb\u690d\u6a21\u578b\uff0cETMR:\u5e26\u6709\u591a\u5c42\u82b1\u7c07\u7684\u80da\u80ce\u6027\u80bf\u7624\uff0cNFB:\u795e\u7ecf\u7ea4\u7ef4\u7624\uff0cMNG:\u8111\u819c\u7624\uff0cSCHW:\u795e\u7ecf\u9798\u7624\uff0cCP:\u8109\u7edc\u4e1b\u80bf\u7624\uff0cCPH:\u9885\u54bd\u7ba1\u7624\uff0cATRT:\u975e\u5178\u578b\u7578\u80ce\u7624\/\u6a2a\u7eb9\u808c\u6837\u80bf\u7624\uff0cEPN:\u5ba4\u7ba1\u819c\u7624\uff0cpedHGG:\u513f\u79d1\u9ad8\u7ea7\u522b\u80f6\u8d28\u7624\uff0cNBL:\u795e\u7ecf\u6bcd\u7ec6\u80de\u7624\uff0cMB:\u9ad3\u6bcd\u7ec6\u80de\u7624\uff0cpedLGG:\u513f\u79d1\u4f4e\u7ea7\u522b\u80f6\u8d28\u7624\u3002\u8bf4\u660e\u5176\u4e2d\u7684\u80bf\u7624\u7c7b\u578b\u8fd8\u662f\u975e\u5e38\u4e30\u5bcc\u7684\u3002<\/span><\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">        <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">Step 2 \u5bf9\u6240\u6709\u7684\u80bf\u7624\u6570\u636e\u8fdb\u884cESTIMATE\u514d\u75ab\u8bc4\u5206\u5206\u6790<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">#\u8bbe\u7f6e\u6570\u7ec4<\/span>    <\/span><o:page><\/o:page><\/section>\n<p><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar <- as.data.frame(matrix(ncol = 7, nrow = 2))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">colnames(emptyvar) <- colnames(estimate_ped_pdx)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar$group <- as.character(emptyvar$group)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar$cohort <- as.character(emptyvar$cohort)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[1,\u201daliquot_id\u201d] <- \u201cempty1\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[2,\u201daliquot_id\u201d] <- \u201cempty2\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[1,\u201dsample_id\u201d] <- \u201cempty1\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[2,\u201dsample_id\u201d] <- \u201cempty2\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[1,\u201dImmuneScore\u201d] <- 3500<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[2,\u201dImmuneScore\u201d] <- 3500<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[1,\u201dcohort\u201d] <- \u201cEMPTY1\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">emptyvar[2,\u201dcohort\u201d] <- \u201cEMPTY2\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">estimate_ped_pdx <- rbind(estimate_ped_pdx,emptyvar)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u8ba1\u7b97ESTIMATE\u514d\u75ab\u8bc4\u5206<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">estimate_ped_pdx$percread <- 8.0947988*exp(estimate_ped_pdx$ImmuneScore*0.0006267)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts <- cbind(NA, unique(estimate_ped_pdx$cohort)) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">colnames(immune.cohorts) <- c(\"group\",\"cohort\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts <- as.data.frame(immune.cohorts)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts$group <- as.character(immune.cohorts$group)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">adults <- c(\"PRAD\", \"LGG\", \"OV\", \"SKCM\", \"COAD\", \"GBM\", \"LUAD\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">peds <- c(\"PDX\",\"ETMR\", \"MB\", \"ATRT\", \"EPN\", \"pedHGG\", \"CP\", \"NBL\", \"pedLGG\", \"CPH\", \"MNG\", \"SCHW\", \"NFB\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts[immune.cohorts$cohort %in% adults, 1] <- \"Adult\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts[immune.cohorts$cohort %in% peds, 1] <- \"Pediatric\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts[immune.cohorts$cohort == \"EMPTY1\",1] <- \"Pediatric\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts[immune.cohorts$cohort == \"EMPTY2\",1] <- \"Pediatric\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u83b7\u53d6\u6bcf\u4e00\u7ec4\u7684\u836f\u7269\u6570\u636e<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(i in <span class=\"code-snippet__number\">1<\/span>:nrow(immune.cohorts)){ immune.cohorts$median_immunereads[i]<-median(estimate_ped_pdx$percread[estimate_ped_pdx$cohort == immune.cohorts$cohort[i]])}<span class=\"code-snippet__comment\">#\u5bf9\u80bf\u7624\u7684\u7c7b\u578b\u8fdb\u884c\u6392\u5e8ftmp <- immune.cohorts[which(immune.cohorts$group == \"Pediatric\"),]tmp1 <- immune.cohorts[which(immune.cohorts$group == \"Adult\"),]immune.cohorts <- rbind(tmp,tmp1)immune.cohorts$cohort <- factor(immune.cohorts$cohort, levels = c(\"PDX\",\"ETMR\", \"MB\", \"ATRT\", \"EPN\", \"pedHGG\", \"CP\", \"NBL\", \"pedLGG\", \"CPH\", \"MNG\", \"SCHW\", \"NFB\", \"EMPTY1\",\"EMPTY2\", \"PRAD\", \"LGG\", \"OV\", \"SKCM\", \"COAD\", \"GBM\", \"LUAD\")) immune.cohorts <- immune.cohorts[order(immune.cohorts$cohort),]# \u8c03\u7528Splot \u5bf9\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u51c6\u5907\u7ed8\u56fedisease.width <- (nrow(estimate_ped_pdx)\/nrow(immune.cohorts)) sorted.estimate_ped_pdx <- estimate_ped_pdx[0,]start = 0for(i in 1:(nrow(immune.cohorts))){ tmp <- estimate_ped_pdx[estimate_ped_pdx$cohort == immune.cohorts$cohort[i],] tmp <- tmp[order(tmp$percread),] #create range of x values to squeeze dots into equal widths of the plot for each Disease regardless of the number of samples div <- disease.width\/nrow(tmp)#If there is only one sample, put the dot in the middle of the alloted spaceif(dim(tmp)[1]==1) { tmp$Xpos<-start+(disease.width\/2) } else tmp$Xpos<-seq(from = start, to = start+disease.width, by = div)[-1] sorted.estimate_ped_pdx<-rbind(sorted.estimate_ped_pdx,tmp) immune.cohorts$Median.start[i] <- tmp$Xpos[1] immune.cohorts$Median.stop[i] <- tmp$Xpos[nrow(tmp)] immune.cohorts$N[i]<-nrow(tmp) start <- start+disease.width+30}immune.cohorts$medianloc <- immune.cohorts$Median.start+((immune.cohorts$Median.stop-immune.cohorts$Median.start)\/2) sorted.estimate_ped_pdx$cohort <- factor(sorted.estimate_ped_pdx$cohort, levels = levels(immune.cohorts$cohort))<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u989c\u8272\u8bbe\u7f6e<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">rmEMPTY <- rep(\"black\",22)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">rmEMPTY[14:15] <- \"white\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts$color_crossbar <- NA<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts$color_crossbar[immune.cohorts$cohort == \"EMPTY1\"] <- \"white\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts$color_crossbar[immune.cohorts$cohort == \"EMPTY2\"] <- \"white\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts$color_crossbar[is.na(immune.cohorts$color_crossbar)] <- \"black\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">immune.cohorts$cohort_n <- paste0(immune.cohorts$cohort, \" (n=\", immune.cohorts$N, \")\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u7ed8\u5236\u56fe\u7247<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fig1b1.fx <- function(x){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ggplot() + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> geom_point(data = sorted.estimate_ped_pdx, aes(x = Xpos ,y = percread, color = cohort), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> size = 7, shape = 20) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> geom_crossbar(data = immune.cohorts, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> aes(x = medianloc,y = median_immunereads, color = color_crossbar,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ymin = median_immunereads,ymax = median_immunereads), width = disease.width) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> myaxis + myplot +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> theme(axis.title.x = element_blank(), axis.title.y = element_text(size = 25),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.text.x = element_text(size = 25, angle = 45, hjust = 1, color = rmEMPTY),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.text.y = element_text(size = 25)) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_color_manual(values = c(cohort_col, \"white\" = \"white\", \"black\" = \"black\"), guide = \"none\") +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_x_continuous(breaks = seq((disease.width)\/2,max(sorted.estimate_ped_pdx$Xpos),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> disease.width+30), labels = immune.cohorts$cohort_n, expand = c(0,20)) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_y_continuous(breaks = seq(0, 70, by = 10)) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> labs(y = \"% Immune Reads\") <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fig1b <- fig1b1.fx(sorted.estimate_ped_pdx)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(file = paste0(plotpath,\"Fig1_B.pdf\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> width = 20, height = 8, useDingbats = FALSE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fig1b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dev.off()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<p><br \/><\/p>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"4.000061\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"0.0\" height=\"4.000061\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015090\" data-ratio=\"0.3990740740740741\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_y315ib3yFicEV2yZ1PpicSWyVSexJw-3.png?resize=553%2C220\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0JvGJMDSf34iawuEEXTO24UpkQSyFxly315ib3yFicEV2yZ1PpicSWyVSexJw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"220 .66998291015625\" width=\"553 .3400268554688\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><br \/><\/p>\n<section style=\"text-align: left;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u5982\u56fe\uff0c\u662f\u57fa\u4e8eESTIMATE\u514d\u75ab\u8bc4\u5206\u7684\u513f\u7ae5\u548c\u6210\u4eba\u764c\u75c7\u7684\u767e\u5206\u6bd4\u514d\u75ab\u8bfb\u6570\u5206\u5e03\u3002ESTIMATE\uff0c\u4e5f\u5c31\u662fEstimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data\uff0c\u662f\u4e00\u79cd\u4f7f\u7528\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u9884\u6d4b\u80bf\u7624\u7eaf\u5ea6\u548c\u80bf\u7624\u7ec4\u7ec7\u4e2d\u6d78\u6da6\u6027\u57fa\u8d28\/\u514d\u75ab\u7ec6\u80de\u5b58\u5728\u7684\u5206\u6570\uff0c\u5305\u542b\u57fa\u8d28\u8bc4\u5206(\u7528\u4e8e\u6355\u6349\u80bf\u7624\u7ec4\u7ec7\u4e2d\u57fa\u8d28\u7684\u5b58\u5728) ,\u514d\u75ab\u8bc4\u5206(\u7528\u4e8e\u8868\u793a\u80bf\u7624\u7ec4\u7ec7\u4e2d\u514d\u75ab\u7ec6\u80de\u7684\u6d78\u6da6) \uff0cestimate\u8bc4\u5206(\u7528\u4e8e\u63a8\u65ad\u80bf\u7624\u7eaf\u5ea6)\u3002<\/span>    <\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;text-align: justify;\">        <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;text-align: justify;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u56fe\u4e2d\u7684PDX\u662f\u4f5c\u4e3a\u514d\u75ab\u6d78\u6da6\u7684\u9634\u6027\u5bf9\u7167\u800c\u8bbe\u7f6e\u7684\uff0c\u6bcf\u79cd\u989c\u8272\u4ee3\u8868\u4e00\u79cd\u7279\u5b9a\u7c7b\u578b\u7684\u764c\u75c7\uff0cy\u8f74\u8868\u793a%\u514d\u75ab\u8bfb\u6570\uff0cx\u8f74\u4e0a\u5217\u51fa\u4e86\u5404\u79cd\u764c\u75c7\u7c7b\u578b\u53ca\u5176\u6837\u672c\u6570\u91cf\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">   <\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">      <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u901a\u8fc7ESTIMATE\u514d\u75ab\u8bc4\u5206\u53ef\u4ee5\u6620\u4e86\u514d\u75ab\u7cfb\u7edf\u5bf9\u80bf\u7624\u7684\u53cd\u5e94\u5f3a\u5ea6\u3002\u4ece\u56fe\u4e2d\u53ef\u4ee5\u770b\u51fa\uff0c\u4e0d\u540c\u7c7b\u578b\u7684\u764c\u75c7\u5728\u514d\u75ab\u8bfb\u6570\u4e0a\u6709\u5f88\u5927\u7684\u5dee\u5f02\uff0c\u80be\u7ec6\u80de\u764c\u3001\u9ed1\u8272\u7d20\u7624\u548c\u5375\u5de2\u764c\u7b49\u764c\u75c7\u7684\u514d\u75ab\u8bfb\u6570\u4e5f\u8f83\u9ad8\u3002\u8fd9\u5bf9\u4e8e\u7814\u7a76\u764c\u75c7\u7684\u514d\u75ab\u6cbb\u7597\u548c\u514d\u75ab\u8010\u53d7\u662f\u6709\u91cd\u8981\u610f\u4e49\u7684\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">Step 3 \u5bf9\u4e0d\u540c\u7684\u514d\u75ab\u96c6\u7fa4\u8fdb\u884c\u5212\u5206<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u52a0\u8f7d\u6570\u636e<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">load(file = paste0(datapath,\"metadata_IC.RData\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">load(file = paste0(datapath, \"geneset_cc_normalized.RData\"))<\/span><\/span><\/code><\/section><\/pre>\n<\/section>\n<p><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">        <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">#\u57fa\u4e8e\u514d\u75ab\u7c07\u8fdb\u884c\u6392\u5e8f<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cluster_cohort <- metadata_IC[order(metadata_IC$immune_cluster, metadata_IC$cohort),]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u63d0\u53d6\u514d\u75ab\u7c07\u4fe1\u606f<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">mycluster <- as.character(cluster_cohort$immune_cluster)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">names(mycluster) <- rownames(cluster_cohort) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cluster_hm <- class_hm.fx(mycluster)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u63d0\u53d6\u80bf\u7624\u7c7b\u578b\u7684\u4fe1\u606f<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">mycohort<\/span> <span class=\"code-snippet__string\"><- cluster_cohort$cohortnames(mycohort) <- rownames(cluster_cohort)mycohorts <- t(as.matrix(mycohort))rownames(mycohorts) <- \"Cohort\"cohorts_hm <- cohorts_hm.fx(mycohorts)cells_mat <- geneset_cc_norm[,rownames(cluster_cohort)]         <\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"># \u7ed8\u5236\u70ed\u56fe<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__selector-tag\">cells_hm<\/span> <<span class=\"code-snippet__selector-tag\">-<\/span> <span class=\"code-snippet__selector-tag\">cells_hm<\/span><span class=\"code-snippet__selector-class\">.fx<\/span>(<span class=\"code-snippet__selector-tag\">cells_mat<\/span>)         <\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u8fdb\u884c\u6ce8\u91ca<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">annotation_order <- c(\"Pediatric Inflammed\", \"Myeloid Predominant\", \"Immune Neutral\", \"Immune Desert\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cluster_ha = HeatmapAnnotation(clusters = anno_mark(at = c(50, 235, 566, 844), labels_rot = 0,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> labels = annotation_order, side = \"top\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> labels_gp = gpar(fontsize = 20), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> link_height = unit(0.5, \"cm\")))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fig1c <- cluster_ha %v% cluster_hm %v% cells_hm %v% cohorts_hm<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"text-align: left;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u8bbe\u7f6e\u53c2\u6570<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code><span class=\"code-snippet_outer\">lgd_cohort = Legend(labels = names(cohort_col)[2:13], title = <span class=\"code-snippet__string\">\"\"<\/span>, nrow = 1, legend_gp = gpar(fill = cohort_col[2:13]))pdf(paste0(plotpath,<span class=\"code-snippet__string\">\"Fig1_C.pdf\"<\/span>), width = 18, height = 10)draw(fig1c, annotation_legend_side = <span class=\"code-snippet__string\">\"bottom\"<\/span>, legend_grouping = <span class=\"code-snippet__string\">\"original\"<\/span>, annotation_legend_list = list(lgd_cohort))dev.off()<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"36.133884\" style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\"><br \/><\/td>\n<td width=\"0.0\" height=\"36.133884\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015088\" data-ratio=\"0.5546296296296296\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_F08mqRuALTkqIT8k0MBM3o0CUXF3bw-3.png?resize=551%2C150\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0JvDKo3mOJtB1ZPB5sv9my4BlllF08mqRuALTkqIT8k0MBM3o0CUXF3bw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"150 .66998291015625\" width=\"551 .3400268554688\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">   <\/span><\/p>\n<p><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"><\/o:p><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5206\u6790\u7684\u7ed3\u679c\u5982\u56fe\u6240\u793a\uff0c\u56fe\u7247\u7684\u9876\u90e8\u6709\u56db\u4e2a\u7c7b\u522b\uff0c\u5206\u522b\u662fPediatric Inflamed\uff08\u708e\u75c7\u578b\uff09\uff0cMyeloid Predominant\uff08\u9ad3\u7cfb\u4e3b\u5bfc\u578b\uff09\uff0cImmune Neutral\uff08\u514d\u75ab\u4e2d\u6027\u578b\uff09\uff0c\u548cImmune Desert\uff08\u514d\u75ab\u6c99\u6f20\u578b\uff09\uff0c\u662f\u6839\u636e\u514d\u75ab\u7ec6\u80de\u7684\u603b\u4f53\u6c34\u5e73\u6216\u6bd4\u4f8b\u8fdb\u884c\u5212\u5206\u7684\u3002<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u800c\u56fe\u7247\u7684\u53f3\u4fa7\u6709\u4e00\u4e2a\u56fe\u4f8b\uff0c\u663e\u793a\u4e86\u4e0d\u540c\u989c\u8272\u4ee3\u8868\u7684\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\uff0c\u4f8b\u5982\u5355\u6838\u7ec6\u80de\uff0c\u7c92\u7ec6\u80de\uff0c\u6811\u7a81\u72b6\u7ec6\u80de\uff0cT\u7ec6\u80de\uff0cNK\u7ec6\u80de\uff0c\u548cB\u7ec6\u80de\u3002\u8fd9\u4e9b\u514d\u75ab\u7ec6\u80de\u90fd\u662f\u4eba\u4f53\u514d\u75ab\u7cfb\u7edf\u7684\u91cd\u8981\u7ec4\u6210\u90e8\u5206\uff0c\u53c2\u4e0e\u62b5\u6297\u611f\u67d3\u548c\u80bf\u7624\u7b49\u75c5\u7406\u8fc7\u7a0b\u3002<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5728\u56fe\u7247\u7684\u5e95\u90e8\u6709\u4e00\u4e9b\u5f69\u8272\u7684\u6761\u5f62\uff0c\u7528\u6765\u8868\u793a\u4e0d\u540c\u7684\u80bf\u7624\u7c7b\u578b\uff0c\u4e2d\u95f4\u90e8\u5206\u662f\u4e00\u4e2a\u77e9\u9635\uff0c\u6bcf\u4e2a\u5c0f\u65b9\u683c\u4e2d\u7684\u989c\u8272\u7528\u6765\u8868\u793a\u67d0\u4e00\u79cd\u514d\u75ab\u7ec6\u80de\u5728\u67d0\u4e00\u7c7b\u522b\u6216\u961f\u5217\u4e2d\u7684\u4e30\u5ea6\uff0c\u989c\u8272\u8d8a\u6df1\u8868\u793a\u4e30\u5ea6\u8d8a\u9ad8\uff0c\u989c\u8272\u8d8a\u6d45\u8868\u793a\u4e30\u5ea6\u8d8a\u4f4e\u3002\u4ece\u77e9\u9635\u4e2d\u53ef\u4ee5\u770b\u51fa\uff0c\u4e0d\u540c\u7c7b\u522b\u6216\u961f\u5217\u4e4b\u95f4\u7684\u514d\u75ab\u7ec6\u80de\u5206\u5e03\u548c\u4e30\u5ea6\u6709\u5f88\u5927\u7684\u5dee\u5f02\uff0c\u4f8b\u5982\uff0cPediatric Inflamed\u7c7b\u522b\u4e2d\u7684NK\u7ec6\u80de\u548c\u6811\u7a81\u72b6\u7ec6\u80de\u4e30\u5ea6\u8f83\u9ad8\uff0c\u800cImmune Desert\u7c7b\u522b\u4e2d\u7684\u514d\u75ab\u7ec6\u80de\u4e30\u5ea6\u666e\u904d\u8f83\u4f4e\uff0c\u8fd9\u4e9b\u5dee\u5f02\u53ef\u80fd\u53cd\u6620\u4e86\u4e0d\u540c\u6761\u4ef6\u4e0b\u7684\u514d\u75ab\u72b6\u6001\u548c\u529f\u80fd\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">    <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">Step 4 \u764c\u75c7\u4e0e\u7279\u5b9a\u514d\u75ab\u96c6\u7fa4\u7684\u76f8\u5173\u6027\u5206\u6790<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">      <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u5bfc\u5165\u6570\u636e<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">load<\/span>(<span class=\"code-snippet__keyword\">file<\/span> = paste0(datapath,<span class=\"code-snippet__string\">\"metadata_IC.RData\"<\/span>)) tab <- as.data.frame(<span class=\"code-snippet__keyword\">table<\/span>(metadata_IC$cohort), stringsAsFactors = F)tab <- tab[<span class=\"code-snippet__keyword\">order<\/span>(tab$Freq, decreasing = F),]         <\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"># \u5c06\u80bf\u7624\u7c07\u548c\u80bf\u7624\u7c7b\u578b\u6c47\u805a\u4e3a\u77e9\u9635<\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">cancer_IC_mat <- matrix(nrow = <span class=\"code-snippet__number\">12<\/span>, ncol = <span class=\"code-snippet__number\">4<\/span>, dimnames = <span class=\"code-snippet__keyword\">list<\/span>(tab$Var1, c(<span class=\"code-snippet__string\">\"Pediatric Inflamed\"<\/span>, <span class=\"code-snippet__string\">\"Myeloid Predominant\"<\/span>, <span class=\"code-snippet__string\">\"Immune Neutral\"<\/span>, <span class=\"code-snippet__string\">\"Immune Desert\"<\/span>)))<span class=\"code-snippet__keyword\">for<\/span>(i in <span class=\"code-snippet__number\">1<\/span>:nrow(cancer_IC_mat)){ mycancer <- metadata_IC[ metadata_IC$cohort == rownames(cancer_IC_mat)[i],] freq_tab <- <span class=\"code-snippet__keyword\">as<\/span>.data.frame(table(mycancer$immune_cluster), stringsAsFactors = F) freq_tab$perc <- freq_tab$Freq\/sum(freq_tab$Freq) cancer_IC_mat[i, freq_tab$Var1] <- freq_tab$perc *<span class=\"code-snippet__number\">100<\/span>}<\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">#\u5904\u7406NA\u6570\u636e<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cancer_IC_mat[is.na(cancer_IC_mat)] <- 0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"># \u5b9a\u4e49\u7c07<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">row_dend <- as.dendrogram(hclust(dist(cancer_IC_mat), \"complete\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">row_dend <- dendextend::rotate(row_dend,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> c(\"NFB\", \"SCHW\", \"MNG\", \"CPH\", \"ATRT\", \"NBL\", \"pedLGG\", \"ETMR\", \"MB\", \"CP\", \"pedHGG\", \"EPN\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># \u6ce8\u91ca<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">ha = rowAnnotation(`cohort size` = anno_barplot(tab$Freq, bar_width = 1,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> gp = gpar(col = \"white\", fill = \"#4d4d4d\"), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> border = FALSE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis_param = list(at = c(0, 100, 200, 300), labels_rot = 45, gp = gpar(fontsize = 20)),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> width = unit(3, \"cm\")), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> show_annotation_name = FALSE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">ha_1 = HeatmapAnnotation(`immune size` = anno_barplot( as.matrix(table(metadata_IC$immune_cluster)), bar_width = 1,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> gp = gpar(col = \"white\", fill = \"#4d4d4d\"), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> border = FALSE, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis_param = list(at = c(0, 100,200,300), labels_rot = 45, gp = gpar(fontsize = 20)),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> height = unit(3, \"cm\")), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> show_annotation_name = FALSE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<p><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u56fecol_fun= colorRamp2(c(0, 100), c(\"white\", \"red\"))cancer_hm = Heatmap(cancer_IC_mat,#titles and namesname = \"% cancer\",show_row_names = TRUE,show_column_names = TRUE,#clusters and orderscluster_columns = FALSE,cluster_rows = row_dend,show_row_dend = TRUE,#aesthesticsrow_names_side = \"left\",col = col_fun,column_names_rot = 45,column_names_gp = gpar(fontsize = 10),row_names_gp = gpar(fontsize = 10), height = unit(nrow(cancer_IC_mat), \"cm\"),width = unit(ncol(cancer_IC_mat), \"cm\"),column_title_gp = gpar(fontsize = 10),column_title = NULL,row_title = NULL,right_annotation = ha,top_annotation = ha_1,show_heatmap_legend = TRUE)pdf(paste0(plotpath,\"Fig1_D.pdf\"),width = 10, height = 10)draw(cancer_hm)dev.off() <\/span><\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"116.66844\" height=\"24.267036\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"116.66844\" height=\"24.267036\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;text-indent: 0em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015091\" data-ratio=\"0.9972222222222222\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_USWInDs9QtCX4Z1bjfCuCeiaJHSVag-2.png?resize=303%2C400\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0Jvse19HNWlib5GxricLqicnaiazgLZVUSWInDs9QtCX4Z1bjfCuCeiaJHSVag\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"400 .010009765625\" width=\"303 .3399658203125\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><br \/><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u7ed3\u679c\u5982\u56fe\uff0c\u663e\u793a\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u764c\u75c7\u4e0e\u7279\u5b9a\u514d\u75ab\u96c6\u7fa4\u7684\u8868\u8fbe\u91cf\u4e4b\u95f4\u7684\u5173\u7cfb\u3002\u56fe\u4e2d\u7eb5\u8f74\u5217\u51fa\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u80bf\u7624\uff08NFB, SCHW, JMNG \u7b49\uff09\uff0c\u6a2a\u8f74\u5217\u51fa\u4e86\u514d\u75ab\u96c6\u7fa4\uff0c\u540c\u65f6\uff0c\u5728\u7eb5\u8f74\u4e0a\u8fd8\u6709\u4e00\u4e2a\u6e10\u53d8\u8272\u6761\uff0c\u8868\u793a0\u5230100%\u7684\u764c\u75c7\u53d1\u751f\u7387\u3002\uff08\u764c\u75c7\u53d1\u751f\u7387\u662f\u6307\u67d0\u4e00\u57fa\u56e0\u5728\u67d0\u4e00\u7c7b\u522b\u4e2d\u7684\u6837\u672c\u4e2d\u8868\u8fbe\u5f02\u5e38\u7684\u6bd4\u4f8b\uff0c\u53cd\u6620\u4e86\u8be5\u80bf\u7624\u4e0e\u514d\u75ab\u96c6\u7fa4\u7684\u76f8\u5173\u6027\uff09\u3002<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u6bcf\u4e2a\u5355\u5143\u683c\u7684\u989c\u8272\u4ee3\u8868\u8be5\u80bf\u7624\u5728\u7279\u5b9a\u96c6\u7fa4\u4e2d\u7684\u764c\u75c7\u53d1\u751f\u7387\uff1b\u989c\u8272\u8d8a\u6df1\uff0c\u767e\u5206\u6bd4\u8d8a\u9ad8\uff0c\u8868\u793a\u8be5\u57fa\u56e0\u4e0e\u8be5\u7c7b\u522b\u66f4\u52a0\u76f8\u5173\uff1b\u989c\u8272\u8d8a\u6d45\uff0c\u767e\u5206\u6bd4\u8d8a\u4f4e\uff0c\u8868\u793a\u8be5\u57fa\u56e0\u4e0e\u8be5\u7c7b\u522b\u4e0d\u592a\u76f8\u5173\u3002\u4f8b\u5982\uff0cNFB\u57fa\u56e0\u5728ImmuDesert\u4e2d\u7684\u764c\u75c7\u53d1\u751f\u7387\u4e3a0%\uff0c\u800cEPN\u5728Immune Neutral\u7c7b\u522b\u4e2d\u7684\u764c\u75c7\u53d1\u751f\u7387\u4e3a100%\uff0c\u8bf4\u660eEPN\u4e0eImmune Neutral\u7c7b\u522b\u6709\u5f88\u5f3a\u7684\u76f8\u5173\u6027\uff0c\u53ef\u80fd\u662fEPN\u7684\u81f4\u75c5\u56e0\u7d20\u6216\u8005\u8bca\u65ad\u6307\u6807\u3002<\/span>    <\/span><o:page><\/o:page><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">Step 5 \u5206\u6790\u514d\u75ab\u7c7b\u578b\u4e0eCRI-iAtlas\u7c07\uff08\u514d\u75ab\u96c6\u7fa4\uff09\u7684\u5173\u7cfb<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/section>\n<p><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5bfc\u5165\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">load(file = paste0(datapath,\"metadata_IC.RData\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tab <- as.data.frame(table(metadata_IC$CRI_cluster), stringsAsFactors = F)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tab <- tab[order(tab$Freq, decreasing = F),]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(0, 112, 192);font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<p><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5b58\u50a8\u6bcf\u4e2a\u514d\u75ab\u96c6\u7fa4\u548c\u514d\u75ab\u7c07\u7684\u767e\u5206\u6bd4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cri_IC_mat <- matrix(nrow = 6, ncol = 4,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> dimnames = list(tab$Var1,c(\"Pediatric Inflamed\", \"Myeloid Predominant\", <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"Immune Neutral\", \"Immune Desert\")))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for(i in 1:nrow(cri_IC_mat)){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mycancer <- metadata_IC[ metadata_IC$CRI_cluster == rownames(cri_IC_mat)[i],] <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> freq_tab <- as.data.frame(table(mycancer$immune_cluster), stringsAsFactors = F)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> freq_tab$perc <- freq_tab$Freq\/sum(freq_tab$Freq) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> cri_IC_mat[i, freq_tab$Var1] <- freq_tab$perc *100<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cri_IC_mat[is.na(cri_IC_mat)] <- 0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">col_fun= colorRamp2(c(0, 100), c(\"white\", \"red\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u8bbe\u7f6e\u70ed\u56fe\u53c2\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cri_hm = Heatmap(cri_IC_mat,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#titles and names <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> name = \"% CRI-iAtlas cluster\", <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> show_row_names = TRUE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> show_column_names = TRUE, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#clusters and orders <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> cluster_columns = FALSE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> cluster_rows = FALSE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> show_column_dend = TRUE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#aesthestics<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> row_names_side = \"left\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> col = col_fun,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> column_names_rot = 45, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> column_names_gp = gpar(fontsize = 15),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> row_names_gp = gpar(fontsize = 15), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> height = unit(nrow(cri_IC_mat), \"cm\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> width = unit(ncol(cri_IC_mat), \"cm\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> column_title_gp = gpar(fontsize = 15),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> column_title = NULL,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> row_title = NULL,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> show_heatmap_legend = TRUE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">ha = rowAnnotation(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> `cohort size` = anno_barplot(tab$Freq, bar_width = 1, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> gp = gpar(col = \"white\", fill = \"#4d4d4d\"), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> border = FALSE, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis_param = list(gp = gpar(fontsize=15), at = c(0, 100,250,500), labels_rot = 45),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> width = unit(4, \"cm\")), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> show_annotation_name = FALSE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(paste0(plotpath, \"Fig1_E.pdf\"), width = 10, height = 10)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">cri_hm + ha<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dev.off()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<p><br \/><\/p>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"0.9333475\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"0.0\" height=\"0.9333475\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015093\" data-ratio=\"0.9768518518518519\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_ZwRTt6mW8c7nW2lfCSPGtQiaeCapMg-2.png?resize=406%2C268\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0JvNuCGYARD1ovwOoDXYY4upNK9hZwRTt6mW8c7nW2lfCSPGtQiaeCapMg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"268 .0\" width=\"406 .010009765625\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><br \/><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5206\u6790\u7684\u7ed3\u679c\u5982\u56fe\uff0c\u5de6\u8fb9\u7684\u70ed\u56fe\u663e\u793a\u4e86pedNST\u4e2d\u6bcf\u4e2aCRI-iAtlas\u7c07\uff08\u514d\u75ab\u96c6\u7fa4\uff09\u4e2d\u8de8\u8d8a\u514d\u75ab\u7c07\u7684\u6837\u672c\u6bd4\u4f8b\uff0c\u800c\u67f1\u72b6\u56fe\u663e\u793a\u4e86\u6bcf\u4e2aCRI-iAtlas\u7c07\u805a\u7c7b\u7684\u6837\u672c\u603b\u6570\uff0c\u4ece\u800c\u5c55\u793a\u4e86\u4e0d\u540c\u514d\u75ab\u53cd\u5e94\u7c7b\u578b\u4e0eCRI-iAtlas\u7c07\u7684\u6570\u91cf\u4e4b\u95f4\u7684\u5173\u7cfb\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">       <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u4f8b\u5982\uff1aY\u8f74\u5217\u51fa\u4e86\u4e03\u79cd\u4e0d\u540c\u7684\u514d\u75ab\u53cd\u5e94\u7c7b\u578b\uff1aTGFbeta dominant\uff08TGF-\u03b2\u5360\u4f18\u52bf\uff09, IFN-gamma dominant\uff08IFN-\u03b3\u5360\u4f18\u52bf\uff09, Wound Healing\uff08\u521b\u4f24\u6108\u5408\uff09, Immunologically quiet\uff08\u514d\u75ab\u9759\u9ed8\uff09, Inflammatory\uff08\u708e\u75c7\uff09, Lymphocyte depleted\uff08<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(17, 17, 17);\">\u6dcb\u5df4\u7ec6\u80de\u8017\u7aed<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\uff09\u548cMixed\uff08\u6df7\u5408\u578b\uff09\uff0c\u8868\u4e2d\u7528\u7ea2\u8272\u3001\u767d\u8272\u6765\u8868\u793a\u6bcf\u79cd\u514d\u75ab\u53cd\u5e94\u7c7b\u578b\u5bf9\u5e94\u7684CRI-iAtlas\u7c07\u7684\u6570\u91cf\u3002\u7ea2\u8272\u4ee3\u8868\u8f83\u9ad8\u6570\u91cf\uff0c\u767d\u8272\u4ee3\u8868\u8f83\u4f4e\u6570\u91cf\u3002<\/span><\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">Step 6 \u7528H&E TIL\u5206\u6570\u5206\u6790\u514d\u75ab\u7cfb\u7edf\u5bf9\u80bf\u7624\u7684\u53cd\u5e94\u5f3a\u5ea6<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">       <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5bfc\u5165\u6570\u636e\uff08HE\u8bc4\u5206\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">load(file = file.path(datapath,\"HE_manifest.RData\"))<\/span><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\">               <\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u7ed8\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">heplot <- ggplot(data = HE_manifest,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">aes(x = immune_cluster, y = agg_tilScore)) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">geom_beeswarm(cex = 1.5, aes(color = cohort), size = 5) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">geom_boxplot(width = 0.5, outlier.colour = NA, fill = NA) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">myaxis + myplot +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">scale_color_manual(values = cohort_col) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">theme(legend.position = \"none\", <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">plot.margin = unit(c(0.2,0.2,0.2,2), \"cm\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">axis.title.x = element_blank(),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">axis.title.y = element_text(size = 30),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">axis.text.x = element_text(size = 30),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">axis.text.y = element_text(size = 30),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">plot.title = element_text(size = 30, hjust = 0.5)) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">geom_signif(comparisons = list(c(\"Pediatric Inflamed\", \"Myeloid Predominant\")), y_position = 0.4,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">map_signif_level=TRUE, textsize = 10, test = \"wilcox.test\", vjust = 0.5) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">geom_signif(comparisons = list(c(\"Pediatric Inflamed\", \"Immune Desert\")), y_position = 0.45,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">map_signif_level=TRUE, textsize = 10, test = \"wilcox.test\", vjust = 0.5) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">labs(y = \"Average TIL score\") + ggtitle(~underline(\"H&E TIL score (n = 355)\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(paste0(plotpath,\"Fig1_F.pdf\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">width = 10, height = 12)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">print(heplot)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dev.off()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<p><br \/><\/p>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"20.66698\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"0.0\" height=\"20.66698\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015094\" data-ratio=\"1.1961325966850829\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_uDctYESoibh4WOL9l0rJgVQ4fKoYGw-2.png?resize=315%2C377\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0JvTQR4vCcdjs0MpPSJhvHTg08REuDctYESoibh4WOL9l0rJgVQ4fKoYGw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"724\" height=\"377 .9399719238281\" width=\"315 .94000244140625\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><\/p>\n<p><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u7ed3\u679c\u5982\u56fe\uff0c\u6211\u4eec\u5728\u8fd9\u4e00\u6b65\u4e2d\u7ed8\u5236\u7684\u70ed\u56fe\u662f\u4e00\u4e2a\u663e\u793aH&E TIL\u5206\u6570\u548c\u514d\u75ab\u96c6\u7fa4\u5173\u7cfb\u7684\u6563\u70b9\u56fe\u3002<\/span><span style=\"letter-spacing: 0.034em;font-family: \u7b49\u7ebf;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-size: 16px;\">        <o:p> <\/o:p><\/span><span style=\"letter-spacing: 0.034em;font-size: 16px;\">    <\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5bf9\u4e8eH&E TIL\u5206\u6570\uff0c\u8fd9\u662f\u4e00\u79cd\u7528\u6765\u8bc4\u4f30\u80bf\u7624\u6d78\u6da6\u6027\u6dcb\u5df4\u7ec6\u80de\uff08TIL\uff09\u7684\u65b9\u6cd5\uff0c\u57fa\u4e8eH&E\u67d3\u8272\u7684\u80bf\u7624\u5207\u7247\uff0c\u7528\u4e8e\u53cd\u6620\u4e86\u514d\u75ab\u7cfb\u7edf\u5bf9\u80bf\u7624\u7684\u53cd\u5e94\u5f3a\u5ea6\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u56fe\u4e2d\u4e0d\u540c\u989c\u8272\u548c\u5f62\u72b6\u7684\u70b9\u8868\u793a\u4e0d\u540c\u75be\u75c5\u6216\u6837\u672c\u6765\u6e90\uff0c\u4f8b\u5982CBTN\uff0cICGC\uff0cTCGA\u3002\u6bcf\u4e2a\u96c6\u7fa4\u4e2d\u70b9\u7684\u4f4d\u7f6e\u8868\u793a\u6bcf\u4e2a\u6837\u672c\u7684H&E TIL\u5206\u6570\uff0c\u8d8a\u9760\u8fd1y\u8f74\u8868\u793a\u5206\u6570\u8d8a\u9ad8\uff0c\u8d8a\u9760\u8fd1x\u8f74\u8868\u793a\u5206\u6570\u8d8a\u4f4e\u3002\u8fd9\u91cc\u7528\u7bb1\u5f62\u56fe\u6765\u663e\u793aTIL\u8bc4\u5206\uff0c\u901a\u8fc7\u5bf9\u6574\u4e2a\u513f\u79d1\u4e2d\u67a2\u795e\u7ecf\u7cfb\u7edf\u80bf\u7624\u6837\u672c(CBTN)\u7684\u75c5\u7406\u56fe\u50cf\u8fdb\u884c\u5206\u5272\u5206\u6790\u800c\u786e\u5b9a\u3002\u6240\u793a\u7684\u6837\u672c\u56fe\u50cf\u5206\u522b\u4ee3\u88681%(\u4e0b)\u300110%(\u4e2d)\u548c15%(\u4e0a)\u7684TIL\u5206\u6570\uff0c\u5206\u522b\u5bf9\u5e94\u4e8e\u4f4e\u56db\u5206\u4f4d\u6570\u3001\u5e73\u5747\u503c\u548c\u9ad8\u56db\u5206\u4f4d\u6570\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u9664\u6b64\u4e4b\u5916\u56fe\u4e2d\u8fd8\u6709\u4e00\u4e9b\u663e\u8457\u6027\u6807\u8bb0\uff0c\u7528\u6765\u663e\u793a\u4e0d\u540c\u7c7b\u522b\u4e4b\u95f4\u7684H&E TIL\u5206\u6570\u662f\u5426\u6709\u663e\u8457\u5dee\u5f02\uff0c\u4f8b\u5982\uff0cPediatric Inflamed\u548cMyeloid Predominant\u4e4b\u95f4\u6709\u4e00\u4e2a\u661f\u53f7\uff0c\u8868\u793a\u5b83\u4eec\u4e4b\u95f4\u7684\u5dee\u5f02\u662f\u663e\u8457\u7684\uff0c\u800cPediatric Inflamed\u548cImmune Desert\u4e4b\u95f4\u6709\u4e00\u4e2a\u661f\u53f7\uff0c\u540c\u6837\u8868\u793a\u5b83\u4eec\u4e4b\u95f4\u7684\u5dee\u5f02\u662f\u975e\u5e38\u663e\u8457\u7684\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\">        <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">Step 7 \u80bf\u7624\u4e0e\u4fe1\u53f7\u901a\u8def\u9891\u7387\u5206\u6790<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5bfc\u5165\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">load(file = paste0(datapath,\"metadata_IC.RData\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">n_x <- 4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">lggp_c <- subgroupcount_IC.fx(metadata_IC, \"pedLGG\") <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">lggp_f <- subgroupfreq_IC.fx(metadata_IC, \"pedLGG\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">hggp_c <- subgroupcount_IC.fx(metadata_IC, \"pedHGG\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">hggp_f <- subgroupfreq_IC.fx(metadata_IC, \"pedHGG\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">nblp_c <- subgroupcount_IC.fx(metadata_IC, \"NBL\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">nblp_f <- subgroupfreq_IC.fx(metadata_IC, \"NBL\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">atrtp_c <- subgroupcount_IC.fx(metadata_IC, \"ATRT\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">atrtp_f <- subgroupfreq_IC.fx(metadata_IC, \"ATRT\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">mbp_c <- subgroupcount_IC.fx(metadata_IC, \"MB\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">mbp_f <- subgroupfreq_IC.fx(metadata_IC, \"MB\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">epnp_c <- subgroupcount_IC.fx(metadata_IC, \"EPN\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">epnp_f <- subgroupfreq_IC.fx(metadata_IC, \"EPN\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u7ec4\u5408\u6761\u5f62\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">c_ls = list(atrtp_c + ggtitle(expression(~underline(\"ATRT\"))), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> nblp_c+ ggtitle(expression(~underline(\"NBL\"))), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mbp_c+ ggtitle(expression(~underline(\"MB\"))), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> hggp_c + ggtitle(expression(~underline(\"pedHGG\"))), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> lggp_c + ggtitle(expression(~underline(\"pedLGG\"))), <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> epnp_c + ggtitle(expression(~underline(\"EPN\"))))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">f_ls = list(atrtp_f, nblp_f, mbp_f, hggp_f, lggp_f, epnp_f )<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5408\u5e76<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(paste0(plotpath, \"Fig1_G.pdf\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> width = 20, height = 10, useDingbats = FALSE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">wrap_plots(c(c_ls, f_ls), nrow = 2)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dev.off()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\">          <\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"7.333445\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"0.0\" height=\"7.333445\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015095\" data-ratio=\"0.49907407407407406\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_v3MblgaVEUlR3dNVrdpkiatSIfjZ1g-2.png?resize=552%2C276\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxPOe9tUFY5Qb6zia1UHx0JvUtvXbM1BHYETOuTjhSYcbU7B6v3MblgaVEUlR3dNVrdpkiatSIfjZ1g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"276 .0\" width=\"552 .6799926757812\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><br \/><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u8fd9\u662f\u4eca\u5929\u7684\u6700\u540e\u4e00\u5e45\u56fe\u5566\uff0c\u8fd9\u5e45\u56fe\u662f\u4e00\u4e2a\u663e\u793a\u4e0d\u540c\u7c7b\u578b\u764c\u75c7\u9891\u7387\u548c\u5206\u6570\u7684\u6761\u5f62\u56fe\u3002\u56fe\u4e2d\u6709\u516d\u4e2a\u7c7b\u522b\u7684\u80bf\u7624\uff0c\u6bcf\u4e2a\u7c7b\u522b\u90fd\u6709\u4e00\u4e2a\u9891\u7387\u6761\u5f62\u56fe\u548c\u4e00\u4e2a\u5206\u6570\u5806\u53e0\u6761\u5f62\u56fe\uff0c\u5728\u6761\u5f62\u56fe\u4e2d\uff0c\u7528\u7070\u8272\u9634\u5f71\u8868\u793a\u6bcf\u4e2a\u7c7b\u522b\u7684\u6837\u672c\u6570\uff0c\u5206\u6570\u5806\u53e0\u6761\u5f62\u56fe\u5219\u7528\u591a\u79cd\u989c\u8272\u8868\u793a\u6bcf\u4e2a\u7c7b\u522b\u4e2d\u4e0d\u540c\u4e9a\u578b\u7684\u767e\u5206\u6bd4\uff0c\u6bcf\u4e2a\u4e9a\u578b\u7684\u7f29\u5199\u548c\u4ee3\u7801\u5728\u56fe\u7684\u5e95\u90e8\u6807\u6ce8\uff0c\u4f8b\u5982\uff0cATRT-TYR\u8868\u793aATRT\u4e2d\u7684\u916a\u6c28\u9178\u4e9a\u578b\uff0cMB-WNT\u8868\u793aMB\u4e2d\u7684WNT\u4fe1\u53f7\u901a\u8def\u4e9a\u578b\uff0c\u8fd9\u4e9b\u4e9a\u578b\u662f\u6839\u636e\u57fa\u56e0\u7ec4\u6216\u8f6c\u5f55\u7ec4\u6570\u636e\u8fdb\u884c\u5206\u6790\u548c\u5206\u7c7b\u7684\uff0c\u53cd\u6620\u4e86\u4e0d\u540c\u764c\u75c7\u7c7b\u578b\u7684\u751f\u7269\u5b66\u7279\u5f81\u548c\u9884\u540e\u7279\u5f81\u3002<\/span>    <\/span><o:page><\/o:page><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u901a\u8fc7\u4ee5\u4e0a\u7684\u5206\u6790\uff0c\u6211\u4eec\u5728pedNST\u4e2d\u627e\u5230\u4e86\u56db\u4e2a\u5e7f\u6cdb\u7684\u514d\u75ab\u96c6\u7fa4\uff0c\u5e76\u4e14\u8fdb\u884c\u4e86\u548c\u514d\u75ab\u96c6\u7fa4\u6709\u5173\u7684\u76f8\u5173\u6027\u5206\u6790\u3002<\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 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