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solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-recalc-dims=\"1\" \/><\/p>\n\u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u4f7f\u7528\u80bf\u7624\u514d\u75ab\u529f\u80fd\u969c\u788d\u548c\u6392\u65a5\uff08TIDE\uff09\u9884\u6d4b\u7b97\u6cd5\u8bc4\u4f30\u4e24\u79cd\u4e9a<\/span>\u578b\u7684\u514d\u75ab\u6cbb\u7597\u53cd\u5e94<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<\/span> <\/p>\n\u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u4f7f\u7528\u80bf\u7624\u514d\u75ab\u529f\u80fd\u969c\u788d\u548c\u6392\u65a5\uff08TIDE\uff09\u9884\u6d4b\u7b97\u6cd5\u8bc4\u4f30\u4e24\u79cd\u4e9a<\/span>\u578b\u7684\u514d\u75ab\u6cbb\u7597\u53cd\u5e94\uff0c\u8be5\u5206\u6790\u5728\u80bf\u7624\u76f8\u5173\u751f\u4fe1\u6587\u7ae0\u4e2d\u51fa\u73b0\u7684\u9891\u7387\u975e\u5e38\u9ad8\uff0c\u662f\u4e00\u4e2a\u503c\u5f97\u5c0f\u4f19\u4f34\u5b66\u4e60\u7684\u5206\u6790\u5185\u5bb9\uff0c\u63a5\u4e0b\u6765\u9a6c\u4e0a\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\u5b66\u4e60\u5427\uff01<\/span><\/span><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n\u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code>#\u5b89\u88c5\u9700\u8981\u7684R\u5305<\/span><\/span><\/code><code>install.packages(\"ggplot2\"<\/span>)<\/span><\/code><code>install.packages(\"tidyverse\"<\/span>)<\/span><\/code><code>install.packages(\"cowplot\"<\/span>)<\/span><\/code><code>install.packages(\"ggsignif\"<\/span>)<\/span><\/code><code>install.packages(\"ggsci\"<\/span>)<\/span><\/code><code>#\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/span><\/span><\/code><code>library<\/span>(tidyverse)<\/span><\/code><code>library<\/span>(ggplot2)<\/span><\/code><code>library<\/span>(ggsci)<\/span><\/code><code>library<\/span>(ggpubr)<\/span><\/code><code>library<\/span>(ggsignif)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n\u5982\u679c\u9700\u8981\u5b8c\u6574\u7684\u4ee3\u7801\u53ef\u4ee5\u70b9\u51fb\u4ed8\u8d39\u83b7\u53d6\u54e6!\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u5b63\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965!<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" data-type=\"png\" data-w=\"1080\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-16.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/span><\/span><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6690751445086706\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/10_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWlWbhwzZQIQKw2OPd4ZwR9pJLZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6623376623376623\" data-s=\"300,640\" data-type=\"png\" data-w=\"693\" style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/11_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWKtxDNTGOuhyAZb1n2uwFBOGjd5YWNtWPt9nwkrEwicowmcqtJdMMGrA\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><\/span><\/em><\/strong><\/p>\n <\/span><\/em><\/strong><\/p>\n\u8f93\u5165\u6570\u636e<\/span><\/em><\/strong><\/p>\n <\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>#EXP.txt\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u5217\u540d\u4e3a\u6837\u672c\u540d<\/span><\/code><code>dat <-<\/span> read.table<\/span>(\"EXP.txt<\/span>\",sep<\/span> = \"t\"<\/span>,row.names<\/span> = 1,header<\/span> = T,stringsAsFactors<\/span> = F,check.names<\/span> = F)<\/span><\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.27890173410404623\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_ibeadGkncvK9vLyicHur8qNhIQ6VKA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWYJAllbekvBxicFK8z7l3sP68PhCibeadGkncvK9vLyicHur8qNhIQ6VKA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>#\u5c06\u6837\u672c\u8fdb\u884c\u6807\u51c6\u5316\uff0c\u5c06\u6837\u672c\u6309\u5747\u503c\u6807\u51c6\u5316\uff0c\u8868\u8fbe\u91cf\u51cf\u53bb\u6bcf\u4e2a\u57fa\u56e0\u6240\u5728\u6837\u672c\u7684\u5747\u503c(\u6309\u884c\u8ba1\u7b97\u5747\u503c\uff0c\u5728\u7528\u6bcf\u4e2a\u8868\u8fbe\u91cf-\u5747\u503c)<\/span><\/code><code>exp<-t(apply(dat,1,function(x){x-(mean(x))}))<\/span><\/code><code>#group.txt\uff0c\u98ce\u9669\u8bc4\u5206\u9ad8\u4f4e\u5206\u7ec4\u6837\u672c\u4fe1\u606f\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3a\u9ad8\u4f4e\u5206\u7ec4\u4fe1\u606f<\/span><\/code><code>ann <- read.table(\"group.txt\",sep = \"t\",header = T,stringsAsFactors = F,check.names = F)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2706222865412446\" data-s=\"300,640\" data-type=\"png\" data-w=\"691\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_pcC4vDJefGAkBWIavWnFweKMyPPoLw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsW0YTOehmvzjQfVFlbmnLlGWuYpcC4vDJefGAkBWIavWnFweKMyPPoLw\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n <\/p>\nTIDE\u8bc4\u5206\u8ba1\u7b97<\/span><\/em><\/strong><\/p>\n#TIDE\u7684\u8ba1\u7b97\u75db\u8fc7\u8be5\u7f51\u5740\uff1a<\/span>http:\/\/tide.dfci.harvard.edu\/login\/<\/span><o:p><\/o:p><\/span><\/p>\n\u5728\u5229\u7528\u8be5\u7f51\u7ad9\u8ba1\u7b97\u4e4b\u524d\uff0c\u9996\u5148\u8981\u5229\u7528\u90ae\u7bb1\u8fdb\u884c\u6ce8\u518c\uff0c\u5982\u4e0b\u56fe\uff1a<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5736994219653179\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_zoxtib7qbwq9PlbFBCJ0rUlyAWORCQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWIkiaDPrf8uXkqia0T6FavHsjfdGzoxtib7qbwq9PlbFBCJ0rUlyAWORCQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n#\u70b9\u51fbPredictresponse\u5c31\u53ef\u4ee5\u8fdb\u884c\u5206\u6790\uff0c\u5f97\u5230\u6700\u540e\u5206\u6790\u7ed3\u679c\uff0c\u70b9\u51fbExport to CSV\u4e0b\u8f7dTIDE\u5206\u6790\u7ed3\u679c\u3002<o:p><\/o:p><\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.34104046242774566\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_RzJ8hdr9fMk0ZnicND5nXYiavFwLwQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsW1CKPxHNe2vduFw00icO8LBvqHLURzJ8hdr9fMk0ZnicND5nXYiavFwLwQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n <\/p>\n <\/span><\/p>\n <\/p>\n<\/section>\n\u200d<\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\nTIDE\u8bc4\u5206\u5728\u9ad8\u4f4e\u98ce\u9669\u7ec4\u4e2d\u7684\u663e\u8457\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><\/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=\"apache\"><code>#\u8bfb\u53d6TIDE\u7ed3\u679c\u6587\u4ef6\uff0c\u5305\u62ec\u6837\u672c\u540d\uff0cTIDE\uff0cExclusion\u7b49\u5217\u4fe1\u606f\u3002<\/span><\/span><\/code><code>TIDE<\/span><-read.csv(\"export.csv\"<\/span>,header=T)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2774566473988439\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_uzBZBugicxHNcPekMYB9jfIVuz9OCA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsW9LtwsjycRIyeECia9dHE37VDsFuzBZBugicxHNcPekMYB9jfIVuz9OCA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>#\u4fee\u6539\u5217\u540d<\/span><\/span><\/code><code>TIDE<\/span><-rename(TIDE,sample=Patient)<\/span><\/code><code>#\u8fde\u63a5TIDE\u7ed3\u679c\u6587\u4ef6\u548c\u9ad8\u4f4e\u98ce\u9669\u7ec4\u4fe1\u606f\u6587\u4ef6<\/span><\/span><\/code><code>final<\/span><-left_join(TIDE,ann,by=\"sample\"<\/span>)<\/span><\/code><code>#\u7ed8\u5236TIDE\u8bc4\u5206\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/span><\/code><code>boxplot_TIDE<\/span><- ggplot(final, aes(x = group, y = TIDE))+ <\/span><\/code><code> labs<\/span>(y=\"TIDE\"<\/span>,x= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes(fill=group))+ <\/span><\/code><code> geom_boxplot<\/span>(width=0.3)+ <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title = element_text(size = 12,color =\"black\"<\/span>), <\/span><\/code><code> axis<\/span>.text = element_text(size= 12,color = \"black\"<\/span>),<\/span><\/code><code> panel<\/span>.grid.minor.y = element_blank(),<\/span><\/code><code> panel<\/span>.grid.minor.x = element_blank(),<\/span><\/code><code> axis<\/span>.text.x = element_text(angle = 45, hjust = 1 ),<\/span><\/code><code> panel<\/span>.grid=element_blank(),<\/span><\/code><code> legend<\/span>.position = \"top\"<\/span>,<\/span><\/code><code> legend<\/span>.text = element_text(size= 12),<\/span><\/code><code> legend<\/span>.title= element_text(size= 12)<\/span><\/code><code> ) +<\/span><\/code><code>#\u663e\u8457\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><code>geom_signif<\/span>(comparisons=list(c(\"High\"<\/span>,\"Low\"<\/span>)),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/code><code> map_signif_level<\/span>=F) <\/span><\/code><code>ggsave<\/span>(file=\"TIDE.pdf\"<\/span>,boxplot_TIDE,height=10,width=15)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6690751445086706\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/10_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWlWbhwzZQIQKw2OPd4ZwR9pJLZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>##\u7ed8\u5236Dysfunction\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/code><code>boxplot_Dysfunction<-<\/span> ggplot<\/span>(final<\/span>, aes<\/span>(x<\/span> = group,<\/span> y<\/span> =Dysfunction<\/span> ))+ <\/span><\/span><\/code><code> labs<\/span>(y<\/span>=\"Dysfunction\"<\/span>,x<\/span>= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes<\/span>(fill<\/span>=group))+<\/span> <\/span><\/code><code> geom_boxplot<\/span>(width<\/span>=0.3)+<\/span> <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title<\/span> = element_text(size<\/span> = 12,color<\/span> =\"black\"<\/span>), <\/span><\/code><code> axis.text<\/span> = element_text(size<\/span>= 12,color<\/span> = \"black\"<\/span>),<\/span><\/code><code> panel.grid.minor.y<\/span> = element_blank(),<\/span><\/span><\/code><code> panel.grid.minor.x<\/span> = element_blank(),<\/span><\/span><\/code><code> axis.text.x<\/span> = element_text(angle<\/span> = 45,<\/span> hjust<\/span> = 1<\/span> ),<\/span><\/code><code> panel.grid<\/span>=element_blank(),<\/span><\/span><\/code><code> legend.position<\/span> = \"top\"<\/span>,<\/span><\/code><code> legend.text<\/span> = element_text(size<\/span>= 12),<\/span><\/span><\/code><code> legend.title<\/span>= element_text(size<\/span>= 12)<\/span><\/span><\/code><code> ) +<\/span><\/code><code>geom_signif<\/span>(comparisons<\/span>=list(c(<\/span>\"High<\/span>\",\"Low<\/span>\")),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/span><\/code><code> map_signif_level<\/span>=F)<\/span> <\/span><\/code><code>ggsave<\/span>(file<\/span>=\"Dysfunction.pdf\"<\/span>,boxplot_Dysfunction<\/span>,height<\/span>=10,width<\/span>=15)<\/span><\/span><\/code><code> <\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6623376623376623\" data-s=\"300,640\" data-type=\"png\" data-w=\"693\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/11_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWKtxDNTGOuhyAZb1n2uwFBOGjd5YWNtWPt9nwkrEwicowmcqtJdMMGrA\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><\/p>\n <\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>###\u7ed8\u5236Exclusion\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/code><code>boxplot_Exclusion<-<\/span> ggplot<\/span>(final<\/span>, aes<\/span>(x<\/span> = group,<\/span> y<\/span> =Exclusion<\/span> ))+ <\/span><\/span><\/code><code> labs<\/span>(y<\/span>=\"Exclusion\"<\/span>,x<\/span>= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes<\/span>(fill<\/span>=group))+<\/span> <\/span><\/code><code> geom_boxplot<\/span>(width<\/span>=0.3)+<\/span> <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title<\/span> = element_text(size<\/span> = 12,color<\/span> =\"black\"<\/span>), <\/span><\/code><code> axis.text<\/span> = element_text(size<\/span>= 12,color<\/span> = \"black\"<\/span>),<\/span><\/code><code> panel.grid.minor.y<\/span> = element_blank(),<\/span><\/span><\/code><code> panel.grid.minor.x<\/span> = element_blank(),<\/span><\/span><\/code><code> axis.text.x<\/span> = element_text(angle<\/span> = 45,<\/span> hjust<\/span> = 1<\/span> ),<\/span><\/code><code> panel.grid<\/span>=element_blank(),<\/span><\/span><\/code><code> legend.position<\/span> = \"top\"<\/span>,<\/span><\/code><code> legend.text<\/span> = element_text(size<\/span>= 12),<\/span><\/span><\/code><code> legend.title<\/span>= element_text(size<\/span>= 12)<\/span><\/span><\/code><code> ) +<\/span><\/code><code>geom_signif<\/span>(comparisons<\/span>=list(c(<\/span>\"High<\/span>\",\"Low<\/span>\")),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/span><\/code><code> map_signif_level<\/span>=F)<\/span> <\/span><\/code><code>ggsave<\/span>(file<\/span>=\"Exclusion.pdf\"<\/span>,boxplot_Exclusion<\/span>,height<\/span>=10,width<\/span>=15)<\/span><\/span><\/code><code> <\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.670995670995671\" data-s=\"300,640\" data-type=\"png\" data-w=\"693\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_sFrFMt0ziaicbwofL41exfpvpqkJHQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWdqxUaAnWMJnYNliadsEWQ24K6icPsFrFMt0ziaicbwofL41exfpvpqkJHQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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\"><code>###\u7ed8\u5236MSI\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/code><code>boxplot_MSI<-<\/span> ggplot<\/span>(final<\/span>, aes<\/span>(x<\/span> = group,<\/span> y<\/span> =MSI.Expr.Sig))+<\/span> <\/span><\/span><\/code><code> labs<\/span>(y<\/span>=\"MSI\"<\/span>,x<\/span>= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes<\/span>(fill<\/span>=group))+<\/span> <\/span><\/code><code> geom_boxplot<\/span>(width<\/span>=0.3)+<\/span> <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title<\/span> = element_text(size<\/span> = 12,color<\/span> =\"black\"<\/span>), <\/span><\/code><code> axis.text<\/span> = element_text(size<\/span>= 12,color<\/span> = \"black\"<\/span>),<\/span><\/code><code> panel.grid.minor.y<\/span> = element_blank(),<\/span><\/span><\/code><code> panel.grid.minor.x<\/span> = element_blank(),<\/span><\/span><\/code><code> axis.text.x<\/span> = element_text(angle<\/span> = 45,<\/span> hjust<\/span> = 1<\/span> ),<\/span><\/code><code> panel.grid<\/span>=element_blank(),<\/span><\/span><\/code><code> legend.position<\/span> = \"top\"<\/span>,<\/span><\/code><code> legend.text<\/span> = element_text(size<\/span>= 12),<\/span><\/span><\/code><code> legend.title<\/span>= element_text(size<\/span>= 12)<\/span><\/span><\/code><code> ) +<\/span><\/code><code>geom_signif<\/span>(comparisons<\/span>=list(c(<\/span>\"High<\/span>\",\"Low<\/span>\")),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/span><\/code><code> map_signif_level<\/span>=F)<\/span> <\/span><\/code><code>ggsave<\/span>(file<\/span>=\"MSI.pdf\"<\/span>,boxplot_MSI<\/span>,height<\/span>=10,width<\/span>=15)<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6719653179190751\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_CTj2HkRqYQdG0WALC5siaQ0Pia63fQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWc3BoOMYFCJ1bISOT3fLugIw76UCTj2HkRqYQdG0WALC5siaQ0Pia63fQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n <\/p>\n<\/section>\n<section style=\"text-align: justify;\" 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textvalue=\"3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" hasload=\"1\" style=\"color: var(--weui-LINK);outline: 0px;cursor: pointer;font-size: 14px;\" rel=\"noopener\">3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8<\/a><\/section>\n<section style=\"outline: 0px;letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491905&idx=1&sn=fb34ebd6282962c7803badaee7a39096&chksm=cf7f7184f808f8929608c0050344ad86193d0fc6455c1c18e16cc17bf4b37832b63d3b18284e&scene=21#wechat_redirect\" textvalue=\"4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" hasload=\"1\" style=\"color: var(--weui-LINK);outline: 0px;cursor: pointer;\" rel=\"noopener\">4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b<\/span><\/a><\/section>\n<section style=\"outline: 0px;letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493633&idx=1&sn=2263dfe7572c0bcf6816c2c1a37d79de&chksm=cf7f78c4f808f1d2209321d6ace39fde5fa60c0691b56f88eac21916f5a2872ce8ee345f1d5f&scene=21#wechat_redirect\" textvalue=\"\u8f6f\u4ef6\u5305\u5b89\u88c5\u3001\u6253\u602a\u5feb\u53c8\u597d\uff0c1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff1b\u8fd8\u6709\u6bd4\u8fd9\u66f4\u7701\u94b1\u7684\u561b\uff01\uff01\uff01\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" hasload=\"1\" style=\"color: var(--weui-LINK);outline: 0px;cursor: pointer;letter-spacing: 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Mono\",Menlo,Courier,monospace}.code-snippet__comment,.code-snippet__quote{color:#afafaf;font-style:italic}.code-snippet__keyword,.code-snippet__selector-tag,.code-snippet__subst{color:#ca7d37}.code-snippet__number,.code-snippet__literal,.code-snippet__variable,.code-snippet__template-variable,.code-snippet__tag .code-snippet__attr{color:#0e9ce5}.code-snippet__string,.code-snippet__doctag{color:#d14}.code-snippet__title,.code-snippet__section,.code-snippet__selector-id{color:#d14}.code-snippet__subst{font-weight:normal}.code-snippet__type,.code-snippet__class 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0;align-items:center}.flex_bd{padding-left:14px;}.account_nickname{display:inline-block;vertical-align:middle;line-height:1.2;color:#576b95;font-size:14px}.account_desc{overflow:hidden;text-overflow:ellipsis;display:-webkit-box;-webkit-box-orient:vertical;-webkit-line-clamp:1;color:rgba(0,0,0,0.3);font-size:14px;line-height:1.2;padding-top:.4em}.msg_source_url{text-align:left;word-break:break-all;margin-top:20px;}.msg_source_url a{padding-right:10px;}.msg_source_url .url_text{color:#a8a8a8;}.video-desc{font-size:14px;margin-top:15px;color:#6c6c6c;}.msg_source_url{text-align:left;}.original_primary_card_tips{color:rgba(0,0,0,0.3);line-height:1.4;font-size:15px;}.weui-flex__item{margin-bottom:20px;padding:20px 16px;margin-top:16px;line-height:1.4;align-items:center;background-color:#f7f7f7;border-radius:8px;position:relative;}.original_primary_desc{color:rgba(0,0,0,0.5);font-size:14px;padding-top:4px;width:auto;overflow:hidden;text-overflow:ellipsis;}.msgBodyReplyList{border-top:1px solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-recalc-dims=\"1\" \/><\/p>\n\u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u4f7f\u7528\u80bf\u7624\u514d\u75ab\u529f\u80fd\u969c\u788d\u548c\u6392\u65a5\uff08TIDE\uff09\u9884\u6d4b\u7b97\u6cd5\u8bc4\u4f30\u4e24\u79cd\u4e9a<\/span>\u578b\u7684\u514d\u75ab\u6cbb\u7597\u53cd\u5e94<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<\/span> <\/p>\n\u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u4f7f\u7528\u80bf\u7624\u514d\u75ab\u529f\u80fd\u969c\u788d\u548c\u6392\u65a5\uff08TIDE\uff09\u9884\u6d4b\u7b97\u6cd5\u8bc4\u4f30\u4e24\u79cd\u4e9a<\/span>\u578b\u7684\u514d\u75ab\u6cbb\u7597\u53cd\u5e94\uff0c\u8be5\u5206\u6790\u5728\u80bf\u7624\u76f8\u5173\u751f\u4fe1\u6587\u7ae0\u4e2d\u51fa\u73b0\u7684\u9891\u7387\u975e\u5e38\u9ad8\uff0c\u662f\u4e00\u4e2a\u503c\u5f97\u5c0f\u4f19\u4f34\u5b66\u4e60\u7684\u5206\u6790\u5185\u5bb9\uff0c\u63a5\u4e0b\u6765\u9a6c\u4e0a\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\u5b66\u4e60\u5427\uff01<\/span><\/span><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n\u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code>#\u5b89\u88c5\u9700\u8981\u7684R\u5305<\/span><\/span><\/code><code>install.packages(\"ggplot2\"<\/span>)<\/span><\/code><code>install.packages(\"tidyverse\"<\/span>)<\/span><\/code><code>install.packages(\"cowplot\"<\/span>)<\/span><\/code><code>install.packages(\"ggsignif\"<\/span>)<\/span><\/code><code>install.packages(\"ggsci\"<\/span>)<\/span><\/code><code>#\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/span><\/span><\/code><code>library<\/span>(tidyverse)<\/span><\/code><code>library<\/span>(ggplot2)<\/span><\/code><code>library<\/span>(ggsci)<\/span><\/code><code>library<\/span>(ggpubr)<\/span><\/code><code>library<\/span>(ggsignif)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n\u5982\u679c\u9700\u8981\u5b8c\u6574\u7684\u4ee3\u7801\u53ef\u4ee5\u70b9\u51fb\u4ed8\u8d39\u83b7\u53d6\u54e6!\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u5b63\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965!<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" data-type=\"png\" data-w=\"1080\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-16.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/span><\/span><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6690751445086706\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/10_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWlWbhwzZQIQKw2OPd4ZwR9pJLZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6623376623376623\" data-s=\"300,640\" data-type=\"png\" data-w=\"693\" style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/11_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWKtxDNTGOuhyAZb1n2uwFBOGjd5YWNtWPt9nwkrEwicowmcqtJdMMGrA\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><\/span><\/em><\/strong><\/p>\n <\/span><\/em><\/strong><\/p>\n\u8f93\u5165\u6570\u636e<\/span><\/em><\/strong><\/p>\n <\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>#EXP.txt\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u5217\u540d\u4e3a\u6837\u672c\u540d<\/span><\/code><code>dat <-<\/span> read.table<\/span>(\"EXP.txt<\/span>\",sep<\/span> = \"t\"<\/span>,row.names<\/span> = 1,header<\/span> = T,stringsAsFactors<\/span> = F,check.names<\/span> = F)<\/span><\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.27890173410404623\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_ibeadGkncvK9vLyicHur8qNhIQ6VKA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWYJAllbekvBxicFK8z7l3sP68PhCibeadGkncvK9vLyicHur8qNhIQ6VKA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>#\u5c06\u6837\u672c\u8fdb\u884c\u6807\u51c6\u5316\uff0c\u5c06\u6837\u672c\u6309\u5747\u503c\u6807\u51c6\u5316\uff0c\u8868\u8fbe\u91cf\u51cf\u53bb\u6bcf\u4e2a\u57fa\u56e0\u6240\u5728\u6837\u672c\u7684\u5747\u503c(\u6309\u884c\u8ba1\u7b97\u5747\u503c\uff0c\u5728\u7528\u6bcf\u4e2a\u8868\u8fbe\u91cf-\u5747\u503c)<\/span><\/code><code>exp<-t(apply(dat,1,function(x){x-(mean(x))}))<\/span><\/code><code>#group.txt\uff0c\u98ce\u9669\u8bc4\u5206\u9ad8\u4f4e\u5206\u7ec4\u6837\u672c\u4fe1\u606f\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3a\u9ad8\u4f4e\u5206\u7ec4\u4fe1\u606f<\/span><\/code><code>ann <- read.table(\"group.txt\",sep = \"t\",header = T,stringsAsFactors = F,check.names = F)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2706222865412446\" data-s=\"300,640\" data-type=\"png\" data-w=\"691\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_pcC4vDJefGAkBWIavWnFweKMyPPoLw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsW0YTOehmvzjQfVFlbmnLlGWuYpcC4vDJefGAkBWIavWnFweKMyPPoLw\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n <\/p>\nTIDE\u8bc4\u5206\u8ba1\u7b97<\/span><\/em><\/strong><\/p>\n#TIDE\u7684\u8ba1\u7b97\u75db\u8fc7\u8be5\u7f51\u5740\uff1a<\/span>http:\/\/tide.dfci.harvard.edu\/login\/<\/span><o:p><\/o:p><\/span><\/p>\n\u5728\u5229\u7528\u8be5\u7f51\u7ad9\u8ba1\u7b97\u4e4b\u524d\uff0c\u9996\u5148\u8981\u5229\u7528\u90ae\u7bb1\u8fdb\u884c\u6ce8\u518c\uff0c\u5982\u4e0b\u56fe\uff1a<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5736994219653179\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_zoxtib7qbwq9PlbFBCJ0rUlyAWORCQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWIkiaDPrf8uXkqia0T6FavHsjfdGzoxtib7qbwq9PlbFBCJ0rUlyAWORCQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n#\u70b9\u51fbPredictresponse\u5c31\u53ef\u4ee5\u8fdb\u884c\u5206\u6790\uff0c\u5f97\u5230\u6700\u540e\u5206\u6790\u7ed3\u679c\uff0c\u70b9\u51fbExport to CSV\u4e0b\u8f7dTIDE\u5206\u6790\u7ed3\u679c\u3002<o:p><\/o:p><\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.34104046242774566\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_RzJ8hdr9fMk0ZnicND5nXYiavFwLwQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsW1CKPxHNe2vduFw00icO8LBvqHLURzJ8hdr9fMk0ZnicND5nXYiavFwLwQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n <\/p>\n <\/span><\/p>\n <\/p>\n<\/section>\n\u200d<\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\nTIDE\u8bc4\u5206\u5728\u9ad8\u4f4e\u98ce\u9669\u7ec4\u4e2d\u7684\u663e\u8457\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><\/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=\"apache\"><code>#\u8bfb\u53d6TIDE\u7ed3\u679c\u6587\u4ef6\uff0c\u5305\u62ec\u6837\u672c\u540d\uff0cTIDE\uff0cExclusion\u7b49\u5217\u4fe1\u606f\u3002<\/span><\/span><\/code><code>TIDE<\/span><-read.csv(\"export.csv\"<\/span>,header=T)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2774566473988439\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_uzBZBugicxHNcPekMYB9jfIVuz9OCA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsW9LtwsjycRIyeECia9dHE37VDsFuzBZBugicxHNcPekMYB9jfIVuz9OCA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>#\u4fee\u6539\u5217\u540d<\/span><\/span><\/code><code>TIDE<\/span><-rename(TIDE,sample=Patient)<\/span><\/code><code>#\u8fde\u63a5TIDE\u7ed3\u679c\u6587\u4ef6\u548c\u9ad8\u4f4e\u98ce\u9669\u7ec4\u4fe1\u606f\u6587\u4ef6<\/span><\/span><\/code><code>final<\/span><-left_join(TIDE,ann,by=\"sample\"<\/span>)<\/span><\/code><code>#\u7ed8\u5236TIDE\u8bc4\u5206\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/span><\/code><code>boxplot_TIDE<\/span><- ggplot(final, aes(x = group, y = TIDE))+ <\/span><\/code><code> labs<\/span>(y=\"TIDE\"<\/span>,x= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes(fill=group))+ <\/span><\/code><code> geom_boxplot<\/span>(width=0.3)+ <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title = element_text(size = 12,color =\"black\"<\/span>), <\/span><\/code><code> axis<\/span>.text = element_text(size= 12,color = \"black\"<\/span>),<\/span><\/code><code> panel<\/span>.grid.minor.y = element_blank(),<\/span><\/code><code> panel<\/span>.grid.minor.x = element_blank(),<\/span><\/code><code> axis<\/span>.text.x = element_text(angle = 45, hjust = 1 ),<\/span><\/code><code> panel<\/span>.grid=element_blank(),<\/span><\/code><code> legend<\/span>.position = \"top\"<\/span>,<\/span><\/code><code> legend<\/span>.text = element_text(size= 12),<\/span><\/code><code> legend<\/span>.title= element_text(size= 12)<\/span><\/code><code> ) +<\/span><\/code><code>#\u663e\u8457\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><code>geom_signif<\/span>(comparisons=list(c(\"High\"<\/span>,\"Low\"<\/span>)),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/code><code> map_signif_level<\/span>=F) <\/span><\/code><code>ggsave<\/span>(file=\"TIDE.pdf\"<\/span>,boxplot_TIDE,height=10,width=15)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6690751445086706\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/10_ZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWlWbhwzZQIQKw2OPd4ZwR9pJLZAnrEqtM2kETDBeWb2eSIZ0nkA9C0A\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>##\u7ed8\u5236Dysfunction\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/code><code>boxplot_Dysfunction<-<\/span> ggplot<\/span>(final<\/span>, aes<\/span>(x<\/span> = group,<\/span> y<\/span> =Dysfunction<\/span> ))+ <\/span><\/span><\/code><code> labs<\/span>(y<\/span>=\"Dysfunction\"<\/span>,x<\/span>= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes<\/span>(fill<\/span>=group))+<\/span> <\/span><\/code><code> geom_boxplot<\/span>(width<\/span>=0.3)+<\/span> <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title<\/span> = element_text(size<\/span> = 12,color<\/span> =\"black\"<\/span>), <\/span><\/code><code> axis.text<\/span> = element_text(size<\/span>= 12,color<\/span> = \"black\"<\/span>),<\/span><\/code><code> panel.grid.minor.y<\/span> = element_blank(),<\/span><\/span><\/code><code> panel.grid.minor.x<\/span> = element_blank(),<\/span><\/span><\/code><code> axis.text.x<\/span> = element_text(angle<\/span> = 45,<\/span> hjust<\/span> = 1<\/span> ),<\/span><\/code><code> panel.grid<\/span>=element_blank(),<\/span><\/span><\/code><code> legend.position<\/span> = \"top\"<\/span>,<\/span><\/code><code> legend.text<\/span> = element_text(size<\/span>= 12),<\/span><\/span><\/code><code> legend.title<\/span>= element_text(size<\/span>= 12)<\/span><\/span><\/code><code> ) +<\/span><\/code><code>geom_signif<\/span>(comparisons<\/span>=list(c(<\/span>\"High<\/span>\",\"Low<\/span>\")),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/span><\/code><code> map_signif_level<\/span>=F)<\/span> <\/span><\/code><code>ggsave<\/span>(file<\/span>=\"Dysfunction.pdf\"<\/span>,boxplot_Dysfunction<\/span>,height<\/span>=10,width<\/span>=15)<\/span><\/span><\/code><code> <\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6623376623376623\" data-s=\"300,640\" data-type=\"png\" data-w=\"693\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png?w=640\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-11-19_\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0c\u9884\u6d4b\u5bf9\u514d\u75ab\u7597\u6cd5\u7684\u53cd\u5e94\uff08TIDE\u8bc4\u5206\uff09\/11_5YWNtWPt9nwkrEwicowmcqtJdMMGrA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWKtxDNTGOuhyAZb1n2uwFBOGjd5YWNtWPt9nwkrEwicowmcqtJdMMGrA\/640?wx_fmt=png''\" data-recalc-dims=\"1\" \/><\/p>\n <\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><code>###\u7ed8\u5236Exclusion\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/code><code>boxplot_Exclusion<-<\/span> ggplot<\/span>(final<\/span>, aes<\/span>(x<\/span> = group,<\/span> y<\/span> =Exclusion<\/span> ))+ <\/span><\/span><\/code><code> labs<\/span>(y<\/span>=\"Exclusion\"<\/span>,x<\/span>= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes<\/span>(fill<\/span>=group))+<\/span> <\/span><\/code><code> geom_boxplot<\/span>(width<\/span>=0.3)+<\/span> <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title<\/span> = element_text(size<\/span> = 12,color<\/span> =\"black\"<\/span>), <\/span><\/code><code> axis.text<\/span> = element_text(size<\/span>= 12,color<\/span> = \"black\"<\/span>),<\/span><\/code><code> panel.grid.minor.y<\/span> = element_blank(),<\/span><\/span><\/code><code> panel.grid.minor.x<\/span> = element_blank(),<\/span><\/span><\/code><code> axis.text.x<\/span> = element_text(angle<\/span> = 45,<\/span> hjust<\/span> = 1<\/span> ),<\/span><\/code><code> panel.grid<\/span>=element_blank(),<\/span><\/span><\/code><code> legend.position<\/span> = \"top\"<\/span>,<\/span><\/code><code> legend.text<\/span> = element_text(size<\/span>= 12),<\/span><\/span><\/code><code> legend.title<\/span>= element_text(size<\/span>= 12)<\/span><\/span><\/code><code> ) +<\/span><\/code><code>geom_signif<\/span>(comparisons<\/span>=list(c(<\/span>\"High<\/span>\",\"Low<\/span>\")),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/span><\/code><code> map_signif_level<\/span>=F)<\/span> <\/span><\/code><code>ggsave<\/span>(file<\/span>=\"Exclusion.pdf\"<\/span>,boxplot_Exclusion<\/span>,height<\/span>=10,width<\/span>=15)<\/span><\/span><\/code><code> <\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.670995670995671\" data-s=\"300,640\" data-type=\"png\" data-w=\"693\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_sFrFMt0ziaicbwofL41exfpvpqkJHQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWdqxUaAnWMJnYNliadsEWQ24K6icPsFrFMt0ziaicbwofL41exfpvpqkJHQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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\"><code>###\u7ed8\u5236MSI\u663e\u8457\u5dee\u5f02\u5c0f\u63d0\u7434\u56fe+\u7bb1\u7ebf\u56fe<\/span><\/code><code>boxplot_MSI<-<\/span> ggplot<\/span>(final<\/span>, aes<\/span>(x<\/span> = group,<\/span> y<\/span> =MSI.Expr.Sig))+<\/span> <\/span><\/span><\/code><code> labs<\/span>(y<\/span>=\"MSI\"<\/span>,x<\/span>= \"RiskGroup\"<\/span>)+ <\/span><\/code><code> geom_violin<\/span>(aes<\/span>(fill<\/span>=group))+<\/span> <\/span><\/code><code> geom_boxplot<\/span>(width<\/span>=0.3)+<\/span> <\/span><\/code><code> scale_fill_npg<\/span>()+<\/span><\/code><code> #\u4fee\u6539\u4e3b\u9898<\/span><\/code><code>theme_classic<\/span>() + <\/span><\/code><code> theme<\/span>(axis.title<\/span> = element_text(size<\/span> = 12,color<\/span> =\"black\"<\/span>), <\/span><\/code><code> axis.text<\/span> = element_text(size<\/span>= 12,color<\/span> = \"black\"<\/span>),<\/span><\/code><code> panel.grid.minor.y<\/span> = element_blank(),<\/span><\/span><\/code><code> panel.grid.minor.x<\/span> = element_blank(),<\/span><\/span><\/code><code> axis.text.x<\/span> = element_text(angle<\/span> = 45,<\/span> hjust<\/span> = 1<\/span> ),<\/span><\/code><code> panel.grid<\/span>=element_blank(),<\/span><\/span><\/code><code> legend.position<\/span> = \"top\"<\/span>,<\/span><\/code><code> legend.text<\/span> = element_text(size<\/span>= 12),<\/span><\/span><\/code><code> legend.title<\/span>= element_text(size<\/span>= 12)<\/span><\/span><\/code><code> ) +<\/span><\/code><code>geom_signif<\/span>(comparisons<\/span>=list(c(<\/span>\"High<\/span>\",\"Low<\/span>\")),<\/span><\/code><code> test<\/span>=t.test,<\/span><\/span><\/code><code> step_increase<\/span>=0.2,<\/span><\/span><\/code><code> map_signif_level<\/span>=F)<\/span> <\/span><\/code><code>ggsave<\/span>(file<\/span>=\"MSI.pdf\"<\/span>,boxplot_MSI<\/span>,height<\/span>=10,width<\/span>=15)<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6719653179190751\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_CTj2HkRqYQdG0WALC5siaQ0Pia63fQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxE3xicWeDGnp9JiarvglLnsWc3BoOMYFCJ1bISOT3fLugIw76UCTj2HkRqYQdG0WALC5siaQ0Pia63fQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/p>\n <\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u6700\u7ec8\u5c0f\u679c\u6210\u529f\u7684\u5b8c\u6210\u4e86<\/span>TIDE\u8bc4\u5206\u7684\u8ba1\u7b97\uff0c\u770b\u8d77\u6765\u56fe\u7247\u6548\u679c\u975e\u5e38\u4e0d\u9519\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u5440<\/span><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;outline: 0px;font-family: system-ui, -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;background-color: rgb(255, 255, 255);text-align: left;\">\n<section style=\"outline: 0px;font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;outline: 0px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;outline: 0px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 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style=\"outline: 0px;letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" hasload=\"1\" style=\"color: var(--weui-LINK);outline: 0px;cursor: pointer;font-size: 14px;\" rel=\"noopener\">1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4<\/a> <\/section>\n<section style=\"outline: 0px;letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" 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