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0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;width: 30%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 30% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;text-align: center;line-height: 0;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"162\" data-cropsely1=\"0\" data-cropsely2=\"162\" data-ratio=\"1\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_ib2l1ye6HNIkwTG696C2pf9yAtdeGA-23.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyB69UyXDLG0wQcISNwmL6DlpIKVBnCSOXHTWJhLcxic2qtibaib2l1ye6HNIkwTG696C2pf9yAtdeGA\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"400\" style=\"height: 111px;vertical-align: middle;width: 111px;\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<ul class=\"list-paddingleft-1\" style=\"padding-left: 30px;width: 100%;list-style-position: outside;\">\n<li>\n<section><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u57fa\u4e8e\u4e4b\u524d\u5bf9CIBERSORT\u8f6f\u4ef6\u5305\u7684\u4ecb\u7ecd\u548c\u4f7f\u7528\uff0c\u4eca\u5929\u5c0f\u679c\u8981\u6559\u5927\u5bb6\u5982\u4f55\u5728\u4f7f\u7528CIBERSORT\u5305\u7684\u524d\u63d0\u4e0b\u5bf9\u5176\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u53ef\u89c6\u5316\u6211\u4eec\u8981\u7528\u5230\u7684R\u5305\u4e3b\u8981\u4e3aggplot2\uff0c\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/span><br \/><\/section>\n<\/li>\n<\/ul>\n<section>\n<section>\n<section><br \/><\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_QiaOCcR0jFpvjkSAu3UmKL82ohCV5Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNXhQ4GD7nqK0jxIA9vNfaZMfcibQiaOCcR0jFpvjkSAu3UmKL82ohCV5Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;color: rgb(62, 62, 62);\">\u51c6\u5907\u5de5\u4f5c\u53ca\u514d\u75ab\u7ec6\u80de\u5206\u6790<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd9\u4e00\u90e8\u5206\u5176\u5b9e\u5728\u4e4b\u524d\u5c0f\u679c\u5df2\u7ecf\u7ed9\u5927\u5bb6\u505a\u8fc7\u8be6\u7ec6\u7684\u4ecb\u7ecd\uff0c\u5728\u8fd9\u91cc\u6211\u4eec\u518d\u6b21\u7b80\u5355\u7684\u56de\u987e\u4e00\u4e0b\u5427\uff01\u8fd9\u4e00\u6b65\u6211\u4eec\u4e3b\u8981\u8981\u505a\u7684\u5de5\u4f5c\u6709\uff1a<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5b89\u88c5\u4ee5\u4e0b R \u5e93\uff1aggplot2, ggpubr, reshape2, dplyr, CIBERSORT\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4e0b\u8f7d LM22.txt\u6570\u636e\u96c6 \u548c TCGA deg_fpkm.tsv \u6570\u636e\u6587\u4ef6\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4ece LM22.txt \u548c TCGA deg_fpkm.tsv \u6587\u4ef6\u4e2d\u8bfb\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4f7f\u7528 CIBERSORT \u5e93\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u5206\u6790\uff0c\u5e76\u4f7f\u7528 CIBERSORT \u51fd\u6570\u8ba1\u7b97\u51fa\u5404\u79cd\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u6bd4\u4f8b\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06 CIBERSORT \u8ba1\u7b97\u7ed3\u679c\u8f93\u51fa\u5230\u6587\u4ef6\u4e2d<\/span><\/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=\"c\"><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\">library(reshape2)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggpubr)<\/span><\/code><code><span class=\"code-snippet_outer\">library(dplyr)<\/span><\/code><code><span class=\"code-snippet_outer\">lm22.file <- <span class=\"code-snippet__string\">\"LM22.txt\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rawdata_file.file<-<span class=\"code-snippet__string\">\"TCGA deg_fpkm.tsv\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cibersort_file <- <span class=\"code-snippet__string\">\"TCGA cibersort.txt\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">'CIBERSORT'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8ba1\u7b97\u514d\u75ab\u7ec6\u80de<\/span><\/code><code><span class=\"code-snippet_outer\">TCGA_TME.results <- CIBERSORT(lm22.file ,rawdata_file.file, perm = <span class=\"code-snippet__number\">50<\/span>, QN = F)<\/span><\/code><code><span class=\"code-snippet_outer\">TCGA_TME.results<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(TCGA_TME.results, <span class=\"code-snippet__string\">\"TCGA_CIBERSORT_Results_fromRcode.csv\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u73b0\u5728\uff0c\u4f60\u5df2\u7ecf\u6210\u529f\u5b8c\u6210\u4e86\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u5206\u6790\u54e6\uff01\u600e\u4e48\u6837\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u5462\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06CIBERSORT\u7684\u8f93\u51fa\u6570\u636e\u8fdb\u884c\u6574\u7406\uff0c\u4ee5\u9002\u5e94ggplot2\u7684\u7ed8\u56fe\u8981\u6c42<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">data <- t(TCGA_TME.results[,-c(<span class=\"code-snippet__number\">9<\/span>:<span class=\"code-snippet__number\">11<\/span>)])<\/span><\/code><code><span class=\"code-snippet_outer\">col=rainbow(nrow(data),s=<span class=\"code-snippet__number\">0.85<\/span>,v=<span class=\"code-snippet__number\">0.85<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">df.<span class=\"code-snippet__keyword\">long<\/span> <- reshape2::melt(data, value.name=<span class=\"code-snippet__string\">'abundance'<\/span>, variable.name=<span class=\"code-snippet__string\">'group'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">\u4f7f\u7528ggplot2\u5305\u751f\u6210\u70ed\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(df.<span class=\"code-snippet__keyword\">long<\/span>, aes(x=Var2, y=abundance, group=Var1)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_classic()+<\/span><\/code><code><span class=\"code-snippet_outer\"> geom_bar(stat=<span class=\"code-snippet__string\">\"identity\"<\/span>, position=<span class=\"code-snippet__string\">\"fill\"<\/span>, aes(fill=Var1))+<\/span><\/code><code><span class=\"code-snippet_outer\"> scale_y_continuous(labels = scales::percent) +<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__built_in\">labs<\/span>(x=<span class=\"code-snippet__string\">'',y='<\/span>Relative Percent<span class=\"code-snippet__number\">'<\/span>,title=<span class=\"code-snippet__string\">'Immune Cell Subset Proportions'<\/span>)+<\/span><\/code><code><span class=\"code-snippet_outer\"> scale_fill_manual(values =col)+<\/span><\/code><code><span class=\"code-snippet_outer\"> theme( panel.grid=element_blank(),legend.title=element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> plot.title = element_text(hjust = <span class=\"code-snippet__number\">0.5<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\"> axis.text.x = element_text(angle =<span class=\"code-snippet__number\">90<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u751f\u6210\u7684\u7ed3\u679c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06\u56fe\u50cf\u4fdd\u5b58\u4e3aPDF\u683c\u5f0f<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.4214765100671141\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_kicctZWQbdN1bSwPCFk0GiaLR2Kvpg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN7pncKOAAowyOBZZpNc067GoeEakicctZWQbdN1bSwPCFk0GiaLR2Kvpg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"745\" style=\"\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">ggsave(“cibersort_barplot.pdf”,height=10,width=25)<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5728\u4e0a\u8ff0\u4ee3\u7801\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528reshape2\u5305\u7684melt\u51fd\u6570\u5c06CIBERSORT\u7684\u8f93\u51fa\u6570\u636e\u8fdb\u884c\u6574\u7406\uff0c\u751f\u6210\u957f\u683c\u5f0f\u7684\u6570\u636e\u6846\u3002\u7136\u540e\uff0c\u6211\u4eec\u4f7f\u7528ggplot2\u5305\u7684geom_bar\u51fd\u6570\u751f\u6210\u5806\u79ef\u6761\u5f62\u56fe\uff0c\u5e76\u4f7f\u7528scale_fill_manual\u51fd\u6570\u8bbe\u7f6e\u989c\u8272\uff0ctheme\u51fd\u6570\u8bbe\u7f6e\u6837\u5f0f\uff0clabs\u51fd\u6570\u8bbe\u7f6e\u56fe\u50cf\u6807\u9898\u548c\u8f74\u6807\u7b7e\u3002\u6700\u540e\uff0c\u6211\u4eec\u4f7f\u7528ggsave\u51fd\u6570\u5c06\u56fe\u50cf\u4fdd\u5b58\u4e3aPDF\u683c\u5f0f\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5230\u6b64\u4e3a\u6b62\uff0c\u6211\u4eec\u5df2\u7ecf\u6210\u529f\u5730\u5b8c\u6210\u4e86\u514d\u75ab\u7ec6\u80de\u6bd4\u4f8b\u5206\u6790\uff0c\u5e76\u53ef\u89c6\u5316\u4e86\u7ed3\u679c\u3002\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u5206\u6790\u7ed3\u679c\u6765\u8fdb\u4e00\u6b65\u7814\u7a76\u514d\u75ab\u7ec6\u80de\u5728\u80bf\u7624\u7ec4\u7ec7\u4e2d\u7684\u4f5c\u7528\u548c\u673a\u5236\uff0c\u4e3a\u80bf\u7624\u514d\u75ab\u6cbb\u7597\u63d0\u4f9b\u79d1\u5b66\u4f9d\u636e\u548c\u6307\u5bfc\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u600e\u4e48\u6837\uff0c\u4eca\u5929\u7684\u70ed\u56fe\u7ed8\u5236\u4f60\u5b66\u4f1a\u600e\u4e48\u7528\u4e86\u5417\uff01<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 10.5pt;letter-spacing: 0.578px;\"><\/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 data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 26%;max-width: 26% !important;\">\n<section style=\"padding: 7px;border-radius: 15px;box-shadow: rgba(169, 187, 223, 0.45) 4px 4px 8px, rgb(255, 255, 255) -2.5px -2.5px 5px;\">\n<section data-width=\"100%\" style=\"width: 100%;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.005281690140845\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_0WFLKBMicbm6iawtkrNrMxpSVU9GBQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN261llpmfF6btPBTUKkibEdnRz5Y0WFLKBMicbm6iawtkrNrMxpSVU9GBQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"568\" data-width=\"100%\" style=\"vertical-align: inherit;width: 100%;display: block;border-radius: 7px;\" title=\"\u5c0f\u4e91-\u5fae\u4fe1\u4e8c\u7ef4\u7801.png\"><\/section>\n<\/section>\n<\/section>\n<section data-width=\"62%\" style=\"width: 62%;max-width: 62% !important;\">\n<section style=\"display: inline-block;\">\n<section style=\"padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u5fae\u4fe1\u53f7 | 18502195490<\/span><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-top: 12px;padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u77e5\u4e4e | \u751f\u4fe1\u679c<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"letter-spacing: 0.578px;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u9c9c\u6d3b\u7684\u70ed\u56fe\uff0c\u8be0\u91ca\u514d\u75ab\u7ec6\u80de\u7ec4\u6210\uff1a\u4f7f\u7528CIBERSORT\u5e76\u5b9e\u73b0\u53ef\u89c6\u5316\u5206\u6790\uff01 \u539f\u521b xiao& […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/53970"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=53970"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/53970\/revisions"}],"predecessor-version":[{"id":53975,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/53970\/revisions\/53975"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=53970"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=53970"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=53970"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":53970,"date":"2024-06-16T13:30:28","date_gmt":"2024-06-16T05:30:28","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=53970"},"modified":"2024-06-16T13:30:28","modified_gmt":"2024-06-16T05:30:28","slug":"%e9%b2%9c%e6%b4%bb%e7%9a%84%e7%83%ad%e5%9b%be%ef%bc%8c%e8%af%a0%e9%87%8a%e5%85%8d%e7%96%ab%e7%bb%86%e8%83%9e%e7%bb%84%e6%88%90%ef%bc%9a%e4%bd%bf%e7%94%a8cibersort%e5%b9%b6%e5%ae%9e%e7%8e%b0%e5%8f%af-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=53970","title":{"rendered":"\u9c9c\u6d3b\u7684\u70ed\u56fe\uff0c\u8be0\u91ca\u514d\u75ab\u7ec6\u80de\u7ec4\u6210\uff1a\u4f7f\u7528CIBERSORT\u5e76\u5b9e\u73b0\u53ef\u89c6\u5316\u5206\u6790\uff01"},"content":{"rendered":"

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solid;border-width: 1px;border-color: rgb(67, 67, 67);flex: 0 0 auto;align-self: flex-start;height: auto;box-shadow: rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;width: 70%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70% !important;\">\n<section style=\"margin-top: 10px;\">\n<section style=\"text-align: center;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;width: 30%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 30% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;text-align: center;line-height: 0;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"162\" data-cropsely1=\"0\" data-cropsely2=\"162\" data-ratio=\"1\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_ib2l1ye6HNIkwTG696C2pf9yAtdeGA-23.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyB69UyXDLG0wQcISNwmL6DlpIKVBnCSOXHTWJhLcxic2qtibaib2l1ye6HNIkwTG696C2pf9yAtdeGA\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"400\" style=\"height: 111px;vertical-align: middle;width: 111px;\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<ul class=\"list-paddingleft-1\" style=\"padding-left: 30px;width: 100%;list-style-position: outside;\">\n<li>\n<section><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u57fa\u4e8e\u4e4b\u524d\u5bf9CIBERSORT\u8f6f\u4ef6\u5305\u7684\u4ecb\u7ecd\u548c\u4f7f\u7528\uff0c\u4eca\u5929\u5c0f\u679c\u8981\u6559\u5927\u5bb6\u5982\u4f55\u5728\u4f7f\u7528CIBERSORT\u5305\u7684\u524d\u63d0\u4e0b\u5bf9\u5176\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u53ef\u89c6\u5316\u6211\u4eec\u8981\u7528\u5230\u7684R\u5305\u4e3b\u8981\u4e3aggplot2\uff0c\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/span><br \/><\/section>\n<\/li>\n<\/ul>\n<section>\n<section>\n<section><br \/><\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_QiaOCcR0jFpvjkSAu3UmKL82ohCV5Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNXhQ4GD7nqK0jxIA9vNfaZMfcibQiaOCcR0jFpvjkSAu3UmKL82ohCV5Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;color: rgb(62, 62, 62);\">\u51c6\u5907\u5de5\u4f5c\u53ca\u514d\u75ab\u7ec6\u80de\u5206\u6790<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd9\u4e00\u90e8\u5206\u5176\u5b9e\u5728\u4e4b\u524d\u5c0f\u679c\u5df2\u7ecf\u7ed9\u5927\u5bb6\u505a\u8fc7\u8be6\u7ec6\u7684\u4ecb\u7ecd\uff0c\u5728\u8fd9\u91cc\u6211\u4eec\u518d\u6b21\u7b80\u5355\u7684\u56de\u987e\u4e00\u4e0b\u5427\uff01\u8fd9\u4e00\u6b65\u6211\u4eec\u4e3b\u8981\u8981\u505a\u7684\u5de5\u4f5c\u6709\uff1a<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5b89\u88c5\u4ee5\u4e0b R \u5e93\uff1aggplot2, ggpubr, reshape2, dplyr, CIBERSORT\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4e0b\u8f7d LM22.txt\u6570\u636e\u96c6 \u548c TCGA deg_fpkm.tsv \u6570\u636e\u6587\u4ef6\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4ece LM22.txt \u548c TCGA deg_fpkm.tsv \u6587\u4ef6\u4e2d\u8bfb\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4f7f\u7528 CIBERSORT \u5e93\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u5206\u6790\uff0c\u5e76\u4f7f\u7528 CIBERSORT \u51fd\u6570\u8ba1\u7b97\u51fa\u5404\u79cd\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u6bd4\u4f8b\uff1b<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06 CIBERSORT \u8ba1\u7b97\u7ed3\u679c\u8f93\u51fa\u5230\u6587\u4ef6\u4e2d<\/span><\/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=\"c\"><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\">library(reshape2)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggpubr)<\/span><\/code><code><span class=\"code-snippet_outer\">library(dplyr)<\/span><\/code><code><span class=\"code-snippet_outer\">lm22.file <- <span class=\"code-snippet__string\">\"LM22.txt\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rawdata_file.file<-<span class=\"code-snippet__string\">\"TCGA deg_fpkm.tsv\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cibersort_file <- <span class=\"code-snippet__string\">\"TCGA cibersort.txt\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">'CIBERSORT'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8ba1\u7b97\u514d\u75ab\u7ec6\u80de<\/span><\/code><code><span class=\"code-snippet_outer\">TCGA_TME.results <- CIBERSORT(lm22.file ,rawdata_file.file, perm = <span class=\"code-snippet__number\">50<\/span>, QN = F)<\/span><\/code><code><span class=\"code-snippet_outer\">TCGA_TME.results<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(TCGA_TME.results, <span class=\"code-snippet__string\">\"TCGA_CIBERSORT_Results_fromRcode.csv\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u73b0\u5728\uff0c\u4f60\u5df2\u7ecf\u6210\u529f\u5b8c\u6210\u4e86\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u5206\u6790\u54e6\uff01\u600e\u4e48\u6837\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u5462\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06CIBERSORT\u7684\u8f93\u51fa\u6570\u636e\u8fdb\u884c\u6574\u7406\uff0c\u4ee5\u9002\u5e94ggplot2\u7684\u7ed8\u56fe\u8981\u6c42<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">data <- t(TCGA_TME.results[,-c(<span class=\"code-snippet__number\">9<\/span>:<span class=\"code-snippet__number\">11<\/span>)])<\/span><\/code><code><span class=\"code-snippet_outer\">col=rainbow(nrow(data),s=<span class=\"code-snippet__number\">0.85<\/span>,v=<span class=\"code-snippet__number\">0.85<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">df.<span class=\"code-snippet__keyword\">long<\/span> <- reshape2::melt(data, value.name=<span class=\"code-snippet__string\">'abundance'<\/span>, variable.name=<span class=\"code-snippet__string\">'group'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">\u4f7f\u7528ggplot2\u5305\u751f\u6210\u70ed\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(df.<span class=\"code-snippet__keyword\">long<\/span>, aes(x=Var2, y=abundance, group=Var1)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_classic()+<\/span><\/code><code><span class=\"code-snippet_outer\"> geom_bar(stat=<span class=\"code-snippet__string\">\"identity\"<\/span>, position=<span class=\"code-snippet__string\">\"fill\"<\/span>, aes(fill=Var1))+<\/span><\/code><code><span class=\"code-snippet_outer\"> scale_y_continuous(labels = scales::percent) +<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__built_in\">labs<\/span>(x=<span class=\"code-snippet__string\">'',y='<\/span>Relative Percent<span class=\"code-snippet__number\">'<\/span>,title=<span class=\"code-snippet__string\">'Immune Cell Subset Proportions'<\/span>)+<\/span><\/code><code><span class=\"code-snippet_outer\"> scale_fill_manual(values =col)+<\/span><\/code><code><span class=\"code-snippet_outer\"> theme( panel.grid=element_blank(),legend.title=element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> plot.title = element_text(hjust = <span class=\"code-snippet__number\">0.5<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\"> axis.text.x = element_text(angle =<span class=\"code-snippet__number\">90<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u751f\u6210\u7684\u7ed3\u679c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06\u56fe\u50cf\u4fdd\u5b58\u4e3aPDF\u683c\u5f0f<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.4214765100671141\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_kicctZWQbdN1bSwPCFk0GiaLR2Kvpg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN7pncKOAAowyOBZZpNc067GoeEakicctZWQbdN1bSwPCFk0GiaLR2Kvpg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"745\" style=\"\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">ggsave(“cibersort_barplot.pdf”,height=10,width=25)<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5728\u4e0a\u8ff0\u4ee3\u7801\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528reshape2\u5305\u7684melt\u51fd\u6570\u5c06CIBERSORT\u7684\u8f93\u51fa\u6570\u636e\u8fdb\u884c\u6574\u7406\uff0c\u751f\u6210\u957f\u683c\u5f0f\u7684\u6570\u636e\u6846\u3002\u7136\u540e\uff0c\u6211\u4eec\u4f7f\u7528ggplot2\u5305\u7684geom_bar\u51fd\u6570\u751f\u6210\u5806\u79ef\u6761\u5f62\u56fe\uff0c\u5e76\u4f7f\u7528scale_fill_manual\u51fd\u6570\u8bbe\u7f6e\u989c\u8272\uff0ctheme\u51fd\u6570\u8bbe\u7f6e\u6837\u5f0f\uff0clabs\u51fd\u6570\u8bbe\u7f6e\u56fe\u50cf\u6807\u9898\u548c\u8f74\u6807\u7b7e\u3002\u6700\u540e\uff0c\u6211\u4eec\u4f7f\u7528ggsave\u51fd\u6570\u5c06\u56fe\u50cf\u4fdd\u5b58\u4e3aPDF\u683c\u5f0f\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 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