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\/><\/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>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;caret-color: red;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 10px 0% 8px;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 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style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">\u5c0f\u679c\u53c8\u6765\u5206\u4eab\u5566\uff01\u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u5229\u7528<\/span><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">quanTIseq\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790\uff0c\u7136\u540e\u57fa\u4e8e\u4e9a\u578b\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\uff0c\u8fdb\u884c\u4e9a\u578b\u95f4\u514d\u75ab\u7ec6\u80de\u542b\u91cf\u663e\u8457\u5dee\u5f02\u5206\u6790\uff0c\u8be5\u5206\u6790\u5728\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u4e2d\u5fc5\u5907\u7684\u5206\u6790\u5185\u5bb9\uff0c\u975e\u5e38\u503c\u5f97\u5c0f\u4f19\u4f34\u5b66\u4e60\uff0c\u5c0f\u679c\u5f3a\u70c8\u63a8\u8350\u5440\uff01\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u542f\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\u5b66\u4e60\u3002<\/span><\/span><\/p>\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;text-align: justify;\"><em><span style=\"font-size: 20px;\">1.quanTIseq\u7b97\u6cd5\u4ecb\u7ecd<\/span><\/em><\/strong><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">\u5728\u8fdb\u884c\u8be5\u5206\u6790\u4e4b\u524d\uff0c\u5c0f\u679c\u5148\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b<\/span><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">quanTIseq\u7b97\u6cd5\uff0cquanTIseq\u57fa\u4e8e\u53cd\u5377\u79ef\u7b97\u6cd5\uff0c\u5229\u7528bulk samples\u7684RNA_seq\u6570\u636e\uff0c\u53ef\u4ee5\u5bf9\u80bf\u7624\u6837\u672c\u4e2d\u4e0d\u540c\u79cd\u7c7b\u514d\u75ab\u7ec6\u80de\u7684\u7ec4\u6210\u8fdb\u884c\u9884\u6d4b\uff0c\u652f\u630110\u79cd\u7c7b\u578b\u7684\u514d\u75ab\u7ec6\u80de\uff0c\u5305\u62ecB cells\uff0cClassically activated macrophages (M1)\uff0cAlternatively activated macrophages (M2)\uff0cMonocytes\uff0cNeutrophils\uff0cNatural killer (NK) cells\uff0cNon-regulatory CD4+ T cells \uff0cCD8+ T cells\uff0cDendritic cells\uff0cOther uncharacterized cells\u3002<\/span><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">\u8fd9\u5c31\u662f\u5c0f\u679c\u5bf9\u8be5\u7b97\u6cd5\u7684\u4ecb\u7ecd\uff0c\u60f3\u6df1\u5165\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5230\u8be5\u7f51\u5740:https:\/\/icbi.i-med.ac.at\/software\/quantiseq\/doc\/index.html#Figure1<\/span><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><\/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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"ruby\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u9996\u5148\u4e0b\u8f7dquanTIseq\u6d41\u7a0b\u5206\u6790\u811a\u672c\uff0c\u5982\u4e0b\u6587:<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">wget <span class=\"code-snippet__symbol\">https:<\/span>\/<span class=\"code-snippet__regexp\">\/icbi.i-med.ac.at\/software<\/span><span class=\"code-snippet__regexp\">\/quantiseq\/doc<\/span><span class=\"code-snippet__regexp\">\/downloads\/quan<\/span>TIseq_pipeline.sh<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#quanTIseq\u6d41\u7a0b\u8fd0\u884c\u53c2\u6570\u4f7f\u7528\u65b9\u6cd5<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3621933621933622\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_aldaOcJ3DaXHo78wORIkED0FK0ibcw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DKibspBqGU2FgFadfJXua9HL62ic7ialdaOcJ3DaXHo78wORIkED0FK0ibcw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/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<li><\/li>\n<li><\/li>\n<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><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5b89\u88c5\u9700\u8981\u7684\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggplot2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggsci\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"tidyverse\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"reshape2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggpubr\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(reshape2)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(ggpubr)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(ggsci)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">3.<\/span><\/em><\/strong><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">\u8f93\u5165\u6570\u636e<\/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=\"perl\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#EXP.txt\uff0c\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u5217\u540d\u4e3a\u6837\u672c\u4fe1\u606f\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">exp<\/span><-read.table(<span class=\"code-snippet__string\">\"EXP.txt\"<\/span>,header=T,row.names=<span class=\"code-snippet__number\">1<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,check.names=F)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\"><\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.24277456647398843\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_TDLtCXInWVVyXWMC2CDyGzHHnUvhPw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DK0slBplKH98TFBAvmvg8IwicjFTDLtCXInWVVyXWMC2CDyGzHHnUvhPw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">4.\u5229\u7528quanTIseq\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\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<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\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5c06\u884c\u540d\u8f6c\u5316\u4e3a\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">exp<\/span><-rownames_to_column(<span class=\"code-snippet__keyword\">exp<\/span>,var=<span class=\"code-snippet__string\">\"GENE\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__number\">4<\/span>.\u5229\u7528quanTIseq\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#quanTIseq\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">bash quanTIseq_pipeline.sh --inputfile=exp.txt --outputdir=quanTIseqTest --prefix=quanTIseqTest --pipelinestart=decon<\/span><\/code><code><span class=\"code-snippet_outer\">input\u8868\u793a\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u5176\u4ed6\u5217\u4e3a\u6837\u672c\u540d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">outputdir\u8868\u793a\u751f\u6210\u7ed3\u679c\u6587\u4ef6\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">prefix\u8868\u793a\u751f\u6210\u7ed3\u679c\u6587\u4ef6\u524d\u7f00<\/span><\/code><code><span class=\"code-snippet_outer\">pipelinestart\u8868\u793aquanTIseq\u5206\u6790\u6d41\u7a0b\uff0c\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u9009\u7528decon<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u751f\u6210\u7ed3\u679c\u6587\u4ef6\u4e3aquanTIseqTest_cell_fractions.txt\uff0c\u8be5\u7ed3\u679c\u4e3a\u8ba1\u7b97\u768410\u79cd\u514d\u75ab\u7ec6\u80de\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u542b\u91cf\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u540d\uff0c\u5176\u4ed6\u5217\u4e3a\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u3002<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><span style=\"display: none;line-height: 0px;\">\u200d<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.23699421965317918\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_HaIpcia4ichypGujqCbryGJeulupvw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DKTdUKWv5gxjhVEuHS7NtNP5qj0bHaIpcia4ichypGujqCbryGJeulupvw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\"><br \/><\/span><\/em><\/strong><\/p>\n<p><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">5.\u4e0d\u540c\u4e9a\u578b\u4e2dquanTIseq\u7b97\u6cd5\u8ba1\u7b97\u7684\u514d\u75ab\u7ec6\u80de\u7684\u663e\u8457\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\"><\/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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6quanTIseq\u5206\u6790\u514d\u75ab\u7ec6\u80de\u7ec4\u6210\u7ed3\u679c\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">immune<-read.table(<span class=\"code-snippet__string\">\"quanTIseqTest_cell_fractions.txt\"<\/span>,header=T,sep=<span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5c06Sample\u5217\u201d.\u201d\u4fee\u6539\u4e3a\u201d-\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">immune<span class=\"code-snippet__variable\">$Sample<\/span><-str_replace_all(immune<span class=\"code-snippet__variable\">$Sample<\/span>,<span class=\"code-snippet__string\">\"\\.\"<\/span>,<span class=\"code-snippet__string\">\"-\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e9a\u578b\u5206\u7ec4\u6587\u4ef6,\u884c\u540d\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e8c\u5217\u4e3a\u4e9a\u578b\u5206\u7ec4\u4fe1\u606f\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">K3<-read.table(<span class=\"code-snippet__string\">\"K3.txt\"<\/span>,header=T,sep=<span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3217893217893218\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_UZGvcVibiaOSnG1cCDxibYc48wPQag.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DK6mAibHySmA2I7ZtKdRHlQ2n03VyMUZGvcVibiaOSnG1cCDxibYc48wPQag\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u5408\u5e76\u514d\u75ab\u7ec6\u80de\u7ec4\u6210\u6587\u4ef6\u548c\u4e9a\u578b\u5206\u7ec4\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">final<-left_join(immune,K3,<span class=\"code-snippet__keyword\">by<\/span>=\u201dSample\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u957f\u5bbd\u6570\u636e\u8f6c\u6362<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">quanTIseq_cluster<-melt(final,id.vars=c(<span class=\"code-snippet__string\">\"Sample\"<\/span>,<span class=\"code-snippet__string\">\"Cluster\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u8bbe\u7f6e\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">colnames(quanTIseq_cluster)<-c(<span class=\"code-snippet__string\">\"Sample\"<\/span>,<span class=\"code-snippet__string\">\"Cluster\"<\/span>,<span class=\"code-snippet__string\">\"celltype\"<\/span>,<span class=\"code-snippet__string\">\"quanTIseq\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u7ed8\u5236\u663e\u8457\u5dee\u5f02\u5206\u6790\u5c0f\u63d0\u7434+\u7bb1\u7ebf\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">boxplot_quanTIseq<- ggplot(quanTIseq_cluster, aes(x = celltype, y =quanTIseq ))+<\/span><\/code><code><span class=\"code-snippet_outer\"> labs(y=<span class=\"code-snippet__string\">\"quanTIseq\"<\/span>,x= <span class=\"code-snippet__string\">\"\"<\/span>)+ <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_boxplot(aes(fill = Cluster),position=position_dodge(<span class=\"code-snippet__number\">0.5<\/span>),width=<span class=\"code-snippet__number\">0.5<\/span>)+ <\/span><\/code><code><span class=\"code-snippet_outer\"> scale_fill_npg()+<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__meta\">#\u4fee\u6539\u4e3b\u9898<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">theme_classic() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme(axis.title = element_text(size = <span class=\"code-snippet__number\">12<\/span>,color =<span class=\"code-snippet__string\">\"black\"<\/span>), <\/span><\/code><code><span class=\"code-snippet_outer\"> axis.text = element_text(size= <span class=\"code-snippet__number\">12<\/span>,color = <span class=\"code-snippet__string\">\"black\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\"> panel.grid.minor.y = element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> panel.grid.minor.x = element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> axis.text.x = element_text(angle = <span class=\"code-snippet__number\">45<\/span>, hjust = <span class=\"code-snippet__number\">1<\/span> ),<\/span><\/code><code><span class=\"code-snippet_outer\"> panel.grid=element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> legend.position = <span class=\"code-snippet__string\">\"top\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> legend.text = element_text(size= <span class=\"code-snippet__number\">12<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\"> legend.title= element_text(size= <span class=\"code-snippet__number\">12<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> ) +<\/span><\/code><code><span class=\"code-snippet_outer\"> stat_compare_means(aes(<span class=\"code-snippet__keyword\">group<\/span> = Cluster),<\/span><\/code><code><span class=\"code-snippet_outer\"> label = <span class=\"code-snippet__string\">\"p.signif\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> method = <span class=\"code-snippet__string\">\"kruskal.test\"<\/span>,<span class=\"code-snippet__meta\">#kruskal.test\u591a\u7ec4\u68c0\u9a8c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> hide.ns = F)<span class=\"code-snippet__meta\">#\u9690\u85cf\u4e0d\u663e\u8457\u7684<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u4fdd\u5b58\u56fe\u7247<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(file=<span class=\"code-snippet__string\">\"quanTIseq.pdf\"<\/span>,boxplot_quanTIseq,height=<span class=\"code-snippet__number\">10<\/span>,width=<span class=\"code-snippet__number\">15<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6705202312138728\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_dYApu9W45B2o4htfDy9emM1UICvjGQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DKwk9QLz5sKtsLf0WlJ7VRtwCqdYApu9W45B2o4htfDy9emM1UICvjGQ\/640?wx_fmt=png'\" 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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>\n<section style=\"display: inline-block;vertical-align: top;width: 29.9652%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 29.9652% !important;\">\n<section style=\"margin-top: 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\/><\/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>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;caret-color: red;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 10px 0% 8px;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;\">\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u7edd\u5bf9\u662f\u751f\u4fe1\u70ed\u70b9\u5206\u6790\u5185\u5bb9\uff0c\u57fa\u4e8e\u4e09\u79cd\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\u8fdb\u884c\u751f\u5b58\u8d44\u6599\u7279\u5f81\u57fa\u56e0\u7b5b\u9009\uff0c\u6700\u7ec8\u5c06\u4e09\u79cd\u7b97\u6cd5\u83b7\u5f97\u7684\u4ea4\u53c9\u57fa\u56e0\u4f5c\u4e3a\u6211\u4eec\u7684\u7279\u5f81\u57fa\u56e0\u3002<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">\u5c0f\u679c\u53c8\u6765\u5206\u4eab\u5566\uff01\u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u5229\u7528<\/span><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">quanTIseq\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790\uff0c\u7136\u540e\u57fa\u4e8e\u4e9a\u578b\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\uff0c\u8fdb\u884c\u4e9a\u578b\u95f4\u514d\u75ab\u7ec6\u80de\u542b\u91cf\u663e\u8457\u5dee\u5f02\u5206\u6790\uff0c\u8be5\u5206\u6790\u5728\u80bf\u7624\u751f\u4fe1\u6587\u7ae0\u4e2d\u5fc5\u5907\u7684\u5206\u6790\u5185\u5bb9\uff0c\u975e\u5e38\u503c\u5f97\u5c0f\u4f19\u4f34\u5b66\u4e60\uff0c\u5c0f\u679c\u5f3a\u70c8\u63a8\u8350\u5440\uff01\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u542f\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\u5b66\u4e60\u3002<\/span><\/span><\/p>\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;text-align: justify;\"><em><span style=\"font-size: 20px;\">1.quanTIseq\u7b97\u6cd5\u4ecb\u7ecd<\/span><\/em><\/strong><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">\u5728\u8fdb\u884c\u8be5\u5206\u6790\u4e4b\u524d\uff0c\u5c0f\u679c\u5148\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b<\/span><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">quanTIseq\u7b97\u6cd5\uff0cquanTIseq\u57fa\u4e8e\u53cd\u5377\u79ef\u7b97\u6cd5\uff0c\u5229\u7528bulk samples\u7684RNA_seq\u6570\u636e\uff0c\u53ef\u4ee5\u5bf9\u80bf\u7624\u6837\u672c\u4e2d\u4e0d\u540c\u79cd\u7c7b\u514d\u75ab\u7ec6\u80de\u7684\u7ec4\u6210\u8fdb\u884c\u9884\u6d4b\uff0c\u652f\u630110\u79cd\u7c7b\u578b\u7684\u514d\u75ab\u7ec6\u80de\uff0c\u5305\u62ecB cells\uff0cClassically activated macrophages (M1)\uff0cAlternatively activated macrophages (M2)\uff0cMonocytes\uff0cNeutrophils\uff0cNatural killer (NK) cells\uff0cNon-regulatory CD4+ T cells \uff0cCD8+ T cells\uff0cDendritic cells\uff0cOther uncharacterized cells\u3002<\/span><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">\u8fd9\u5c31\u662f\u5c0f\u679c\u5bf9\u8be5\u7b97\u6cd5\u7684\u4ecb\u7ecd\uff0c\u60f3\u6df1\u5165\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5230\u8be5\u7f51\u5740:https:\/\/icbi.i-med.ac.at\/software\/quantiseq\/doc\/index.html#Figure1<\/span><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><\/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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"ruby\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u9996\u5148\u4e0b\u8f7dquanTIseq\u6d41\u7a0b\u5206\u6790\u811a\u672c\uff0c\u5982\u4e0b\u6587:<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">wget <span class=\"code-snippet__symbol\">https:<\/span>\/<span class=\"code-snippet__regexp\">\/icbi.i-med.ac.at\/software<\/span><span class=\"code-snippet__regexp\">\/quantiseq\/doc<\/span><span class=\"code-snippet__regexp\">\/downloads\/quan<\/span>TIseq_pipeline.sh<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#quanTIseq\u6d41\u7a0b\u8fd0\u884c\u53c2\u6570\u4f7f\u7528\u65b9\u6cd5<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3621933621933622\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_aldaOcJ3DaXHo78wORIkED0FK0ibcw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DKibspBqGU2FgFadfJXua9HL62ic7ialdaOcJ3DaXHo78wORIkED0FK0ibcw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/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<li><\/li>\n<li><\/li>\n<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><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5b89\u88c5\u9700\u8981\u7684\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggplot2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggsci\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"tidyverse\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"reshape2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"ggpubr\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(reshape2)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(ggpubr)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(ggsci)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">3.<\/span><\/em><\/strong><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">\u8f93\u5165\u6570\u636e<\/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=\"perl\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#EXP.txt\uff0c\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u5217\u540d\u4e3a\u6837\u672c\u4fe1\u606f\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">exp<\/span><-read.table(<span class=\"code-snippet__string\">\"EXP.txt\"<\/span>,header=T,row.names=<span class=\"code-snippet__number\">1<\/span>,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,check.names=F)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\"><\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.24277456647398843\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_TDLtCXInWVVyXWMC2CDyGzHHnUvhPw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DK0slBplKH98TFBAvmvg8IwicjFTDLtCXInWVVyXWMC2CDyGzHHnUvhPw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">4.\u5229\u7528quanTIseq\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\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<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\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5c06\u884c\u540d\u8f6c\u5316\u4e3a\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">exp<\/span><-rownames_to_column(<span class=\"code-snippet__keyword\">exp<\/span>,var=<span class=\"code-snippet__string\">\"GENE\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__number\">4<\/span>.\u5229\u7528quanTIseq\u7b97\u6cd5\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#quanTIseq\u8fdb\u884c\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">bash quanTIseq_pipeline.sh --inputfile=exp.txt --outputdir=quanTIseqTest --prefix=quanTIseqTest --pipelinestart=decon<\/span><\/code><code><span class=\"code-snippet_outer\">input\u8868\u793a\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u5176\u4ed6\u5217\u4e3a\u6837\u672c\u540d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">outputdir\u8868\u793a\u751f\u6210\u7ed3\u679c\u6587\u4ef6\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">prefix\u8868\u793a\u751f\u6210\u7ed3\u679c\u6587\u4ef6\u524d\u7f00<\/span><\/code><code><span class=\"code-snippet_outer\">pipelinestart\u8868\u793aquanTIseq\u5206\u6790\u6d41\u7a0b\uff0c\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u9009\u7528decon<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u751f\u6210\u7ed3\u679c\u6587\u4ef6\u4e3aquanTIseqTest_cell_fractions.txt\uff0c\u8be5\u7ed3\u679c\u4e3a\u8ba1\u7b97\u768410\u79cd\u514d\u75ab\u7ec6\u80de\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u542b\u91cf\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u540d\uff0c\u5176\u4ed6\u5217\u4e3a\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u3002<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><span style=\"display: none;line-height: 0px;\">\u200d<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.23699421965317918\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_HaIpcia4ichypGujqCbryGJeulupvw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DKTdUKWv5gxjhVEuHS7NtNP5qj0bHaIpcia4ichypGujqCbryGJeulupvw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\"><br \/><\/span><\/em><\/strong><\/p>\n<p><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\">5.\u4e0d\u540c\u4e9a\u578b\u4e2dquanTIseq\u7b97\u6cd5\u8ba1\u7b97\u7684\u514d\u75ab\u7ec6\u80de\u7684\u663e\u8457\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><strong style=\"letter-spacing: 0.578px;text-align: center;text-wrap: wrap;\"><em><span style=\"font-size: 20px;\"><\/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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6quanTIseq\u5206\u6790\u514d\u75ab\u7ec6\u80de\u7ec4\u6210\u7ed3\u679c\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">immune<-read.table(<span class=\"code-snippet__string\">\"quanTIseqTest_cell_fractions.txt\"<\/span>,header=T,sep=<span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5c06Sample\u5217\u201d.\u201d\u4fee\u6539\u4e3a\u201d-\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">immune<span class=\"code-snippet__variable\">$Sample<\/span><-str_replace_all(immune<span class=\"code-snippet__variable\">$Sample<\/span>,<span class=\"code-snippet__string\">\"\\.\"<\/span>,<span class=\"code-snippet__string\">\"-\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e9a\u578b\u5206\u7ec4\u6587\u4ef6,\u884c\u540d\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e8c\u5217\u4e3a\u4e9a\u578b\u5206\u7ec4\u4fe1\u606f\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">K3<-read.table(<span class=\"code-snippet__string\">\"K3.txt\"<\/span>,header=T,sep=<span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3217893217893218\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_UZGvcVibiaOSnG1cCDxibYc48wPQag.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DK6mAibHySmA2I7ZtKdRHlQ2n03VyMUZGvcVibiaOSnG1cCDxibYc48wPQag\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u5408\u5e76\u514d\u75ab\u7ec6\u80de\u7ec4\u6210\u6587\u4ef6\u548c\u4e9a\u578b\u5206\u7ec4\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">final<-left_join(immune,K3,<span class=\"code-snippet__keyword\">by<\/span>=\u201dSample\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u957f\u5bbd\u6570\u636e\u8f6c\u6362<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">quanTIseq_cluster<-melt(final,id.vars=c(<span class=\"code-snippet__string\">\"Sample\"<\/span>,<span class=\"code-snippet__string\">\"Cluster\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u8bbe\u7f6e\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">colnames(quanTIseq_cluster)<-c(<span class=\"code-snippet__string\">\"Sample\"<\/span>,<span class=\"code-snippet__string\">\"Cluster\"<\/span>,<span class=\"code-snippet__string\">\"celltype\"<\/span>,<span class=\"code-snippet__string\">\"quanTIseq\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u7ed8\u5236\u663e\u8457\u5dee\u5f02\u5206\u6790\u5c0f\u63d0\u7434+\u7bb1\u7ebf\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">boxplot_quanTIseq<- ggplot(quanTIseq_cluster, aes(x = celltype, y =quanTIseq ))+<\/span><\/code><code><span class=\"code-snippet_outer\"> labs(y=<span class=\"code-snippet__string\">\"quanTIseq\"<\/span>,x= <span class=\"code-snippet__string\">\"\"<\/span>)+ <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_boxplot(aes(fill = Cluster),position=position_dodge(<span class=\"code-snippet__number\">0.5<\/span>),width=<span class=\"code-snippet__number\">0.5<\/span>)+ <\/span><\/code><code><span class=\"code-snippet_outer\"> scale_fill_npg()+<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__meta\">#\u4fee\u6539\u4e3b\u9898<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">theme_classic() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme(axis.title = element_text(size = <span class=\"code-snippet__number\">12<\/span>,color =<span class=\"code-snippet__string\">\"black\"<\/span>), <\/span><\/code><code><span class=\"code-snippet_outer\"> axis.text = element_text(size= <span class=\"code-snippet__number\">12<\/span>,color = <span class=\"code-snippet__string\">\"black\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\"> panel.grid.minor.y = element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> panel.grid.minor.x = element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> axis.text.x = element_text(angle = <span class=\"code-snippet__number\">45<\/span>, hjust = <span class=\"code-snippet__number\">1<\/span> ),<\/span><\/code><code><span class=\"code-snippet_outer\"> panel.grid=element_blank(),<\/span><\/code><code><span class=\"code-snippet_outer\"> legend.position = <span class=\"code-snippet__string\">\"top\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> legend.text = element_text(size= <span class=\"code-snippet__number\">12<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\"> legend.title= element_text(size= <span class=\"code-snippet__number\">12<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> ) +<\/span><\/code><code><span class=\"code-snippet_outer\"> stat_compare_means(aes(<span class=\"code-snippet__keyword\">group<\/span> = Cluster),<\/span><\/code><code><span class=\"code-snippet_outer\"> label = <span class=\"code-snippet__string\">\"p.signif\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> method = <span class=\"code-snippet__string\">\"kruskal.test\"<\/span>,<span class=\"code-snippet__meta\">#kruskal.test\u591a\u7ec4\u68c0\u9a8c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> hide.ns = F)<span class=\"code-snippet__meta\">#\u9690\u85cf\u4e0d\u663e\u8457\u7684<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#\u4fdd\u5b58\u56fe\u7247<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(file=<span class=\"code-snippet__string\">\"quanTIseq.pdf\"<\/span>,boxplot_quanTIseq,height=<span class=\"code-snippet__number\">10<\/span>,width=<span class=\"code-snippet__number\">15<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6705202312138728\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_dYApu9W45B2o4htfDy9emM1UICvjGQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwJ6AG1nswZobxHEGdUN4DKwk9QLz5sKtsLf0WlJ7VRtwCqdYApu9W45B2o4htfDy9emM1UICvjGQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\"><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><br \/><\/p>\n<\/section>\n<p><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">\u6700\u7ec8\u5c0f\u679c\u6210\u529f\u7684\u5bf9\u4e0d\u540c\u4e9a\u578b\u5229\u7528<\/span><span style=\"font-family:\u5fae\u8f6f\u96c5\u9ed1;\">quanTIseq\u7b97\u6cd5\u8fdb\u884c\u4e86\u514d\u75ab\u6d78\u6da6\u5206\u6790\uff0c\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\uff01<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u5fae\u8f6f\u96c5\u9ed1;color:rgb(255,0,0);font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><span 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justify;letter-spacing: 0.5px;text-indent: 0em;color: rgb(0, 150, 136);font-size: 32px;caret-color: rgba(0, 0, 0, 0);\"><\/span><span style=\"outline: 0px;text-align: justify;letter-spacing: 0.5px;text-indent: 0em;color: rgb(0, 150, 136);font-size: 32px;caret-color: rgba(0, 0, 0, 0);\"><\/span><\/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<p><br \/><\/p>\n<p><br \/><\/p>\n<section style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);\">\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: 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