{"id":58988,"date":"2024-06-17T07:20:50","date_gmt":"2024-06-16T23:20:50","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58988"},"modified":"2024-06-17T07:20:50","modified_gmt":"2024-06-16T23:20:50","slug":"r%e8%af%ad%e8%a8%80gsva%e5%8c%85%e5%ae%9e%e7%8e%b0ssgsea%e5%88%86%e6%9e%90%ef%bc%8c%e5%b8%a6%e4%bd%a0%e6%8e%a2%e7%b4%a2%e8%82%bf%e7%98%a4%e7%bb%86%e8%83%9e%e5%85%8d%e7%96%ab%e6%b5%b8%e6%b6%a6-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58988","title":{"rendered":"R\u8bed\u8a00GSVA\u5305\u5b9e\u73b0ssGSEA\u5206\u6790\uff0c\u5e26\u4f60\u63a2\u7d22\u80bf\u7624\u7ec6\u80de\u514d\u75ab\u6d78\u6da6\u7684\u591a\u6837\u6027\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=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_ib2l1ye6HNIkwTG696C2pf9yAtdeGA-50.png?w=640\" 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;\" data-recalc-dims=\"1\" \/><\/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);\">hi\uff01\u4eca\u5929\uff0c\u5c0f\u679c\u8981\u518d\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u597d\u7528\u7684\u514d\u75ab\u6d78\u6da6\u5de5\u5177\u5305\u3002<\/span><\/section>\n<\/li>\n<li>\n<p><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u5728\u8fd9\u4e2a\u6559\u7a0b\u4e2d\uff0c\u6211\u5c06\u4ecb\u7ecd\u5982\u4f55\u4f7f\u7528 GSVA \u5305\u5b9e\u73b0\u5bf9\u57fa\u56e0\u6570\u636e\u96c6\u7684\u514d\u75ab\u6d78\u6da6\u5206\u6790\uff0c\u5e76\u6839\u636e\u7ed3\u679c\u7ed8\u5236 Boxplot \u56fe\uff0c\u4ee5\u6bd4\u8f83\u4e0d\u540c\u6837\u672c\u5206\u7c7b\u4e4b\u95f4\u7684\u7ec6\u80de\u6d78\u6da6\u6c34\u5e73\u5dee\u5f02\u3002\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u5427\uff01<\/span><\/p>\n<\/li>\n<\/ul>\n<section style=\"height: 0px;overflow: hidden;\"><br \/><\/section>\n<section style=\"height: 0px;overflow: hidden;\"><br \/><\/section>\n<section>\n<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=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_QiaOCcR0jFpvjkSAu3UmKL82ohCV5Q-7.png?w=640\" 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%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;white-space: normal;margin-bottom: 8px;\"><strong><em><span style=\"font-size: 20px;color: rgb(62, 62, 62);\">GSVA\u5305\u7684\u5b89\u88c5\u4e0e\u5bfc\u5165<\/span><\/em><\/strong><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (!requireNamespace(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>, quietly = TRUE))<\/span><\/code><code><span class=\"code-snippet_outer\"> install.packages(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"GSVA\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(GSVA)<\/span><\/code><\/pre>\n<\/section>\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;\"><br \/><\/section>\n<\/section>\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=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_s2ZHCtbN9nDKgpfniawYJJzqxT6v6g-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNq0nuSrPNnVriasrjcop8ONDW3ss2ZHCtbN9nDKgpfniawYJJzqxT6v6g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"text-align: center;white-space: normal;margin-bottom: 8px;\"><strong><em><span style=\"font-size: 20px;color: rgb(62, 62, 62);\">\u51c6\u5907\u6570\u636e<\/span><\/em><\/strong><\/section>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u51c6\u5907\u4e24\u4e2a\u6570\u636e\u6587\u4ef6\uff1a<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4e00\u4e2a\u5305\u542b\u57fa\u56e0\u8868\u8fbe\u4fe1\u606f\u7684\u6570\u636e\u6587\u4ef6 \uff1atumor_all_gene_exp.txt\u3002\u8be5\u6587\u4ef6\u7684\u6bcf\u4e00\u5217\u8868\u793a\u4e00\u4e2a\u57fa\u56e0\uff0c\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u60c5\u51b5\u4ee5\u6570\u5b57\u8868\u793a\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4e00\u4e2a\u5305\u542b\u57fa\u56e0\u96c6\u4fe1\u606f\u7684\u7b26\u5408 MMC3 \u6570\u636e\u5e93\u683c\u5f0f\u7684\u6587\u4ef6\uff1ammc3.csv\u3002\u8be5\u6587\u4ef6\u5305\u542b\u591a\u4e2a\u57fa\u56e0\u96c6\uff08pathway\uff09\uff0c\u6bcf\u4e2a\u57fa\u56e0\u96c6\u6709\u4e00\u4e2a\u552f\u4e00\u7684\u7f16\u53f7\u548c\u540d\u79f0\uff0c\u6bcf\u4e00\u6761\u8bb0\u5f55\u4ee3\u8868\u8be5\u57fa\u56e0\u96c6\u4e2d\u7684\u4e00\u4e2a\u57fa\u56e0\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c0f\u679c\u6e29\u99a8\u63d0\u793a\uff0c\u5bf9\u4e8e\u8fd9\u4e24\u4e2a\u6587\u4ef6\uff0c\u5176\u884c\u540d\u548c\u5217\u540d\u9700\u4e0e\u4ee3\u7801\u76f8\u5e94\u4f4d\u7f6e\u8981\u6c42\u4e00\u81f4\uff0c\u5426\u5219\u540e\u7eed\u64cd\u4f5c\u53ef\u80fd\u4f1a\u51fa\u9519\u54e6\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">#\u8bfb\u5165\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u57fa\u56e0\u96c6\u4fe1\u606f:<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">uni_matrix=read.delim(<span class=\"code-snippet__string\">\"tumor_all_gene_exp.txt\"<\/span>,header=T,stringsAsFactors = FALSE,row.names=<span class=\"code-snippet__number\">1<\/span>,check.names = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">gene_set<-read.csv(<span class=\"code-snippet__string\">\"mmc3.csv\"<\/span>,header=T,stringsAsFactors = FALSE)<\/span><\/code><\/pre>\n<\/section>\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;\"><br \/><\/section>\n<\/section>\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=\"0.49899799599198397\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_PSgMgn9cx3xIMRpoK7HUMUxLr0HL3A-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNszG7picpYriceh3kdysIicAjyUtPSgMgn9cx3xIMRpoK7HUMUxLr0HL3A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"499\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"text-align: center;white-space: normal;margin-bottom: 8px;\"><strong><em><span style=\"font-size: 20px;color: rgb(62, 62, 62);\">\u6570\u636e\u9884\u5904\u7406<\/span><\/em><\/strong><\/section>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06 gene_set \u4e2d\u7684\u57fa\u56e0\u6309\u7167\u57fa\u56e0\u540d\u79f0\u5206\u7ec4\uff0c\u4ee5\u4fbf\u540e\u7eed\u76f4\u63a5\u8f93\u5165 GSVA \u51fd\u6570\u4e2d\u4f7f\u7528\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">list<\/span><- split(as.matrix(gene_set)[,1], gene_set[,2])<\/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;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u4f7f\u7528 gsva \u51fd\u6570\u8ba1\u7b97\u57fa\u56e0\u96c6\u53d8\u5316\u5206\u6790\u6307\u6807\uff08GSVA\uff09\uff0cgsva()\u51fd\u6570\u662f\u4e00\u79cd\u57fa\u4e8e\u975e\u53c2\u6570\u65b9\u6cd5\u7684\u901a\u8def\u5bcc\u96c6\u5206\u6790\uff08Pathway Enrichment Analysis\uff09\u5de5\u5177\uff0c\u800c\u901a\u8def\u5bcc\u96c6\u5206\u6790\u4e5f\u662f\u514d\u75ab\u6d78\u6da6\u5206\u6790\u4e2d\u5e38\u89c1\u7684\u4e00\u4e2a\u5e94\u7528\u54e6\uff01\u5b83\u7528\u4e8e\u8ba1\u7b97\u57fa\u56e0\u8868\u8fbe\u8c31\u4e2d\u6bcf\u4e2a\u6837\u672c\u4e0e\u6307\u5b9a\u57fa\u56e0\u96c6\u7684\u5173\u8054\u7a0b\u5ea6\uff0c\u5c06\u5176\u8f6c\u5316\u4e3a\u4e00\u4e2a\u8fde\u7eed\u503c\u5f97\u5206\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6700\u540e\uff0c\u6211\u4eec\u5e76\u7ed3\u679c\u5b58\u50a8\u5230 cellInfiltration_matrix_score.csv \u6587\u4ef6\u4e2d\u3002<\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\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=\"c\"><code><span class=\"code-snippet_outer\">gsva_matrix<- gsva(as.matrix(uni_matrix), <span class=\"code-snippet__built_in\">list<\/span>,method=<span class=\"code-snippet__string\">'ssgsea'<\/span>,kcdf=<span class=\"code-snippet__string\">'Gaussian'<\/span>,<span class=\"code-snippet__built_in\">abs<\/span>.ranking=TRUE)<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(gsva_matrix,<span class=\"code-snippet__string\">\"cellInfiltration_matrix_score.csv\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd0\u884c\u4e0a\u8ff0\u4ee3\u7801\u540e\uff0c\u4f1a\u5728\u5de5\u4f5c\u76ee\u5f55\u4e2d\u751f\u6210\u4e00\u4e2a\u540d\u4e3a cellInfiltration_matrix_score.csv \u7684\u6587\u4ef6\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u6bcf\u4e2a\u6837\u672c\u5728\u4e0d\u540c\u57fa\u56e0\u96c6\u4e2d\u7684 GSVA \u5f97\u5206\u54e6\u3002<\/span><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u81f3\u6b64\uff0c\u6211\u4eec\u5df2\u7ecf\u5b8c\u6210\u4e86GSVA\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u8ba1\u7b97\u5206\u6790\uff0c\u6211\u4eec\u5148\u6765\u770b\u4e00\u4e0b\u8ba1\u7b97\u4e4b\u540e\u7684\u90e8\u5206\u7ed3\u679c\u662f\u4ec0\u4e48\u6837\u5427\uff01<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5974729241877257\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_35g8FPmoX1lKeYibVQCPTnCdQltJyQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNpETfgREQRhZ5lQQV9KfXkgmCH35g8FPmoX1lKeYibVQCPTnCdQltJyQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<\/section>\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;\"><br \/><\/section>\n<\/section>\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=\"0.4400871459694989\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_5b6n1ktWiauTdCD5ibDmDlYhn4Gvlg-3.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNylh9Ot54aFJuqnzRED27naywY85b6n1ktWiauTdCD5ibDmDlYhn4Gvlg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"459\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\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;\"><br \/><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 20px;\" powered-by=\"xiumi.us\">\n<section style=\"margin-bottom: 8px;\"><em style=\"letter-spacing: 0.578px;\"><strong>\u7ed8\u5236\u7bb1\u7ebf\u56fe\u5b9e\u73b0\u7ed3\u679c\u53ef\u89c6\u5316<\/strong><\/em><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8ba1\u7b97\u5b8c\u6210\u540e\uff0c\u6211\u4eec\u5982\u4f55\u5c06\u7ed3\u679c\u53ef\u89c6\u5316\u5c55\u793a\u51fa\u6765\u5462\uff1f\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 ggplot2\u3001ggpubr \u548c ggsignif \u5305\u8fdb\u884c\u7ed8\u56fe\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u9996\u5148\u8bfb\u5165\u6570\u636e\u6587\u4ef6\u548c\u6837\u672c\u4fe1\u606f\u6587\u4ef6\uff1a<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">data=read.csv(<span class=\"code-snippet__string\">\"cellInfiltration_matrix_score.csv\"<\/span>,header=T,row.names=<span class=\"code-snippet__number\">1<\/span>,stringsAsFactors=FALSE,check.names=FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">group=read.delim(<span class=\"code-snippet__string\">\"group.txt\"<\/span>,header=T,stringsAsFactors=FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">row.names(group)=group$sample<\/span><\/code><code><span class=\"code-snippet_outer\">group=group[colnames(data),]<\/span><\/code><code><span class=\"code-snippet_outer\">data=as.data.frame(t(data))<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06 data \u4e2d\u7684 cluster \u5217\u66ff\u6362\u4e3a\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u5e76\u8c03\u6574\u5217\u7684\u987a\u5e8f\uff1a<\/span><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">data$cluster=group$Group<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">data=data[,c(29,1:28)]<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5c06\u8c03\u6574\u540e\u7684\u6570\u636e\u5b58\u50a8\u5230\u8868\u683c\u6587\u4ef6 \u4e2d\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">write.csv(data,”28cell_boxplot_data.csv”)<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8bfb\u5165\u4e0a\u8ff0\u8868\u683c\u6587\u4ef6\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">data=read.csv(<span class=\"code-snippet__string\">\"28cell_boxplot_data.csv\"<\/span>,header=T,row.names=<span class=\"code-snippet__number\">1<\/span>,stringsAsFactors=FALSE,check.names=FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">test=as.<span class=\"code-snippet__built_in\">list<\/span>(data[,<span class=\"code-snippet__number\">-1<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">height<-<span class=\"code-snippet__built_in\">stack<\/span>(test)<\/span><\/code><code><span class=\"code-snippet_outer\">Group=rep(data$cluster,ncol(data)<span class=\"code-snippet__number\">-1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data1=as.data.frame(cbind(Group,height))<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4f7f\u7528 ggplot2\u3001ggpubr\u3001ggsignif \u5305\u751f\u6210 Boxplot \u56fe\uff0c\u5e76\u8bbe\u7f6e Boxplot \u7684\u76f8\u5173\u53c2\u6570\u4e0e\u683c\u5f0f\uff0c\u6700\u7ec8\u8f93\u51fa 28cell_3cluster_boxplot.pdf \u6587\u4ef6\uff0c\u5177\u4f53\u7684\u4ee3\u7801\u6d41\u7a0b\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\uff1a<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">#\u5bfc\u5165\u6240\u9700R\u5305<\/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<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(ggpubr)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggsignif)<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(data1)=c(<span class=\"code-snippet__string\">\"group\"<\/span>,<span class=\"code-snippet__string\">\"Cell_infiltration_level\"<\/span>,<span class=\"code-snippet__string\">\"cell\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">df=data1<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(<span class=\"code-snippet__string\">\"28cell_3cluster_boxplot.pdf\"<\/span>,height=<span class=\"code-snippet__number\">6<\/span>,width=<span class=\"code-snippet__number\">15<\/span>) #\u8bbe\u7f6e\u6587\u4ef6\u5b58\u50a8\u540d\u79f0\u4e0e\u683c\u5f0f<\/span><\/code><code><span class=\"code-snippet_outer\">#\u7ed8\u5236\u7bb1\u7ebf\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">p=ggplot(data=df,aes(x=cell,y=Cell_infiltration_level,fill=group))+<\/span><\/code><code><span class=\"code-snippet_outer\">  geom_boxplot(width=<span class=\"code-snippet__number\">0.3<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">               position = position_dodge(<span class=\"code-snippet__number\">0.5<\/span>),outlier.colour =NA)+<\/span><\/code><code><span class=\"code-snippet_outer\">  theme_bw()+<\/span><\/code><code><span class=\"code-snippet_outer\">  theme(panel.grid = element_blank())+<\/span><\/code><code><span class=\"code-snippet_outer\">  scale_fill_manual(values = c(<span class=\"code-snippet__string\">\"#4DBBD5FF\"<\/span>,<span class=\"code-snippet__string\">\"#E64B35FF\"<\/span>,<span class=\"code-snippet__string\">\"#E18727FF\"<\/span>))+<\/span><\/code><code><span class=\"code-snippet_outer\">  stat_compare_means(aes(group=group),<\/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\">                     hide.ns = TRUE,<\/span><\/code><code><span class=\"code-snippet_outer\">                     label.y = c(<span class=\"code-snippet__number\">0.6<\/span>))+<\/span><\/code><code><span class=\"code-snippet_outer\">  theme(axis.text.x = element_text(size=<span class=\"code-snippet__number\">12<\/span>,colour=<span class=\"code-snippet__string\">\"black\"<\/span>,angle=<span class=\"code-snippet__number\">60<\/span>,hjust = <span class=\"code-snippet__number\">0.9<\/span>),axis.text.y = element_text(size=<span class=\"code-snippet__number\">12<\/span>, angle=<span class=\"code-snippet__number\">0<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">        axis.title.x = element_text(size=<span class=\"code-snippet__number\">15<\/span>),axis.title.y = element_text(size=<span class=\"code-snippet__number\">15<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">print(p)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd0\u884c\u4e0a\u8ff0\u4ee3\u7801\u540e\uff0c\u4f1a\u5728\u5de5\u4f5c\u76ee\u5f55\u4e2d\u751f\u6210\u4e00\u4e2a\u540d\u4e3a 28cell_3cluster_boxplot.pdf \u7684\u6587\u4ef6\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u7ed8\u5236\u597d\u7684 Boxplot \u56fe\u54e6\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span 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