{"id":30326,"date":"2024-02-29T14:49:49","date_gmt":"2024-02-29T06:49:49","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30326"},"modified":"2024-02-29T14:49:50","modified_gmt":"2024-02-29T06:49:50","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%e7%9a%84","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30326","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":"<p><strong>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 <\/strong><\/p>\n<p>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<\/p>\n<p>\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<\/p>\n<p><strong>GSVA\u5305\u7684\u5b89\u88c5\u4e0e\u5bfc\u5165<\/strong><\/p>\n<p>if (!requireNamespace(&#8220;BiocManager&#8221;, quietly = TRUE))<br \/>\ninstall.packages(&#8220;BiocManager&#8221;)<br \/>\nBiocManager::install(&#8220;GSVA&#8221;)<br \/>\nlibrary(GSVA)<\/p>\n<p><strong>\u51c6\u5907\u6570\u636e<\/strong><\/p>\n<p>\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u51c6\u5907\u4e24\u4e2a\u6570\u636e\u6587\u4ef6\uff1a<\/p>\n<ul>\n<li>\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<\/li>\n<li>\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<\/li>\n<\/ul>\n<p>\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<\/p>\n<p>#\u8bfb\u5165\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u57fa\u56e0\u96c6\u4fe1\u606f:<br \/>\nuni_matrix=read.delim(&#8220;tumor_all_gene_exp.txt&#8221;,header=T,stringsAsFactors = FALSE,row.names=1,check.names = FALSE)<br \/>\ngene_set&lt;-read.csv(&#8220;mmc3.csv&#8221;,header=T,stringsAsFactors = FALSE)<\/p>\n<p><strong>\u6570\u636e\u9884\u5904\u7406<\/strong><\/p>\n<p>\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<\/p>\n<p>list&lt;- split(as.matrix(gene_set)[,1], gene_set[,2])<\/p>\n<p>\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<\/p>\n<p>\u6700\u540e\uff0c\u6211\u4eec\u5e76\u7ed3\u679c\u5b58\u50a8\u5230 cellInfiltration_matrix_score.csv \u6587\u4ef6\u4e2d\u3002<\/p>\n<p>gsva_matrix&lt;- gsva(as.matrix(uni_matrix), list,method=&#8217;ssgsea&#8217;,kcdf=&#8217;Gaussian&#8217;,abs.ranking=TRUE)<br \/>\nwrite.csv(gsva_matrix,&#8221;cellInfiltration_matrix_score.csv&#8221;)<\/p>\n<p>\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<\/p>\n<p>\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<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"382\" class=\"wp-image-30327\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-128.png?resize=640%2C382\" alt=\"\u8868\u683c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-128.png?w=1144 1144w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-128.png?resize=300%2C179 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-128.png?resize=1024%2C610 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-128.png?resize=768%2C458 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-128.png?resize=600%2C358 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p><strong>\u7ed8\u5236\u7bb1\u7ebf\u56fe\u5b9e\u73b0\u7ed3\u679c\u53ef\u89c6\u5316<\/strong><\/p>\n<p>\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<\/p>\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 ggplot2\u3001ggpubr \u548c ggsignif \u5305\u8fdb\u884c\u7ed8\u56fe\u3002<\/p>\n<p>\u9996\u5148\u8bfb\u5165\u6570\u636e\u6587\u4ef6\u548c\u6837\u672c\u4fe1\u606f\u6587\u4ef6\uff1a<\/p>\n<p>data=read.csv(&#8220;cellInfiltration_matrix_score.csv&#8221;,header=T,row.names=1,stringsAsFactors=FALSE,check.names=FALSE)<br \/>\ngroup=read.delim(&#8220;group.txt&#8221;,header=T,stringsAsFactors=FALSE)<br \/>\nrow.names(group)=group$sample<br \/>\ngroup=group[colnames(data),]<br \/>\ndata=as.data.frame(t(data))<\/p>\n<p>\u5c06 data \u4e2d\u7684 cluster \u5217\u66ff\u6362\u4e3a\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u5e76\u8c03\u6574\u5217\u7684\u987a\u5e8f\uff1a<\/p>\n<p>data$cluster=group$Group<br \/>\ndata=data[,c(29,1:28)]<\/p>\n<p>\u5c06\u8c03\u6574\u540e\u7684\u6570\u636e\u5b58\u50a8\u5230\u8868\u683c\u6587\u4ef6 \u4e2d\u3002<\/p>\n<p>write.csv(data,&#8221;28cell_boxplot_data.csv&#8221;)<\/p>\n<p>\u8bfb\u5165\u4e0a\u8ff0\u8868\u683c\u6587\u4ef6\uff1a<\/p>\n<p>data=read.csv(&#8220;28cell_boxplot_data.csv&#8221;,header=T,row.names=1,stringsAsFactors=FALSE,check.names=FALSE)<br \/>\ntest=as.list(data[,-1])<br \/>\nheight&lt;-stack(test)<br \/>\nGroup=rep(data$cluster,ncol(data)-1)<br \/>\ndata1=as.data.frame(cbind(Group,height))<\/p>\n<p>\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<\/p>\n<p>#\u5bfc\u5165\u6240\u9700R\u5305<br \/>\nlibrary(ggplot2)<br \/>\nlibrary(ggpubr)<br \/>\nlibrary(ggsignif)<br \/>\n\u200b<br \/>\ncolnames(data1)=c(&#8220;group&#8221;,&#8221;Cell_infiltration_level&#8221;,&#8221;cell&#8221;)<br \/>\ndf=data1<br \/>\npdf(&#8220;28cell_3cluster_boxplot.pdf&#8221;,height=6,width=15) #\u8bbe\u7f6e\u6587\u4ef6\u5b58\u50a8\u540d\u79f0\u4e0e\u683c\u5f0f<br \/>\n\u200b<br \/>\n#\u7ed8\u5236\u7bb1\u7ebf\u56fe<br \/>\np=ggplot(data=df,aes(x=cell,y=Cell_infiltration_level,fill=group))+<br \/>\ngeom_boxplot(width=0.3,<br \/>\nposition = position_dodge(0.5),outlier.colour =NA)+<br \/>\ntheme_bw()+<br \/>\ntheme(panel.grid = element_blank())+<br \/>\nscale_fill_manual(values = c(&#8220;#4DBBD5FF&#8221;,&#8221;#E64B35FF&#8221;,&#8221;#E18727FF&#8221;))+<br \/>\nstat_compare_means(aes(group=group),<br \/>\nlabel=&#8221;p.signif&#8221;,<br \/>\nhide.ns = TRUE,<br \/>\nlabel.y = c(0.6))+<br \/>\ntheme(axis.text.x = element_text(size=12,colour=&#8221;black&#8221;,angle=60,hjust = 0.9),axis.text.y = element_text(size=12, angle=0),<br \/>\naxis.title.x = element_text(size=15),axis.title.y = element_text(size=15))<br \/>\n\u200b<br \/>\nprint(p)<br \/>\ndev.off()<\/p>\n<p>\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<\/p>\n<p>\u5c0f\u679c\u518d\u6b21\u63d0\u9192\uff1a\u4ee5\u4e0a\u4ee3\u7801\u4ec5\u4e3a\u793a\u4f8b\uff0c\u5b9e\u9645\u4f7f\u7528\u65f6\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u6570\u636e\u3001\u5206\u6790\u9700\u6c42\u548c\u73af\u5883\u5bf9\u53c2\u6570\u8fdb\u884c\u76f8\u5e94\u8c03\u6574\u54e6\uff01<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"260\" class=\"wp-image-30328\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?resize=640%2C260\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?w=2001 2001w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?resize=300%2C122 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?resize=1024%2C416 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?resize=768%2C312 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?resize=1536%2C623 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?resize=600%2C243 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?w=1280 1280w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30326-2.png?w=1920 1920w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> \u597d\u5566\uff0c\u73b0\u5728\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u6700\u540e\u7ed8\u5236\u7684\u7ed3\u679c\u957f\u4ec0\u4e48\u6837\u5427\uff01<\/p>\n<p>\u600e\u4e48\u6837\uff0c\u4eca\u5929\u7684R\u5305\u4f60\u5b66\u4f1a\u600e\u4e48\u7528\u4e86\u561b?<\/p>\n<p>\u66f4\u591a\u5b66\u4e60\u8d44\u6e90\u8bf7\u5927\u5bb6\u79fb\u6b65\u5c0f\u679c\u4e13\u5c5e\u4e91\u751f\u4fe1\u5e73\u53f0\u641c\u7d22\u66f4\u591a\u8d44\u6e90\u54e6\uff01<\/p>\n<p>\u5c0f\u679c\u4e13\u5c5e\u4e91\u751f\u4fe1\u5e73\u53f0\uff1a<a href=\"http:\/\/www.biocloudservice.com\/home.html\">\u4e91\u751f\u4fe1 \u00a0&#8211; \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/a><\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"239\" class=\"wp-image-30329\" 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