{"id":30319,"date":"2024-02-29T14:48:25","date_gmt":"2024-02-29T06:48:25","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30319"},"modified":"2024-02-29T14:48:27","modified_gmt":"2024-02-29T06:48:27","slug":"xcell%ef%bc%9a%e5%9f%ba%e5%9b%a0%e8%a1%a8%e8%be%be%e6%95%b0%e6%8d%ae%e7%9a%84%e5%85%8d%e7%96%ab%e6%b5%b8%e6%b6%a6%e5%88%86%e6%9e%90%e4%b8%93%e5%ae%b6%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30319","title":{"rendered":"xCell\uff1a\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u514d\u75ab\u6d78\u6da6\u5206\u6790\u4e13\u5bb6\uff01"},"content":{"rendered":"

xCell\uff1a\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u514d\u75ab\u6d78\u6da6\u5206\u6790\u4e13\u5bb6\uff01<\/strong><\/p>\n

hi\u5927\u5bb6\uff0c\u597d\u4e45\u4e0d\u89c1\uff0c\u5c0f\u679c\u53c8\u6765\u5566\uff01<\/p>\n

xCell\u662f\u4e00\u79cd\u57fa\u4e8e\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u514d\u75ab\u7ec6\u80de\u6d78\u6da6\u8bc4\u4f30\u5de5\u5177\uff0c\u53ef\u4ee5\u8bc6\u522b\u51fa\u6f5c\u5728\u7684\u514d\u75ab\u7ec6\u80de\u4e9a\u7fa4\u5e76\u8ba1\u7b97\u5b83\u4eec\u5728\u7ec4\u7ec7\u4e2d\u7684\u76f8\u5bf9\u4e30\u5ea6\u3002\u5b83\u53ef\u4ee5\u5e7f\u6cdb\u5e94\u7528\u4e8e\u764c\u75c7\u3001\u81ea\u8eab\u514d\u75ab\u6027\u75be\u75c5\u548c\u5176\u4ed6\u75be\u75c5\u7684\u514d\u75ab\u6d78\u6da6\u5206\u6790\u4e2d\u3002<\/p>\n

\u4eca\u5929\u5c0f\u679c\u5c31\u6765\u6559\u5927\u5bb6\u5982\u4f55\u5b9e\u6218\u5e94\u7528xCell\u8fdb\u884c\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u514d\u75ab\u6d78\u6da6\u5206\u6790\uff0c\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e0b\u5427\uff01<\/p>\n

\u6570\u636e\u9884\u5904\u7406<\/strong><\/p>\n

\u4e0b\u8f7dxCell\u5305\u5e76\u5bfc\u5165\uff1a<\/p>\n

install.packages(‘devtools’)
\ndevtools::install_github(‘dviraran\/xCell’)
\nlibrary(xCell)<\/p>\n

xCell\u514d\u75ab\u6d78\u6da6\u5206\u6790<\/h3>\n

\u5bfc\u5165\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u5e76\u901a\u8fc7xCellAnalysis\u5206\u6790\u8868\u8fbe\u77e9\u9635\uff0c\u8be5\u51fd\u6570\u7528\u4e8e\u9884\u6d4b\u7ec6\u80de\u7ec4\u5206\u5728\u7ed9\u5b9a\u6837\u672c\u4e2d\u7684\u76f8\u5bf9\u4e30\u5ea6\uff1a<\/h3>\n

exprSet=read.csv(“GSE57065_ExprMatrix.csv”,header=T,row.names=1)
\nxCell <- xCellAnalysis(exprSet) \u00a0 \u00a0 \u00a0 \u00a0###array data
\nwrite.csv(xCell,”xCell_score.csv”) #\u5c06\u8ba1\u7b97\u540e\u7684\u7ed3\u679c\u5199\u5165\u8868\u683c\u6587\u4ef6\u4e2d<\/p>\n

\u5148\u6765\u4e00\u8d77\u770b\u4e0b\u5206\u6790\u540e\u7684\u6570\u636e\u96c6\u5427\uff01<\/p>\n

\u5904\u7406xCell\u5206\u6790\u540e\u7684\u7ed3\u679c\u6570\u636e\u96c6<\/strong><\/p>\n

\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u6837\u672c\u7684\u5206\u7ec4\u60c5\u51b5\uff0c\u63d0\u53d6\u51fa\u5bf9\u5e94\u7684\u7ec6\u80de\u7c7b\u578b\u5f97\u5206\u3002<\/p>\n

\u9996\u5148\u6211\u4eec\u8981\u8bfb\u53d6 group.txt \u7684\u6587\u4ef6\uff0c\u8fd9\u91cc\u5305\u542b\u4e86\u6837\u672c\u7684\u5206\u7ec4\u4fe1\u606f\uff0c\u6e29\u99a8\u63d0\u793a\uff0c\u7ec6\u80de\u8868\u8fbe\u6837\u672c\u6570\u636e\u5305\u542b\u4e24\u79cd\u7c7b\u578b\u54e6\uff01<\/p>\n

\u6211\u4eec\u53ef\u4ee5\u8bfb\u5165\u8fd9\u4e2a\u6587\u4ef6\uff0c\u5e76\u63d0\u53d6\u51fa\u201cseptic_shock\u201d \u548c \u201chealthy\u201d \u4e24\u7ec4\u6837\u672c\u7684\u5f97\u5206\uff1a<\/p>\n

group=read.delim(“group.txt”,header=T,stringsAsFactors = FALSE,sep=”\\t”)
\nscore=read.csv(“xCell_score.csv”,header=T,row.names=1,stringsAsFactors = FALSE)
\n#\u53d6\u51fa\u7ed3\u679c\u6587\u4ef6\u4e2d\u7684\u524d64\u4e2a\u6837\u672c\uff0c\u5e76\u5206\u522b\u53d6\u51fa\u201cseptic_shock\u201d\uff0c\u5373\u5e26\u6709\u75be\u75c5\u7684\u6837\u672c\u7fa4\u548c\u201chealthy\u201d\uff0c\u5373\u5065\u5eb7\u7684\u6837\u672c\u7fa4\u5230\u5bf9\u5e94\u7684\u6570\u636e\u96c6\u4e2d
\ncase_data=score[1:64,group$group==”septic_shock”]
\ncontrol_data=score[1:64,group$group==”healthy”]
\nall(row.names(case_data)==row.names(control_data))
\nnormal=ncol(control_data)
\ntumor=ncol(case_data)
\nnormal_data=as.data.frame(t(control_data))
\ntumor_data=as.data.frame(t(case_data))
\n#\u5408\u5e76\u4e24\u79cd\u7c7b\u578b\u7684\u7ed3\u679c\u6587\u4ef6
\nrt_total = rbind(normal_data,tumor_data)
\ncell_group_file=read.delim(“cell_type.txt”,header=T,stringsAsFactors = FALSE)
\ncell_group=unique(cell_group_file$Subgroup)<\/p>\n

xCell\u5bf9\u5206\u6790\u7ed3\u679c\u4e0b\u6e38\u5206\u6790<\/strong><\/p>\n

\u540c\u6837\u5730\uff0c\u6211\u4eec\u4e5f\u53ef\u4ee5\u5bf9xCell\u5206\u6790\u7684\u7ed3\u679c\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u5e76\u901a\u8fc7\u5c0f\u63d0\u7434\u56fe\u5bf9\u7ed3\u679c\u8fdb\u884c\u76f4\u89c2\u7684\u5206\u6790\uff0c\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u600e\u6837\u64cd\u4f5c\u5427\uff01<\/p>\n

\u73b0\u5728\u6211\u4eec\u63d0\u53d6\u51fa\u4e86xCellAnalysis\u5206\u6790\u540e\u7684\u6837\u672c\u6570\u636e\u96c6\u5e76\u505a\u4e86\u5c01\u88c5\u5904\u7406\uff0c\u73b0\u5728\u6211\u4eec\u53ef\u4ee5\u9488\u5bf9\u6211\u4eec\u7684\u7ec6\u80de\u7fa4\u6570\u636e\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u4ee5\u53ca\u53ef\u89c6\u5316\u5904\u7406\u7684\u64cd\u4f5c\u3002<\/p>\n

\u4e3b\u8981\u7684\u6d41\u7a0b\u4e3a\uff1a\u6839\u636e\u4e0d\u540c\u7684\u7ec6\u80de\u5b50\u7fa4\u5bf9\u6837\u672c\u8fdb\u884c\u5206\u7c7b\uff0c\u904d\u5386\u6bcf\u4e2a\u7ec6\u80de\u5b50\u7fa4\uff0c\u5e76\u8ba1\u7b97\u6bcf\u4e2a\u5b50\u7fa4\u7684\u5dee\u5f02\u663e\u8457\u6027\uff0c\u5e76\u5bf9\u663e\u8457\u5dee\u5f02\u7684\u7ec6\u80de\u5b50\u7fa4\u8fdb\u884c\u7ed8\u56fe\u5c55\u793a\u548c\u4fdd\u5b58\u7ed3\u679c\u3002\u90a3\u4e48\u5c31\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e0b\u4ee3\u7801\u5b9e\u73b0\u5427\uff01<\/p>\n

for (subgroup in cell_group){
\ns=which( cell_group_file$Subgroup==subgroup) #\u83b7\u53d6\u5f53\u524d\u7ec6\u80de\u6240\u5c5e\u5b50\u7fa4\u7684index
\ncells=cell_group_file$Cell.types[s] #\u63d0\u53d6\u5c5e\u4e8e\u5f53\u524d\u5b50\u7fa4\u7684\u6240\u6709\u7ec6\u80de
\nrt=rt_total[,cells] \u00a0 #\u63d0\u53d6\u5c5e\u4e8e\u5f53\u524d\u5b50\u7fa4\u7684\u6240\u6709\u7ec6\u80de\u7c7b\u578b\u7684\u6570\u636e\uff0c\u5e76\u4fdd\u5b58\u5728 rt \u4e2d
\ncell=c()
\np.value=c()
\nfor(i in 1:ncol(rt)){
\nnormalData=rt[1:normal,i]
\ntumorData=rt[(normal+1):(normal+tumor),i]
\nwilcoxtest=wilcox.test(normalData,tumorData,exact = F) #\u8ba1\u7b97\u5176\u5dee\u5f02\u7684 p-value\uff0c\u5e76\u4fdd\u5b58\u5728p.value\u4e2d\uff0c\u7ec6\u80de\u7c7b\u578b\u540d\u79f0\u4fdd\u5b58\u5728cell\u4e2d
\np=round(wilcoxtest$p.value,3)
\np.value=c(p.value,p) #\u5408\u5e76
\ncell=c(cell,colnames(rt)[i])
\n}
\nsig=data.frame(cell,p.value)
\nsig=sig[sig$p.value<0.05,] #\u9009\u51fap\u503c\u5c0f\u4e8e0.05\u7684\u663e\u8457\u7ec6\u80de\u7c7b\u578b
\ns=which(colnames(rt)%in%as.character(sig$cell))
\nrt=rt[,s]
\nall(colnames(rt)==as.character(sig$cell))<\/p>\n

\u901a\u8fc7\u5c0f\u63d0\u7434\u56fe\u53ef\u89c6\u5316\u4e0b\u6e38\u5206\u6790\u7684\u7ed3\u679c<\/strong><\/p>\n

\u73b0\u5728\uff0c\u6211\u4eec\u53ef\u4ee5\u5c06\u6700\u7ec8\u7684\u8ba1\u7b97\u7ed3\u679c\u901a\u8fc7\u5c0f\u63d0\u7434\u56fe\u5c55\u793a\u51fa\u6765\uff0c\u8ba9\u6211\u4eec\u6765\u770b\u770b\u5177\u4f53\u7684\u4ee3\u7801\u5b9e\u73b0\u5427\uff01<\/p>\n

library(vioplot)
\npdf(paste(subgroup,”Xcell_score.pdf”,sep=”_”),height=8,width=15) #\u8bbe\u7f6e\u53ef\u89c6\u5316\u548c\u4fdd\u5b58\u7684\u6587\u4ef6\u540d\u79f0
\npar(las=1,mar=c(10,6,3,3))
\nx=c(1:ncol(rt))
\ny=c(1:ncol(rt))
\n#\u7ed8\u5236\u7a7a\u767d\u6563\u70b9\u56fe
\nplot(x,y,
\nxlim=c(0,(ncol(rt)-1)*3+2),ylim=c(min(rt),max(rt)+0.02),
\nmain=”GSE57065″,xlab=””, ylab=”Xcell score”,
\npch=21,col=”white”,xaxt=”n”,cex.lab=1.3,cex.main=1.5)
\nfor(i in 1:ncol(rt)){
\nnormalData=rt[1:normal,i]
\ntumorData=rt[(normal+1):(normal+tumor),i]
\nwilcoxtest=wilcox.test(normalData,tumorData,exact = F)
\np=round(wilcoxtest$p.value,3)
\nvioplot(normalData,at=3*(i-1),lty=1,add = T,col = ‘#42B540FF’) \u00a0#\u7ed8\u5236\u6b63\u5e38\u6570\u636e\u7684\u5c0f\u63d0\u7434\u56fe
\nvioplot(tumorData,at=3*(i-1)+1,lty=1,add = T,col = ‘#925E9FFF’) #\u7ed8\u5236\u80bf\u7624\u6570\u636e\u7684\u5c0f\u63d0\u7434\u56fe
\nmx=max(c(normalData,tumorData))
\nlines(c(x=3*(i-1)+0.2,x=3*(i-1)+0.8),c(mx,mx))
\ntext(x=3*(i-1)+1,y=mx+0.02,labels=ifelse(p<0.001,paste0(“p<0.001”),paste0(“p=”,p)),cex = 0.8)
\n}
\ntext(seq(1,((ncol(rt)-1)*3+1),3),-0.01,xpd = NA,labels=colnames(rt),cex = 1,srt = 45,pos=2,font=2)
\ndev.off()
\nwrite.csv(sig,paste(subgroup,”_sig_cell.csv”,sep=””)) \u00a0#\u4fdd\u5b58\u6700\u7ec8\u7ed3\u679c
\n}<\/p>\n

\"\u56fe\u8868, \u73b0\u5728\uff0c\u4f60\u5df2\u7ecf\u6210\u529f\u5b8c\u6210\u4e86xCell\u5206\u6790\u7ec6\u80de\u5230\u53ef\u89c6\u5316\u7684\u5de6\u53f3\u5de5\u4f5c\uff0c\u73b0\u5728\u5c0f\u679c\u7ed9\u5927\u5bb6\u5c55\u793a\u5176\u4e2d\u4e00\u4e2a\u7ec6\u80de\u5b50\u7fa4\u7684\u4e0b\u6e38\u5206\u6790\u53ef\u89c6\u5316\u7ed3\u679c\uff01\u4e00\u8d77\u6765\u770b\u5427\uff01<\/p>\n

\u600e\u4e48\u6837\uff0c\u4f60\u5b66\u4f1a\u600e\u4e48\u4f7f\u7528xCell\u5305\u4e86\u561b? \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

\u5c0f\u679c\u4e13\u5c5e\u4e91\u751f\u4fe1\u5e73\u53f0\uff1a\u4e91\u751f\u4fe1 \u00a0– \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/a><\/p>\n

\"\u8868\u683c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" \u4e91\u751f\u4fe1\u5e73\u53f0\u4e5f\u6709\u514d\u75ab\u4e13\u7248\u7684\u5b66\u4e60\u6a21\u5757\u54e6\uff0c\u5feb\u6765\u627e\u5230\u4f60\u60f3\u5b66\u4e60\u7684\u4e13\u5c5e\u6a21\u5757\u5427\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"

xCell\uff1a\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u514d\u75ab\u6d78\u6da6\u5206\u6790\u4e13\u5bb6\uff01 hi\u5927\u5bb6\uff0c\u597d\u4e45\u4e0d\u89c1\uff0c\u5c0f\u679c\u53c8\u6765\u5566\uff01 xCell\u662f\u4e00\u79cd\u57fa\u4e8e\u57fa\u56e0\u8868\u8fbe\u6570 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","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\/30319"}],"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=30319"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30319\/revisions"}],"predecessor-version":[{"id":30325,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30319\/revisions\/30325"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30319"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30319"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30319"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}