r语言如何绘制蛋白质组和转录组相关性图
r语言如何绘制蛋白质组和转录组相关性图
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目前研究蛋白质组的项目越来越多，经常有蛋白质和转录组相关的分析。
deg_file<-'S-1_S-2_S-3_vs_R-1_R-2_R-3.all'dep_file<-'S-1_S-2_S-3_vs_R-1_R-2_R-3.DEP.all.xls'#设置筛选参数dep_fc<-1.5dep_fdr<-0.05deg_fc<-1.5deg_fdr<-0.05#读取文件deg<-read_delim(deg_file,delim='\t')dep<-read_delim(dep_file,delim='\t')dim(dep)#蛋白ID转换extr_id<-function(x){return(substr(x,start=0,stop=16))}dep$protein_id<-as.character(llply(dep$protein,extr_id))gene_ids<-deg$`#ID`protein_id<-dep$protein_id#共有IDcommon_id<-intersect(gene_ids,protein_id)#提取数据列表dep_common=dep[dep$protein_id%in%common_id,c('protein_id','logFC','P.Value')]colnames(dep_common)<-c('protein_id','logFC_p','FDR_p')dep_common$regulate_p=as.factor(ifelse(dep_common$FDR_p<dep_fdr&abs(dep_common$logFC_p)>=log2(dep_fc),ifelse(dep_common$logFC_p>log2(dep_fc),'Up','Down'),'Normal'))table(dep_common$regulate_p)deg_common=deg[deg$`#ID`%in%common_id,c('#ID','FDR','log2FC')]colnames(deg_common)<-c('#ID','FDR_g','log2FC_g')deg_common$regulate_g=as.factor(ifelse(deg_common$FDR_g<deg_fdr&abs(deg_common$log2FC_g)>=log2(deg_fc),ifelse(deg_common$log2FC_g>log2(deg_fc),'Up','Down'),'Normal'))table(deg_common$regulate_g)#合并转录组和蛋白质结果merge_df<-merge(dep_common,deg_common,by.x='protein_id',by.y='#ID')#基于调控关系进行分组merge_df$type<-paste(merge_df$regulate_p,merge_df$regulate_g,sep='_')types<-c('Down_Down','Down_Up','Up_Down','Up_Up')merge_df[!merge_df$type%in%types,'type']<-'Other'#绘图mycol<-c("#e41a1c","#ff7f00","#984ea3","#4daf4a","#80b1d3")ggplot(data=merge_df,aes(x=logFC_p,y=log2FC_g,colour=type))+geom_point()+scale_color_manual(values=c("Up_Up"=mycol[1],"Up_Down"=mycol[2],"Down_Up"=mycol[3],"Down_Down"=mycol[4],"Other"=mycol[5]))+geom_hline(aes(yintercept=log2(deg_fc)),linetype="dashed",colour="grey11")+geom_hline(aes(yintercept=-log2(deg_fc)),linetype="dashed",colour="grey11")+geom_vline(aes(xintercept=-log2(dep_fc)),linetype="dashed",colour="grey11")+geom_vline(aes(xintercept=log2(dep_fc)),linetype="dashed",colour="grey11")+labs(x="Protein_logFC",y="Gene_logFC",title="Protein_Gene_relation")+theme_bw()+theme(panel.grid=element_blank(),axis.text.x=element_text(colour="black"),axis.text.y=element_text(colour="black"),panel.border=element_rect(colour="black"),legend.key=element_blank(),legend.title=element_blank())
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