?基因瀑布圖（oncoplot）和熱圖組合堪稱癌癥基因?qū)W研究利器

setwd("F:/work/個性化/基因瀑布圖") test<-read.delim("test.txt",?header=TRUE?,check.names?=?F) #此處讀取的是四個文件的基因交集，只有一列基因，這樣最后呈現(xiàn)的圖的樣本和基因個數(shù)一樣。 library(ComplexHeatmap) png("test.png",type="cairo",width=2000,height=800) color.1?<-?colorRampPalette(rev(c("red",?"white",?"#3CB34E")))(100) data<-?read.delim("mRNA_fpkm.list",?row.names?=?1,?header=TRUE?,check.names?=?F) row.names(data)<-data$Symbol data<-data[which(rownames(data)%in%test$gene_symbol),] data=?data[,?-1] data?<-?log10(data+0.000001) data<-as.matrix(data) ht1<-Heatmap(data,col=color.1,cluster_columns??=?T,cluster_rows?=?F,name="gene",column_title?=?"gene",show_row_names?=?T,show_column_names?=?T) #此處既顯示樣品名又顯示基因名 col<-c("frameshift_mutation"="red","other"="#3CB34E","nonsynonymous_SNV"="red") alter_fun<-list( ??background=function(x,y,w,h){ ????grid.rect(x,y,w-unit(0.5,"mm"),h-unit(0.5,"mm"), ??????????????gp=gpar(fill="#cccccc",col=NA)) ??}, ??frameshift_mutation=function(x,y,w,h){ ????grid.rect(x,y,w-unit(0.5,"mm"),h-unit(0.5,"mm"), ??????????????gp=gpar(fill=col["frameshift_mutation"],col=NA)) ??}, ??other=function(x,y,w,h){ ????grid.rect(x,y,w-unit(0.5,"mm"),h-unit(0.5,"mm"), ??????????????gp=gpar(fill=col["other"],col=NA)) ??}, ??nonsynonymous_SNV=function(x,y,w,h){ ????grid.rect(x,y,w-unit(0.5,"mm"),h-unit(0.5,"mm"), ??????????????gp=gpar(fill=col["nonsynonymous_SNV"],col=NA)) ??} ) library(do) mat?<-read.table("indel_keygene.xls",head=T,sep="\t",stringsAsFactors?=?FALSE)

rownames(mat)<-mat$Gene mat<-mat[which(rownames(mat)%in%test$gene_symbol),] mat<-mat[,-1] mat[is.na(mat)]<-"" mat<-Replace(mat,from?=?"^.$",to?=?"?",pattern?=?"") #此處Replace是R包do中的函數(shù)，將文件中的內(nèi)容替換成自己所需要的內(nèi)容 mat<-Replace(mat,from?=?"^,.",to?=?"?",pattern?=?"") mat<-Replace(mat,from?=?",.$",to?=?"?",pattern?=?"") mat<-Replace(mat,from?=?"^.,",to?=?"?",pattern?=?"") mat<-Replace(mat,from?=?"nonframeshift?deletion,frameshift?deletion",to?=?"frameshift_mutation",pattern?=?"") mat<-Replace(mat,from?=?"frameshift?deletion,nonframeshift?deletion",to?=?"frameshift_mutation",pattern?=?"") mat<-Replace(mat,from?=?"nonframeshift?deletion",to?=?"other",pattern?=?"") mat<-Replace(mat,from?=?"nonframeshift?insertion",to?=?"other",pattern?=?"") mat<-Replace(mat,from?=?"frameshift?deletion",to?=?"frameshift_mutation",pattern?=?"") mat<-Replace(mat,from?=?"frameshift?insertion",to?=?"frameshift_mutation",pattern?=?"") mat<-Replace(mat,from?=?"unknown",to?=?"other",pattern?=?"") #oncoPrint(mat) #指定變異類型的標簽，和數(shù)據(jù)中的類型對應 heatmap_legend_param<-list(title="Indel",at=c("frameshift_mutation",?"other"),labels=c("frameshift_mutation",?"other")) #設(shè)定標題 column_title<-"Indel?Oncoplot" ht2<-oncoPrint(mat,alter_fun?=?alter_fun,col=col,column_title=column_title,heatmap_legend_param?=?heatmap_legend_param,remove_empty_columns?=?F,remove_empty_rows?=?F,show_column_names?=?T,show_row_names?=T) mat?<-read.table("keygene.SNP.xls",head=T,sep="\t",stringsAsFactors?=?FALSE)

rownames(mat)<-mat$Gene mat<-mat[which(rownames(mat)%in%test$gene_symbol),] mat<-mat[,-1] mat[is.na(mat)]<-"" #mat<-str_replace("nonframeshift?insertion","other","") mat<-Replace(mat,from?=?"^.$",to?=?"",pattern?=?"") mat<-Replace(mat,from?=?"^,.",to?=?"",pattern?=?"") mat<-Replace(mat,from?=?",.$",to?=?"",pattern?=?"") mat<-Replace(mat,from?=?"^.,",to?=?"",pattern?=?"") mat<-Replace(mat,from?=?"stopgain",to?=?"other",pattern?=?"") mat<-Replace(mat,from?=?"stoploss",to?=?"other",pattern?=?"") mat<-Replace(mat,from?=?"unknown",to?=?"other",pattern?=?"") mat<-Replace(mat,from?=?"^synonymous?SNV$",to?=?"other",pattern?=?"") mat<-Replace(mat,from?=?"^nonsynonymous?SNV$",to?=?"nonsynonymous_SNV",pattern?=?"") mat<-Replace(mat,from?=?"synonymous?SNV,nonsynonymous?SNV",to?=?"nonsynonymous_SNV",pattern?=?"") mat<-Replace(mat,from?=?"nonsynonymous?SNV,synonymous?SNV",to?=?"nonsynonymous_SNV",pattern?=?"") #oncoPrint(mat) mat<-as.matrix(mat) #指定變異類型的標簽，和數(shù)據(jù)中的類型對應 heatmap_legend_param<-list(title="SNP",at=c("nonsynonymous_SNV",?"other"),labels=c("nonsynonymous_SNV",?"other")) #設(shè)定標題 column_title<-"SNP?Oncoplot" ht3<-oncoPrint(mat,alter_fun?=?alter_fun,col=col,column_title=column_title,heatmap_legend_param?=?heatmap_legend_param,remove_empty_columns?=?F,remove_empty_rows?=?F,show_column_names?=?T,show_row_names?=T) data<-?read.delim("ATAC_promoter_1kb.xls",?row.names?=?1,?header=TRUE?,check.names?=?F) row.names(data)<-data$gene_symbol data<-data[which(rownames(data)%in%test$gene_symbol),] data=?data[,?5:19] data[is.na(data)]<-0 data<-data[which(rowSums(data)>0),] data?<-?log10(data+0.000001) data<-as.matrix(data) library(ComplexHeatmap) color.1?<-?colorRampPalette(rev(c("red",?"white",?"#3CB34E")))(100) ht4<-Heatmap(data,col=color.1,cluster_columns??=?T,cluster_rows?=?F,name?=?"ATAC_promoter_1kb",column_title?=?"ATAC_promoter_1kb",show_row_names?=?T,show_column_names?=?T) draw(ht1+ht2+ht3+ht4,gap=unit(0.8,"cm")) dev.off()