R/modifyPlot.R

In nthomasCUBE/KEGGexpressionmapper:

modifyPlot=function(id, df, gois, expr, cand){
        options(stringsAsFactors=FALSE)
        system(paste("wget http://www.kegg.jp/kegg/pathway/map/",id,".png",sep=""),ignore.stdout = TRUE, ignore.stderr = TRUE)
        img=readPNG(paste(id,".png",sep=""))
        nmb_genes=0; ovl=0
        for(x in 1:dim(df)[1]){
                A=df[x,1];B=df[x,2];C=df[x,3];D=df[x,4];E=df[x,5]
                A=as.integer(A);B=as.integer(B);C=as.integer(C);D=as.integer(D)
                A=A;B=B+3;C=C+3;D=D+3
                if(dim(df)[1]>0 && E %in% gois[,2]){
                        if(E %in% cand){
                                for(p1 in (A-3):(C+3)){ for(p2 in (B-3):(D+3)){ img[p2,p1,1]=0; img[p2,p1,2]=0; img[p2,p1,3]=0; img[p2,p1,4]=1 }}
                                ovl=ovl+1
                        }
                        c_g=subset(gois,gois[,2]==E); c_g=c_g[1,1]
                        for(p in 2:dim(expr)[2]){
                                my_expr=subset(expr,expr[,1]==c_g); my_expr=my_expr[1,p]
                                all_expr=expr[,p]; all_expr=all_expr[all_expr>0]
                                nmb_genes=nmb_genes+1
                                A_=A+(p-2)*(C-A)/(dim(expr)[2]-1); C_=A+(p-1)*(C-A)/(dim(expr)[2]-1)
                                if(length(my_expr) > 0){
                                     if(!is.na(my_expr)){
                                             if(sum(my_expr)==0){
                                             }else if(my_expr>0 && my_expr<=quantile(all_expr,0.25)){ col1=255;col2=255;col3=1
                                             }else if(my_expr>=quantile(all_expr,0.25) && my_expr<quantile(all_expr,0.50)){ col1=155;col2=1;col3=155
                                             }else if(my_expr>=quantile(all_expr,0.50) && my_expr<quantile(all_expr,0.75)){ col1=1;col2=100;col3=200
                                             }else if(my_expr>=quantile(all_expr,0.75) && my_expr<=quantile(all_expr,1)){ col1=1;col2=255;col3=255 }
                                             for(p1 in A_:C_){ for(p2 in B:D){ img[p2,p1,1]=col1;img[p2,p1,2]=col2;img[p2,p1,3]=col3;img[p2,p1,4]=1 }}
                                     }
                                }
                        }
                }
        }
        cur_entry=(c(id,"genes in total:",nmb_genes,ovl))
        system(paste("rm",paste(id,".png",sep="")))
        writePNG(img,paste(id,"_modified",".png",sep=""))
        return(cur_entry)
}