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)
}
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