|
0
|
1 args <- commandArgs(trailingOnly = TRUE)
|
|
|
2 fileR=args[1]
|
|
|
3 fileT=args[2]
|
|
|
4 signCoff=args[3]
|
|
|
5 oname=args[4]
|
|
|
6 data_R=read.table(fileR,header=T)
|
|
|
7 data_T=read.table(fileT,header=T)
|
|
|
8
|
|
|
9
|
|
|
10
|
|
|
11 n=0;
|
|
|
12 m=min(data_R$VINYL_score)
|
|
|
13 M=max(data_R$VINYL_score)
|
|
|
14 Genes=levels(data_R$gene)
|
|
|
15 GeneP=c()
|
|
|
16 for (gene in Genes)
|
|
|
17 {
|
|
|
18 F=1
|
|
|
19 if (length(data_T[data_T$gene==gene,"VINYL_score"])>=5 && length(data_R[data_R$gene==gene,"VINYL_score"])>=5)
|
|
|
20 {
|
|
|
21 F=round(wilcox.test(data_R[data_R$gene==gene,"VINYL_score"],data_T[data_T$gene==gene,"VINYL_score"],alternative="gr")$p.value,3)
|
|
|
22 }
|
|
|
23 n=n+1
|
|
|
24 GeneP[n]=F
|
|
|
25 }
|
|
|
26
|
|
|
27 Genes=Genes[order(GeneP)]
|
|
|
28 GeneP=GeneP[order(GeneP)]
|
|
|
29 n=0
|
|
|
30 file=paste(oname)
|
|
|
31 pdf(file)#,width=1600,height=1600);
|
|
|
32 par(mfrow=c(3,3),mar=c(3,3,3,2))
|
|
|
33
|
|
|
34
|
|
|
35 for (gene in Genes)
|
|
|
36 {
|
|
|
37
|
|
|
38 n=n+1
|
|
|
39 F=GeneP[n]
|
|
|
40 boxplot(data_T[data_T$gene==gene,"VINYL_score"],data_R[data_R$gene==gene,"VINYL_score"],col=c("purple","orange"),main=paste(gene,"p-value=" ,F,sep=" "),names=c("Cont","Aff"),ylim=c(m,M))
|
|
|
41 abline(a=signCoff,b=0,lwd=2,col="red",lty=3)
|
|
|
42 abline(a=0,b=0,lwd=2,col="blue",lty=3)
|
|
|
43 #if (n %% 16==0)
|
|
|
44 #{
|
|
|
45 # dev.off();
|
|
|
46 # file=paste(oname,n,"png",sep=".")
|
|
|
47 # png(file,width=1600,height=1600,res=160);
|
|
|
48 # par(mfrow=c(4,4),mar=c(2,2,2,1.5))
|
|
|
49 #}
|
|
|
50 }
|
|
|
51
|
|
|
52 dev.off();
|
