|
0
|
1 '''
|
|
|
2 python wrapper for cdf plot
|
|
|
3 '''
|
|
|
4
|
|
|
5 import os,sys
|
|
|
6
|
|
|
7 filename = sys.argv[1]
|
|
|
8 output = sys.argv[2]
|
|
|
9 c1, c2 = sys.argv[3].strip().split(',')
|
|
|
10 label1,label2 = sys.argv[5].strip().split(',')
|
|
|
11 title = sys.argv[6].strip()
|
|
|
12 log = sys.argv[4]
|
|
|
13
|
|
|
14 rf = open('tmp.r','w')
|
|
|
15
|
|
|
16 rf.write("options(warn=-1)\n")
|
|
|
17
|
|
|
18 rf.write("x <- read.table('"+filename+"')\n")
|
|
|
19
|
|
|
20 rf.write("mycdf <- function(x1,x2) {\n")
|
|
|
21 rf.write(" sx1 <- sort(x1)\n")
|
|
|
22 rf.write(" sy1 <- c(1:length(sx1))/length(sx1)\n")
|
|
|
23 rf.write(" sx2 <- sort(x2)\n")
|
|
|
24 rf.write(" sy2 <- c(1:length(sx2))/length(sx2)\n")
|
|
|
25 rf.write(" mi <- min(c(x1,x2))\n")
|
|
|
26 rf.write(" ma <- max(c(x1,x2))\n")
|
|
|
27 rf.write(" sx1 <- c(mi,sx1,ma)\n")
|
|
|
28 rf.write(" sx2 <- c(mi,sx2,ma)\n")
|
|
|
29 rf.write(" sy1 <- c(0,sy1,1)\n")
|
|
|
30 rf.write(" sy2 <- c(0,sy2,1)\n")
|
|
|
31 rf.write(" pv <- ks.test(x1,x2)$p.value\n")
|
|
|
32 rf.write(" list(sx1,sy1,sx2,sy2,pv)\n")
|
|
|
33 rf.write("}\n")
|
|
|
34
|
|
|
35 rf.write("list1 <- x[,"+c1+"]\n")
|
|
|
36 rf.write("list2 <- x[,"+c2+"]\n")
|
|
|
37
|
|
|
38 if log == 'log':
|
|
|
39 rf.write("list1 <- log2(1+list1) \n")
|
|
|
40 rf.write("list2 <- log2(1+list2) \n")
|
|
|
41 #rf.write("list1[list1 == -Inf] <- min(list1[list1 != -Inf])\n")
|
|
|
42 rf.write("res <- mycdf(list1,list2)\n")
|
|
|
43
|
|
|
44 rf.write("pdf('"+output+"')\n")
|
|
|
45 rf.write("plot(res[[1]],res[[2]],type='l',lty=1,lwd=2,col='red',main=paste('"+title+"',format(res[[5]], digit=2,scientific = T),sep=' , p='),xlab='value',ylab='cumulative frequency')\n")
|
|
|
46 rf.write("lines(res[[3]],res[[4]],type='l',lty=2,lwd=2,col='blue')\n")
|
|
|
47 rf.write("label1 <- paste('"+label1+"','( n1=',length(list1),')')\n")
|
|
|
48 rf.write("label2 <- paste('"+label2+"','( n2=',length(list2),')')\n")
|
|
|
49 rf.write("legend('bottomright',c(label1,label2),col=c('red','blue'), lty=1:2, lwd=2, bty='n')\n")
|
|
|
50 rf.write("boxplot(list1,list2,names=c(label1,label2))\n")
|
|
|
51 rf.write("dev.off()\n")
|
|
|
52
|
|
|
53 rf.close()
|
|
|
54 os.system("R --vanilla < tmp.r")
|
|
|
55 os.system('rm tmp.r')
|
