Mercurial > repos > xuebing > sharplabtool

comparison plotmatrix.py @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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comparison
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10:1558594a3c2e 11:b7f1d9f8f3bc
1 import sys,os
2
3 infile = sys.argv[1]
4 outfile = sys.argv[2]
5 uselog = sys.argv[3]
6 subset = sys.argv[4]
7 reorder = sys.argv[5]
8 color = sys.argv[6]
9 scale = sys.argv[7] # rescale each row
10 cols = sys.argv[8]
11 rscript = open('tmp.r','w')
12
13 rscript.write("x <- read.table('"+infile+"')\n")
14 rscript.write("x <- x[,c("+cols+")]\n")
15 rscript.write("nr <- nrow(x) \n")
16 rscript.write("nc <- ncol(x)\n")
17 rscript.write("rowsum <- apply(x,1,sum)\n")
18
19 if subset =='subset':
20 rscript.write("if (nr*nc > 100000) {\n")
21 rscript.write(" nr2 <- as.integer(100000/nc)\n")
22 rscript.write(" subind <- sample(seq(nr),nr2)\n")
23 rscript.write(" x <- x[subind,]\n")
24 rscript.write(" rowsum <- rowsum[subind]\n")
25 rscript.write("}\n")
26
27 rscript.write("pdf('"+outfile+"')\n")
28
29 if uselog == 'uselog':
30 rscript.write("x <- -(log(as.matrix(x,nc=nc)))\n")
31 else:
32 rscript.write("x <- -as.matrix(x,nc=nc)\n")
33 if scale == 'scale':
34 rscript.write("x <- scale(x)\n")
35 if reorder == 'average':
36 rscript.write("hc <- hclust(dist(x),method= 'average')\n")
37 rscript.write("x <- x[hc$order,]\n")
38 elif reorder == 'centroid':
39 rscript.write("hc <- hclust(dist(x),method= 'centroid')\n")
40 rscript.write("x <- x[hc$order,]\n")
41 elif reorder == 'complete':
42 rscript.write("hc <- hclust(dist(x),method= 'complete')\n")
43 rscript.write("x <- x[hc$order,]\n")
44 elif reorder == 'single':
45 rscript.write("hc <- hclust(dist(x),method= 'single')\n")
46 rscript.write("x <- x[hc$order,]\n")
47 elif reorder == 'median':
48 rscript.write("hc <- hclust(dist(x),method= 'median')\n")
49 rscript.write("x <- x[hc$order,]\n")
50 elif reorder == 'sort_by_total':
51 rscript.write("srt <- sort(rowsum,index.return=T)\n")
52 rscript.write("x <- x[srt$ix,]\n")
53 elif reorder == 'sort_by_center':
54 rscript.write("srt <- sort(x[,as.integer(nc/2)],index.return=T)\n")
55 rscript.write("x <- x[srt$ix,]\n")
56 if color == 'heat':
57 rscript.write("colormap = heat.colors(1000)\n")
58 elif color == 'topo':
59 rscript.write("colormap = topo.colors(1000)\n")
60 elif color == 'rainbow':
61 rscript.write("colormap = rainbow(1000)\n")
62 elif color == 'terrain':
63 rscript.write("colormap = terrain.colors(1000)\n")
64 else:
65 rscript.write("colormap = gray.colors(1000)\n")
66
67 #rscript.write("qt <- quantile(as.vector(x),probs=c(0.1,0.9))\n")
68 #rscript.write("breaks <- c(min(as.vector(x)),seq(qt[1],qt[2],length.out=99),max(as.vector(x)))\n")
69 #rscript.write("image(t(x),col=colormap,breaks=breaks,axes=F)\n")
70 rscript.write("image(t(x),col=colormap,axes=F)\n")
71 rscript.write("dev.off()\n")
72
73 rscript.close()
74
75 os.system("R --slave < tmp.r")
76 os.system("rm tmp.r")
77