|
0
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 from galaxy import eggs
|
|
|
4 import sys, string
|
|
|
5 from rpy import *
|
|
|
6 import numpy
|
|
|
7
|
|
|
8 def stop_err(msg):
|
|
|
9 sys.stderr.write(msg)
|
|
|
10 sys.exit()
|
|
|
11
|
|
|
12 infile = sys.argv[1]
|
|
|
13 x_cols = sys.argv[2].split(',')
|
|
|
14 method = sys.argv[3]
|
|
|
15 outfile = sys.argv[4]
|
|
|
16 outfile2 = sys.argv[5]
|
|
|
17
|
|
|
18 if method == 'svd':
|
|
|
19 scale = center = "FALSE"
|
|
|
20 if sys.argv[6] == 'both':
|
|
|
21 scale = center = "TRUE"
|
|
|
22 elif sys.argv[6] == 'center':
|
|
|
23 center = "TRUE"
|
|
|
24 elif sys.argv[6] == 'scale':
|
|
|
25 scale = "TRUE"
|
|
|
26
|
|
|
27 fout = open(outfile,'w')
|
|
|
28 elems = []
|
|
|
29 for i, line in enumerate( file ( infile )):
|
|
|
30 line = line.rstrip('\r\n')
|
|
|
31 if len( line )>0 and not line.startswith( '#' ):
|
|
|
32 elems = line.split( '\t' )
|
|
|
33 break
|
|
|
34 if i == 30:
|
|
|
35 break # Hopefully we'll never get here...
|
|
|
36
|
|
|
37 if len( elems )<1:
|
|
|
38 stop_err( "The data in your input dataset is either missing or not formatted properly." )
|
|
|
39
|
|
|
40 x_vals = []
|
|
|
41
|
|
|
42 for k,col in enumerate(x_cols):
|
|
|
43 x_cols[k] = int(col)-1
|
|
|
44 x_vals.append([])
|
|
|
45
|
|
|
46 NA = 'NA'
|
|
|
47 skipped = 0
|
|
|
48 for ind,line in enumerate( file( infile )):
|
|
|
49 if line and not line.startswith( '#' ):
|
|
|
50 try:
|
|
|
51 fields = line.strip().split("\t")
|
|
|
52 valid_line = True
|
|
|
53 for k,col in enumerate(x_cols):
|
|
|
54 try:
|
|
|
55 xval = float(fields[col])
|
|
|
56 except:
|
|
|
57 skipped += 1
|
|
|
58 valid_line = False
|
|
|
59 break
|
|
|
60 if valid_line:
|
|
|
61 for k,col in enumerate(x_cols):
|
|
|
62 xval = float(fields[col])
|
|
|
63 x_vals[k].append(xval)
|
|
|
64 except:
|
|
|
65 skipped += 1
|
|
|
66
|
|
|
67 x_vals1 = numpy.asarray(x_vals).transpose()
|
|
|
68 dat= r.list(array(x_vals1))
|
|
|
69
|
|
|
70 set_default_mode(NO_CONVERSION)
|
|
|
71 try:
|
|
|
72 if method == "cor":
|
|
|
73 pc = r.princomp(r.na_exclude(dat), cor = r("TRUE"))
|
|
|
74 elif method == "cov":
|
|
|
75 pc = r.princomp(r.na_exclude(dat), cor = r("FALSE"))
|
|
|
76 elif method=="svd":
|
|
|
77 pc = r.prcomp(r.na_exclude(dat), center = r(center), scale = r(scale))
|
|
|
78 except RException, rex:
|
|
|
79 stop_err("Encountered error while performing PCA on the input data: %s" %(rex))
|
|
|
80
|
|
|
81 set_default_mode(BASIC_CONVERSION)
|
|
|
82 summary = r.summary(pc, loadings="TRUE")
|
|
|
83 ncomps = len(summary['sdev'])
|
|
|
84
|
|
|
85 if type(summary['sdev']) == type({}):
|
|
|
86 comps_unsorted = summary['sdev'].keys()
|
|
|
87 comps=[]
|
|
|
88 sd = summary['sdev'].values()
|
|
|
89 for i in range(ncomps):
|
|
|
90 sd[i] = summary['sdev'].values()[comps_unsorted.index('Comp.%s' %(i+1))]
|
|
|
91 comps.append('Comp.%s' %(i+1))
|
|
|
92 elif type(summary['sdev']) == type([]):
|
|
|
93 comps=[]
|
|
|
94 for i in range(ncomps):
|
|
|
95 comps.append('Comp.%s' %(i+1))
|
|
|
96 sd = summary['sdev']
|
|
|
97
|
|
|
98 print >>fout, "#Component\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
|
|
|
99 print >>fout, "#Std. deviation\t%s" %("\t".join(["%.4g" % el for el in sd]))
|
|
|
100 total_var = 0
|
|
|
101 vars = []
|
|
|
102 for s in sd:
|
|
|
103 var = s*s
|
|
|
104 total_var += var
|
|
|
105 vars.append(var)
|
|
|
106 for i,var in enumerate(vars):
|
|
|
107 vars[i] = vars[i]/total_var
|
|
|
108
|
|
|
109 print >>fout, "#Proportion of variance explained\t%s" %("\t".join(["%.4g" % el for el in vars]))
|
|
|
110
|
|
|
111 print >>fout, "#Loadings\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
|
|
|
112 xcolnames = ["c%d" %(el+1) for el in x_cols]
|
|
|
113 if 'loadings' in summary: #in case of princomp
|
|
|
114 loadings = 'loadings'
|
|
|
115 elif 'rotation' in summary: #in case of prcomp
|
|
|
116 loadings = 'rotation'
|
|
|
117 for i,val in enumerate(summary[loadings]):
|
|
|
118 print >>fout, "%s\t%s" %(xcolnames[i], "\t".join(["%.4g" % el for el in val]))
|
|
|
119
|
|
|
120 print >>fout, "#Scores\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
|
|
|
121 if 'scores' in summary: #in case of princomp
|
|
|
122 scores = 'scores'
|
|
|
123 elif 'x' in summary: #in case of prcomp
|
|
|
124 scores = 'x'
|
|
|
125 for obs,sc in enumerate(summary[scores]):
|
|
|
126 print >>fout, "%s\t%s" %(obs+1, "\t".join(["%.4g" % el for el in sc]))
|
|
|
127
|
|
|
128 r.pdf( outfile2, 8, 8 )
|
|
|
129 r.biplot(pc)
|
|
|
130 r.dev_off() |
