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