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80
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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 rpy2.robjects as robjects
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6 import rpy2.rlike.container as rlc
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7 from rpy2.robjects.packages import importr
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8 r = robjects.r
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9 grdevices = importr('grDevices')
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10 import numpy
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11
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12 def stop_err(msg):
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13 sys.stderr.write(msg)
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14 sys.exit()
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15
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16 infile = sys.argv[1]
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17 x_cols = sys.argv[2].split(',')
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18 method = sys.argv[3]
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19 outfile = sys.argv[4]
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20 outfile2 = sys.argv[5]
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21
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22 if method == 'svd':
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23 scale = center = "FALSE"
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24 if sys.argv[6] == 'both':
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25 scale = center = "TRUE"
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26 elif sys.argv[6] == 'center':
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27 center = "TRUE"
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28 elif sys.argv[6] == 'scale':
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29 scale = "TRUE"
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30
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31 fout = open(outfile,'w')
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32 elems = []
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33 for i, line in enumerate( file ( infile )):
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34 line = line.rstrip('\r\n')
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35 if len( line )>0 and not line.startswith( '#' ):
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36 elems = line.split( '\t' )
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37 break
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38 if i == 30:
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39 break # Hopefully we'll never get here...
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40
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41 if len( elems )<1:
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42 stop_err( "The data in your input dataset is either missing or not formatted properly." )
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43
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44 x_vals = []
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45
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46 for k,col in enumerate(x_cols):
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47 x_cols[k] = int(col)-1
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48 # x_vals.append([])
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49
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50 NA = 'NA'
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51 skipped = 0
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52 for ind,line in enumerate( file( infile )):
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53 if line and not line.startswith( '#' ):
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54 try:
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55 fields = line.strip().split("\t")
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56 valid_line = True
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57 for k,col in enumerate(x_cols):
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58 try:
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59 xval = float(fields[col])
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60 except:
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61 skipped += 1
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62 valid_line = False
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63 break
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64 if valid_line:
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65 for k,col in enumerate(x_cols):
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66 xval = float(fields[col])
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67 #x_vals[k].append(xval)
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68 x_vals.append(xval)
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69 except:
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70 skipped += 1
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71
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72 #x_vals1 = numpy.asarray(x_vals).transpose()
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73 #dat= r.list(array(x_vals1))
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74 dat = r['matrix'](robjects.FloatVector(x_vals),ncol=len(x_cols),byrow=True)
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75
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76 #set_default_mode(NO_CONVERSION)
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77 try:
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78 if method == "cor":
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79 #pc = r.princomp(r.na_exclude(dat), cor = r("TRUE"))
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80 pc = r.princomp(r['na.exclude'](dat), cor = r("TRUE"))
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81 elif method == "cov":
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82 #pc = r.princomp(r.na_exclude(dat), cor = r("FALSE"))
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83 pc = r.princomp(r['na.exclude'](dat), cor = r("FALSE"))
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84 elif method=="svd":
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85 #pc = r.prcomp(r.na_exclude(dat), center = r(center), scale = r(scale))
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86 pc = r.prcomp(r['na.exclude'](dat), center = r(center), scale = r(scale))
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87 #except RException, rex:
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88 except Exception, rex: # need to find rpy2 RException
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89 stop_err("Encountered error while performing PCA on the input data: %s" %(rex))
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90
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91 #set_default_mode(BASIC_CONVERSION)
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92 summary = r.summary(pc, loadings="TRUE")
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93 #ncomps = len(summary['sdev'])
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94 ncomps = len(summary.rx2('sdev'))
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95
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96 #if type(summary['sdev']) == type({}):
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97 # comps_unsorted = summary['sdev'].keys()
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98 # comps=[]
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99 # sd = summary['sdev'].values()
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100 # for i in range(ncomps):
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101 # sd[i] = summary['sdev'].values()[comps_unsorted.index('Comp.%s' %(i+1))]
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102 # comps.append('Comp.%s' %(i+1))
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103 #elif type(summary['sdev']) == type([]):
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104 # comps=[]
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105 # for i in range(ncomps):
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106 # comps.append('Comp.%s' %(i+1))
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107 # sd = summary['sdev']
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108
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109 comps=[]
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110 for i in range(ncomps):
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111 comps.append('Comp.%s' %(i+1))
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112 sd = summary.rx2('sdev')
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113
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114 print >>fout, "#Component\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
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115 #print >>fout, "#Std. deviation\t%s" %("\t".join(["%.4g" % el for el in sd]))
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116 print >>fout, "#Std. deviation\t%s" %("\t".join(["%.4g" % el for el in sd]))
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117 total_var = 0
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118 vars = []
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119 for s in sd:
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120 var = s*s
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121 total_var += var
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122 vars.append(var)
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123 for i,var in enumerate(vars):
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124 vars[i] = vars[i]/total_var
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125
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126 print >>fout, "#Proportion of variance explained\t%s" %("\t".join(["%.4g" % el for el in vars]))
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127
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128 print >>fout, "#Loadings\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
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129 xcolnames = ["c%d" %(el+1) for el in x_cols]
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130 #if 'loadings' in summary: #in case of princomp
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131 if 'loadings' in summary.names: #in case of princomp
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132 loadings = 'loadings'
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133 #elif 'rotation' in summary: #in case of prcomp
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134 elif 'rotation' in summary.names: #in case of prcomp
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135 loadings = 'rotation'
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136 #for i,val in enumerate(summary[loadings]):
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137 # print >>fout, "%s\t%s" %(xcolnames[i], "\t".join(["%.4g" % el for el in val]))
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138 vm = summary.rx2(loadings)
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139 for i in range(vm.nrow):
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140 vals = []
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141 for j in range(vm.ncol):
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142 vals.append("%.4g" % vm.rx2(i+1,j+1)[0])
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143 print >>fout, "%s\t%s" %(xcolnames[i], "\t".join(vals))
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144
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145 print >>fout, "#Scores\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
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146 #if 'scores' in summary: #in case of princomp
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147 if 'scores' in summary.names: #in case of princomp
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148 scores = 'scores'
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149 #elif 'x' in summary: #in case of prcomp
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150 elif 'x' in summary.names: #in case of prcomp
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151 scores = 'x'
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152 #for obs,sc in enumerate(summary[scores]):
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153 # print >>fout, "%s\t%s" %(obs+1, "\t".join(["%.4g" % el for el in sc]))
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154 vm = summary.rx2(scores)
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155 for i in range(vm.nrow):
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156 vals = []
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157 for j in range(vm.ncol):
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158 vals.append("%.4g" % vm.rx2(i+1,j+1)[0])
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159 print >>fout, "%s\t%s" %(i+1, "\t".join(vals))
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160 r.pdf( outfile2, 8, 8 )
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161 r.biplot(pc)
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162 #r.dev_off()
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163 grdevices.dev_off()
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164
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