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128 lines
3.7 KiB
Python
128 lines
3.7 KiB
Python
#!/usr/bin/env python
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from galaxy import eggs
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import sys, string
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from rpy import *
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import numpy
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def stop_err(msg):
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sys.stderr.write(msg)
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sys.exit()
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infile = sys.argv[1]
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x_cols = sys.argv[2].split(',')
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method = sys.argv[3]
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outfile = sys.argv[4]
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outfile2 = sys.argv[5]
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if method == 'svd':
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scale = center = "FALSE"
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if sys.argv[6] == 'both':
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scale = center = "TRUE"
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elif sys.argv[6] == 'center':
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center = "TRUE"
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elif sys.argv[6] == 'scale':
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scale = "TRUE"
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fout = open(outfile,'w')
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elems = []
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for i, line in enumerate( file ( infile )):
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line = line.rstrip('\r\n')
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if len( line )>0 and not line.startswith( '#' ):
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elems = line.split( '\t' )
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break
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if i == 30:
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break # Hopefully we'll never get here...
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if len( elems )<1:
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stop_err( "The data in your input dataset is either missing or not formatted properly." )
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x_vals = []
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for k,col in enumerate(x_cols):
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x_cols[k] = int(col)-1
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x_vals.append([])
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NA = 'NA'
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skipped = 0
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for ind,line in enumerate( file( infile )):
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if line and not line.startswith( '#' ):
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try:
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fields = line.strip().split("\t")
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valid_line = True
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for k,col in enumerate(x_cols):
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try:
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xval = float(fields[col])
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except:
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skipped += 1
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valid_line = False
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break
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if valid_line:
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for k,col in enumerate(x_cols):
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xval = float(fields[col])
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x_vals[k].append(xval)
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except:
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skipped += 1
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x_vals1 = numpy.asarray(x_vals).transpose()
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dat= r.list(array(x_vals1))
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set_default_mode(NO_CONVERSION)
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try:
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if method == "cor":
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pc = r.princomp(r.na_exclude(dat), cor = r("TRUE"))
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elif method == "cov":
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pc = r.princomp(r.na_exclude(dat), cor = r("FALSE"))
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elif method=="svd":
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pc = r.prcomp(r.na_exclude(dat), center = r(center), scale = r(scale))
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except RException, rex:
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stop_err("Encountered error while performing PCA on the input data: %s" %(rex))
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set_default_mode(BASIC_CONVERSION)
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summary = r.summary(pc, loadings="TRUE")
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ncomps = len(summary['sdev'])
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if type(summary['sdev']) == type({}):
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comps = summary['sdev'].keys()
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sd = summary['sdev'].values()
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for i in range(ncomps):
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sd[comps.index('Comp.%s' %(i+1))] = summary['sdev'].values()[i]
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elif type(summary['sdev']) == type([]):
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comps=[]
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for i in range(ncomps):
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comps.append('Comp.%s' %(i+1))
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sd = summary['sdev']
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print >>fout, "#Component\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
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print >>fout, "#Std. deviation\t%s" %("\t".join(["%.4g" % el for el in sd]))
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total_var = 0
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vars = []
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for s in sd:
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var = s*s
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total_var += var
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vars.append(var)
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for i,var in enumerate(vars):
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vars[i] = vars[i]/total_var
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print >>fout, "#Proportion of variance explained\t%s" %("\t".join(["%.4g" % el for el in vars]))
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print >>fout, "#Loadings\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
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xcolnames = ["c%d" %(el+1) for el in x_cols]
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if 'loadings' in summary: #in case of princomp
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loadings = 'loadings'
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elif 'rotation' in summary: #in case of prcomp
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loadings = 'rotation'
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for i,val in enumerate(summary[loadings]):
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print >>fout, "%s\t%s" %(xcolnames[i], "\t".join(["%.4g" % el for el in val]))
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print >>fout, "#Scores\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)]))
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if 'scores' in summary: #in case of princomp
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scores = 'scores'
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elif 'x' in summary: #in case of prcomp
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scores = 'x'
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for obs,sc in enumerate(summary[scores]):
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print >>fout, "%s\t%s" %(obs+1, "\t".join(["%.4g" % el for el in sc]))
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r.pdf( outfile2, 8, 8 )
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r.biplot(pc)
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r.dev_off() |