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1 #!/usr/bin/env python
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2 #Greg Von Kuster
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3
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4 import sys
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5 from rpy import *
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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 def main():
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12
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13 in_fname = sys.argv[1]
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14 out_fname = sys.argv[2]
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15 try:
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16 columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
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17 except:
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18 stop_err( "Columns not specified, your query does not contain a column of numerical data." )
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19 title = sys.argv[5]
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20 xlab = sys.argv[6]
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21 ylab = sys.argv[7]
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22
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23 matrix = []
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24 skipped_lines = 0
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25 first_invalid_line = 0
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26 invalid_value = ''
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27 invalid_column = 0
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28 i = 0
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29 for i, line in enumerate( file( in_fname ) ):
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30 valid = True
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31 line = line.rstrip( '\r\n' )
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32 if line and not line.startswith( '#' ):
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33 row = []
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34 fields = line.split( "\t" )
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35 for column in columns:
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36 try:
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37 val = fields[column]
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38 if val.lower() == "na":
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39 row.append( float( "nan" ) )
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40 else:
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41 row.append( float( fields[column] ) )
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42 except:
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43 valid = False
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44 skipped_lines += 1
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45 if not first_invalid_line:
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46 first_invalid_line = i + 1
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47 try:
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48 invalid_value = fields[column]
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49 except:
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50 invalid_value = ''
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51 invalid_column = column + 1
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52 break
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53 else:
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54 valid = False
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55 skipped_lines += 1
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56 if not first_invalid_line:
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57 first_invalid_line = i+1
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58
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59 if valid:
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60 matrix.append( row )
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61
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62 if skipped_lines < i:
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63 try:
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64 r.pdf( out_fname, 8, 8 )
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65 r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
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66 r.dev_off()
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67 except Exception, exc:
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68 stop_err( "%s" %str( exc ) )
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69 else:
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70 stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
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71
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72 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
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73 if skipped_lines > 0:
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74 print "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
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75
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76 r.quit( save="no" )
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77
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78 if __name__ == "__main__":
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79 main()
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