Mercurial > repos > mvdbeek > scatterplot_test

annotate scatterplot.py @ 1:b4102b163488 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
author mvdbeek
date Wed, 14 Sep 2016 12:42:56 -0400
parents 11627baf830e
children
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11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
1 #!/usr/bin/env python
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
2 # Greg Von Kuster
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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3
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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4 import sys
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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5
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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6 from numpy import array
1
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
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7 import rpy2.rpy_classic as rpy
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
diff changeset
8 from rpy2.robjects.numpy2ri import numpy2ri
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
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9
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
diff changeset
10
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
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11 rpy.set_default_mode(rpy.NO_CONVERSION)
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
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12 r = rpy.r
0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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13
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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14
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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15 def stop_err(msg):
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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16 sys.stderr.write(msg)
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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17 sys.exit()
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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18
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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19
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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20 def main():
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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21
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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22 in_fname = sys.argv[1]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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23 out_fname = sys.argv[2]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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24 try:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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25 columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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26 except:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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27 stop_err( "Columns not specified, your query does not contain a column of numerical data." )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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28 title = sys.argv[5]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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29 xlab = sys.argv[6]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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30 ylab = sys.argv[7]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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31
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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32 matrix = []
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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33 skipped_lines = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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34 first_invalid_line = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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35 invalid_value = ''
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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36 invalid_column = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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37 i = 0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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38 for i, line in enumerate( file( in_fname ) ):
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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39 valid = True
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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40 line = line.rstrip( '\r\n' )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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41 if line and not line.startswith( '#' ):
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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42 row = []
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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43 fields = line.split( "\t" )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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44 for column in columns:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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45 try:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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46 val = fields[column]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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47 if val.lower() == "na":
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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48 row.append( float( "nan" ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
49 else:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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50 row.append( float( fields[column] ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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51 except:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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52 valid = False
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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53 skipped_lines += 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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54 if not first_invalid_line:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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55 first_invalid_line = i + 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
56 try:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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57 invalid_value = fields[column]
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
58 except:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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59 invalid_value = ''
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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60 invalid_column = column + 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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61 break
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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62 else:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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63 valid = False
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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64 skipped_lines += 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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65 if not first_invalid_line:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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66 first_invalid_line = i + 1
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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67
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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68 if valid:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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69 matrix.append( row )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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70
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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71 if skipped_lines < i:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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72 try:
1
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
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73 a = numpy2ri(array( matrix ))
0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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74 r.pdf( out_fname, 8, 8 )
1
b4102b163488 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents: 0
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75 r.plot( a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
0
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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76 r.dev_off()
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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77 except Exception, exc:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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78 stop_err( "%s" % str( exc ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
79 else:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
80 stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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81
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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82 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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83 if skipped_lines > 0:
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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84 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 )
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff changeset
85
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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86 if __name__ == "__main__":
11627baf830e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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87 main()