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comparison scatterplot.py @ 2:4f8b9e70fda0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 93df3895fbf2fa44ff279303093fb89b79081687
author devteam
date Thu, 15 Sep 2016 11:14:37 -0400
parents c12b0759203b
children efda9a4a50e7
comparison
equal deleted inserted replaced
1:d243056b22ed 2:4f8b9e70fda0
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 #Greg Von Kuster 2 # Greg Von Kuster
3 3
4 import sys 4 import sys
5 from rpy import * 5
6 from numpy import array
7 import rpy2.rpy_classic as rpy
8 from rpy2.robjects.numpy2ri import numpy2ri
9
10
11 rpy.set_default_mode(rpy.NO_CONVERSION)
12 r = rpy.r
13
6 14
7 def stop_err(msg): 15 def stop_err(msg):
8 sys.stderr.write(msg) 16 sys.stderr.write(msg)
9 sys.exit() 17 sys.exit()
18
10 19
11 def main(): 20 def main():
12 21
13 in_fname = sys.argv[1] 22 in_fname = sys.argv[1]
14 out_fname = sys.argv[2] 23 out_fname = sys.argv[2]
27 invalid_column = 0 36 invalid_column = 0
28 i = 0 37 i = 0
29 for i, line in enumerate( file( in_fname ) ): 38 for i, line in enumerate( file( in_fname ) ):
30 valid = True 39 valid = True
31 line = line.rstrip( '\r\n' ) 40 line = line.rstrip( '\r\n' )
32 if line and not line.startswith( '#' ): 41 if line and not line.startswith( '#' ):
33 row = [] 42 row = []
34 fields = line.split( "\t" ) 43 fields = line.split( "\t" )
35 for column in columns: 44 for column in columns:
36 try: 45 try:
37 val = fields[column] 46 val = fields[column]
38 if val.lower() == "na": 47 if val.lower() == "na":
39 row.append( float( "nan" ) ) 48 row.append( float( "nan" ) )
40 else: 49 else:
41 row.append( float( fields[column] ) ) 50 row.append( float( fields[column] ) )
42 except: 51 except:
43 valid = False 52 valid = False
52 break 61 break
53 else: 62 else:
54 valid = False 63 valid = False
55 skipped_lines += 1 64 skipped_lines += 1
56 if not first_invalid_line: 65 if not first_invalid_line:
57 first_invalid_line = i+1 66 first_invalid_line = i + 1
58 67
59 if valid: 68 if valid:
60 matrix.append( row ) 69 matrix.append( row )
61 70
62 if skipped_lines < i: 71 if skipped_lines < i:
63 try: 72 try:
73 a = numpy2ri(array( matrix ))
64 r.pdf( out_fname, 8, 8 ) 74 r.pdf( out_fname, 8, 8 )
65 r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) 75 r.plot( a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
66 r.dev_off() 76 r.dev_off()
67 except Exception, exc: 77 except Exception, exc:
68 stop_err( "%s" %str( exc ) ) 78 stop_err( "%s" % str( exc ) )
69 else: 79 else:
70 stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) ) 80 stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
71 81
72 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] ) 82 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
73 if skipped_lines > 0: 83 if skipped_lines > 0:
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 ) 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 )
75 85
76 r.quit( save="no" )
77
78 if __name__ == "__main__": 86 if __name__ == "__main__":
79 main() 87 main()