/tools/plotting/histogram.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 101 lines · 85 code · 11 blank · 5 comment · 30 complexity · a6b4b022439f285578766354544feb80 MD5 · raw file

  1. #!/usr/bin/env python
  2. #Greg Von Kuster
  3. import sys
  4. from rpy import *
  5. assert sys.version_info[:2] >= ( 2, 4 )
  6. def stop_err(msg):
  7. sys.stderr.write(msg)
  8. sys.exit()
  9. def main():
  10. # Handle input params
  11. in_fname = sys.argv[1]
  12. out_fname = sys.argv[2]
  13. try:
  14. column = int( sys.argv[3] ) - 1
  15. except:
  16. stop_err( "Column not specified, your query does not contain a column of numerical data." )
  17. title = sys.argv[4]
  18. xlab = sys.argv[5]
  19. breaks = int( sys.argv[6] )
  20. if breaks == 0:
  21. breaks = "Sturges"
  22. if sys.argv[7] == "true":
  23. density = True
  24. else: density = False
  25. if len( sys.argv ) >= 9 and sys.argv[8] == "true":
  26. frequency = True
  27. else: frequency = False
  28. matrix = []
  29. skipped_lines = 0
  30. first_invalid_line = 0
  31. invalid_value = ''
  32. i = 0
  33. for i, line in enumerate( file( in_fname ) ):
  34. valid = True
  35. line = line.rstrip('\r\n')
  36. # Skip comments
  37. if line and not line.startswith( '#' ):
  38. # Extract values and convert to floats
  39. row = []
  40. try:
  41. fields = line.split( "\t" )
  42. val = fields[column]
  43. if val.lower() == "na":
  44. row.append( float( "nan" ) )
  45. except:
  46. valid = False
  47. skipped_lines += 1
  48. if not first_invalid_line:
  49. first_invalid_line = i+1
  50. else:
  51. try:
  52. row.append( float( val ) )
  53. except ValueError:
  54. valid = False
  55. skipped_lines += 1
  56. if not first_invalid_line:
  57. first_invalid_line = i+1
  58. invalid_value = fields[column]
  59. else:
  60. valid = False
  61. skipped_lines += 1
  62. if not first_invalid_line:
  63. first_invalid_line = i+1
  64. if valid:
  65. matrix += row
  66. if skipped_lines < i:
  67. try:
  68. a = r.array( matrix )
  69. r.pdf( out_fname, 8, 8 )
  70. histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks )
  71. if density:
  72. density = r.density( a )
  73. if frequency:
  74. scale_factor = len( matrix ) * ( histogram['mids'][1] - histogram['mids'][0] ) #uniform bandwidth taken from first 2 midpoints
  75. density[ 'y' ] = map( lambda x: x * scale_factor, density[ 'y' ] )
  76. r.lines( density )
  77. r.dev_off()
  78. except Exception, exc:
  79. stop_err( "%s" %str( exc ) )
  80. else:
  81. if i == 0:
  82. stop_err("Input dataset is empty.")
  83. else:
  84. stop_err( "All values in column %s are non-numeric." %sys.argv[3] )
  85. print "Histogram of column %s. " %sys.argv[3]
  86. if skipped_lines > 0:
  87. print "Skipped %d invalid lines starting with line #%d, '%s'." % ( skipped_lines, first_invalid_line, invalid_value )
  88. r.quit( save="no" )
  89. if __name__ == "__main__":
  90. main()