/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
- #!/usr/bin/env python
- #Greg Von Kuster
- import sys
- from rpy import *
- assert sys.version_info[:2] >= ( 2, 4 )
- def stop_err(msg):
- sys.stderr.write(msg)
- sys.exit()
- def main():
- # Handle input params
- in_fname = sys.argv[1]
- out_fname = sys.argv[2]
- try:
- column = int( sys.argv[3] ) - 1
- except:
- stop_err( "Column not specified, your query does not contain a column of numerical data." )
- title = sys.argv[4]
- xlab = sys.argv[5]
- breaks = int( sys.argv[6] )
- if breaks == 0:
- breaks = "Sturges"
- if sys.argv[7] == "true":
- density = True
- else: density = False
- if len( sys.argv ) >= 9 and sys.argv[8] == "true":
- frequency = True
- else: frequency = False
- matrix = []
- skipped_lines = 0
- first_invalid_line = 0
- invalid_value = ''
- i = 0
- for i, line in enumerate( file( in_fname ) ):
- valid = True
- line = line.rstrip('\r\n')
- # Skip comments
- if line and not line.startswith( '#' ):
- # Extract values and convert to floats
- row = []
- try:
- fields = line.split( "\t" )
- val = fields[column]
- if val.lower() == "na":
- row.append( float( "nan" ) )
- except:
- valid = False
- skipped_lines += 1
- if not first_invalid_line:
- first_invalid_line = i+1
- else:
- try:
- row.append( float( val ) )
- except ValueError:
- valid = False
- skipped_lines += 1
- if not first_invalid_line:
- first_invalid_line = i+1
- invalid_value = fields[column]
- else:
- valid = False
- skipped_lines += 1
- if not first_invalid_line:
- first_invalid_line = i+1
- if valid:
- matrix += row
- if skipped_lines < i:
- try:
- a = r.array( matrix )
- r.pdf( out_fname, 8, 8 )
- histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks )
- if density:
- density = r.density( a )
- if frequency:
- scale_factor = len( matrix ) * ( histogram['mids'][1] - histogram['mids'][0] ) #uniform bandwidth taken from first 2 midpoints
- density[ 'y' ] = map( lambda x: x * scale_factor, density[ 'y' ] )
- r.lines( density )
- r.dev_off()
- except Exception, exc:
- stop_err( "%s" %str( exc ) )
- else:
- if i == 0:
- stop_err("Input dataset is empty.")
- else:
- stop_err( "All values in column %s are non-numeric." %sys.argv[3] )
- print "Histogram of column %s. " %sys.argv[3]
- if skipped_lines > 0:
- print "Skipped %d invalid lines starting with line #%d, '%s'." % ( skipped_lines, first_invalid_line, invalid_value )
- r.quit( save="no" )
-
- if __name__ == "__main__":
- main()