Source code for plot_chromatogram

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import os
import sys

import pymzml
from pymzml.plot import Factory


[docs]def main(mzml_file): ''' Plots a chromatogram for the given mzML file. File is saved as 'chromatogram_<mzml_file>.html'. usage: ./plot_chromatogram.py <path_to_mzml_file> ''' run = pymzml.run.Reader( mzml_file ) mzml_basename = os.path.basename( mzml_file ) pf = Factory() pf.new_plot() pf.add( run['TIC'].peaks(), color = (0, 0, 0), style = 'lines', title = mzml_basename ) pf.save( 'chromatogram_{0}.html'.format( mzml_basename ), layout = { 'xaxis' : { 'title' : 'Retention time' }, 'yaxis' : { 'title' : 'TIC' } } ) return
if __name__ == '__main__': if len(sys.argv) < 2: print(main.__doc__) exit() mzml_file = sys.argv[1] main(mzml_file)