# Source code for plot_chromatogram

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

    from __future__ import print_function
    import sys
    import pymzml
    import os
    from pymzml.plot import Factory

    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)