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)