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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import pymzml
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",
"ticks": 'outside',
"ticklen": 2,
"tickwidth": 0.25,
"showgrid": False,
"linecolor": 'black',
},
"yaxis": {
"title": "TIC",
"ticks": 'outside',
"ticklen": 2,
"tickwidth": 0.25,
"showgrid": False,
"linecolor": 'black',
},
"plot_bgcolor": 'rgba(255, 255, 255, 0)',
"paper_bgcolor": 'rgba(255, 255, 255, 0)',
},
)
return
if __name__ == "__main__":
if len(sys.argv) < 2:
print(main.__doc__)
exit()
mzml_file = sys.argv[1]
main(mzml_file)
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