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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This function shows how to plot a simple spectrum. It can be directly
plotted via this script or using the python console
Example of plotting a spectrum:
>>> import pymzml, get_example_file
>>> mzMLFile = 'profile-mass-spectrum.mzml'
>>> example_file = get_example_file.open_example(mzMLFile)
>>> run = pymzml.run.Reader("../mzML_example_files/"+mzMLFile, MSn_Precision = 250e-6)
>>> p = pymzml.plot.Factory()
>>> for spec in run:
>>> p.newPlot()
>>> p.add(spec.peaks, color=(200,00,00), style='circles')
>>> p.add(spec.centroidedPeaks, color=(00,00,00), style='sticks')
>>> p.add(spec.reprofiledPeaks, color=(00,255,00), style='circles')
>>> p.save( filename="output/plotAspect.xhtml" , mzRange = [744.7,747] )
"""
from __future__ import print_function
import sys
import pymzml
import get_example_file
def main( file = None):
if file == None:
mzMLFile = 'profile-mass-spectrum.mzml'
example_file = get_example_file.open_example(mzMLFile)
else:
example_file = file
run = pymzml.run.Reader(example_file, MSn_Precision = 250e-6)
p = pymzml.plot.Factory()
specs = [ 4927,4930,4934,4936,4938,4942,4946,4948,4950,4954,4955,4957,4959,4962,4965,4967,4971,4976,4979,4982,4985,4990,4991,4995,4999,5004]
for specID in specs:
spec = run[ specID ]
p.newPlot()
# p.add(spec.peaks, color=(200,00,00), style='circles')
p.add(spec.reprofiledPeaks, color=(100,100,100), style='triangle')
p.add(spec.centroidedPeaks, color=(00,00,00), style='sticks')
# break
p.save( filename="output/plotAspect.xhtml" , mzRange = [840.,853.] )
return
if __name__ == '__main__':
if len(sys.argv) == 1:
main()
else:
main( file = sys.argv[1] )
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