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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'
>>> get_example_file.open_example(mzMLFile)
>>> run = pymzml.run.Reader("mzML_example_files/"+mzMLFile, MSn_Precision = 25e-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 pymzml
import get_example_file
def main( file = None ):
mzMLFile = 'profile-mass-spectrum.mzml'
get_example_file.open_example(mzMLFile)
run = pymzml.run.Reader("mzML_example_files/"+mzMLFile, MSn_Precision = 25e-6)
p = pymzml.plot.Factory()
for spec in run:
p.newPlot()
p.add(spec.peaks, color=(200,00,00), style='squares')
p.add(spec.centroidedPeaks, color=(00,00,00), style='sticks')
p.add(spec.reprofiledPeaks, color=(025,000,200), style='circles')
p.save( filename="output/plotAspect.xhtml" , mzRange = [744.7,747] )
if __name__ == '__main__':
main()
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