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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import pymzml
def main():
"""
This function shows how to plot a simple spectrum. It can be directly
plotted via this script or using the python console.
usage:
./plot_spectrum.py
"""
example_file = os.path.join(
os.path.dirname(__file__), os.pardir, "tests", "data", "example.mzML"
)
run = pymzml.run.Reader(example_file)
p = pymzml.plot.Factory()
for spec in run:
p.new_plot()
p.add(spec.peaks("centroided"), color=(0, 0, 0), style="sticks", name="peaks")
filename = "example_plot_{0}_{1}.html".format(
os.path.basename(example_file), spec.ID
)
p.save(
filename=filename,
layout={
"xaxis":{
"ticks": 'outside',
"ticklen": 2,
"tickwidth": 0.25,
"showgrid": False,
"linecolor": 'black',
},
"yaxis": {
"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)',
},
)
print("Plotted file: {0}".format(filename))
break
if __name__ == "__main__":
main()
|
