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
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
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
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
class PlotTest(unittest.TestCase):
"""
"""
def setUp(self):
self.paths = test_file_paths.paths
self.path = self.paths[2]
self.Run = pymzml.run.Reader(self.path)
self.spec = self.Run[6]
self.layout = {
"font": {"family": "Arial", "size": 20, "color": "#000000"},
"autosize": False,
"width": 1700,
"height": 700,
"margin": {"l": 100, "r": 80, "t": 100, "b": 60},
# 'separatethousands' : False,
# 'autoexpand':True,
"xaxis1": {
"type": "linear",
"color": "#000000",
"title": "<i>m/z</i>",
"titlefont": {"family": "Arial", "size": 24, "color": "#000000"},
"tickmode": "auto",
"nticks": 0,
"tickprefix": "",
"ticksuffix": "",
"showticklabels": True,
"tickfont": {"family": "Arial", "size": 20, "color": "rgb(0, 0, 0)"},
"tickangle": "auto",
"tickformat": "",
"showexponent": "all",
"exponentformat": "B",
"ticklen": 5,
"tickwidth": 1,
"tickcolor": "#000000",
"ticks": "outside",
"showline": True,
"mirror": False,
"showgrid": False,
"zerolinecolor": "rgb(0, 0, 0)",
"zerolinewidth": 1,
"zeroline": False,
"anchor": "y",
"side": "bottom",
"tick0": 0,
"dtick": 100,
},
"yaxis1": {
"type": "linear",
"color": "#000000",
"title": "Intensity",
"titlefont": {"family": "Arial", "size": 24, "color": "#000000"},
"nticks": 0,
"tickprefix": "",
"ticksuffix": "",
"showticklabels": True,
"tickfont": {"family": "Arial", "size": 20, "color": "rgb(0, 0, 0)"},
"tickangle": "auto",
"tickformat": "",
"showexponent": "all",
"exponentformat": "B",
# 'separatethousands' : True,
"ticklen": 5,
"tickwidth": 1,
"tickcolor": "#000000",
"ticks": "outside",
"showline": True,
"mirror": False,
"showgrid": False,
"zerolinecolor": "rgb(0, 0, 0)",
"zerolinewidth": 1,
"zeroline": False,
"anchor": "x",
"side": "left",
"tick0": 0,
"dtick": 20000000,
},
"legend": {
"bgcolor": "#fff",
"bordercolor": "#444",
"borderwidth": 0,
"font": {"family": "Arial", "size": 20, "color": "#000000"},
"orientation": "v",
"traceorder": "normal",
"x": 1.02,
"xanchor": "left",
"y": 1,
"yanchor": "auto",
},
}
self.test_styles = [
("lines", (200, 200, 200), "solid", 0.8, None, None),
("sticks", (200, 0, 0), "solid", 0.8, None, (200, 300)),
("points", (0, 0, 200), "solid", 0.8, None, None),
("label.sticks", (0, 0, 200), "dot", 0.8, None, None),
("triangle.big", (200, 0, 200), "solid", 0.8, None, None),
("triangle.small", (200, 0, 0), "solid", 0.8, None, None),
("label.triangle.MS_precision", (0, 200, 0), "dash", 0.8, None, None),
("label.spline", (0, 200, 0), "dash", 0.3, None, None),
("label.triangle.small", (0, 200, 0), "solid", 0.8, None, None),
("label.linear.bottom", (0, 200, 100), "solid", 0.8, self.layout, None),
]
self.pf = Factory()
self.file_name = os.path.join(os.path.dirname(self.path), "test_plot.html")
def test_new_plot(self):
self.pf.new_plot(MS_precision="100e-6", title="test")
self.assertEqual(self.pf.MS_precisions[0], "100e-6")
self.assertEqual(self.pf.titles[0], "test")
self.pf.new_plot()
self.assertEqual(len(self.pf.plots), 2)
self.assertEqual(self.pf.MS_precisions[1], "5e-6")
self.assertEqual(self.pf.titles[1], None)
self.pf = Factory()
def test_add_plots(self):
for plotnumber, plot in enumerate(self.test_styles):
self.pf.new_plot()
style, color, dash, opacity, layout, mz_range = plot
split_style = style.split(".")
if split_style[0] == "label":
self.pf.add(
self.spec.highest_peaks(100),
color=(200, 200, 200),
style="lines",
name="datapoints",
title="test spec plot",
plot_num=plotnumber,
mz_range=mz_range,
)
label_list = []
for peak in self.spec.highest_peaks(100):
label_list.append((peak[0], 100, "spline_top", "label"))
self.pf.add(
label_list,
color=color,
style=style,
name="Label",
opacity=opacity,
dash=dash,
title="test spec plot",
plot_num=plotnumber,
mz_range=mz_range,
)
self.assertEqual(len(self.pf.plots[plotnumber]), 2)
else:
peak_list = self.spec.highest_peaks(100)
self.pf.add(
peak_list,
color=color,
style=style,
name="Label",
opacity=opacity,
dash=dash,
title="test spec plot",
plot_num=plotnumber,
mz_range=mz_range,
)
self.assertEqual(
self.pf.plots[plotnumber][-1]["line"]["color"],
"rgba({0}, {1}, {2}, {3})".format(
color[0], color[1], color[2], opacity
),
)
self.assertEqual(self.pf.plots[plotnumber][-1]["line"]["dash"], dash)
if "label" in style:
if "spline" in style:
mode = "lines+markers+text"
else:
mode = "text+lines"
elif style == "points":
mode = "markers"
else:
mode = "lines"
self.assertEqual(self.pf.plots[plotnumber][-1]["mode"], mode)
if mz_range is not None:
self.assertLessEqual(self.pf.x_max[plotnumber], mz_range[1])
self.assertEqual(len(self.pf.plots), len(self.test_styles))
def test_save_plot(self):
self.pf.add(
self.spec.highest_peaks(100),
color=(200, 200, 200),
style="sticks",
name="datapoints",
)
self.pf.save(filename=self.file_name, layout=self.layout)
self.assertTrue(os.path.exists(self.file_name))
def tearDown(self):
if os.path.exists(self.file_name):
os.remove(self.file_name)
class PlotTest(unittest.TestCase):
"""
"""
def setUp(self):
self.paths = test_file_paths.paths
self.path = self.paths[2]
self.Run = pymzml.run.Reader(self.path)
self.spec = self.Run[6]
self.layout = {
"font": {
"family": "Arial",
"size": 20,
"color": "#000000"
},
"autosize": False,
"width": 1700,
"height": 700,
"margin": {
"l": 100,
"r": 80,
"t": 100,
"b": 60
},
# 'separatethousands' : False,
# 'autoexpand':True,
"xaxis1": {
"type": "linear",
"color": "#000000",
"title": "<i>m/z</i>",
"titlefont": {
"family": "Arial",
"size": 24,
"color": "#000000"
},
"tickmode": "auto",
"nticks": 0,
"tickprefix": "",
"ticksuffix": "",
"showticklabels": True,
"tickfont": {
"family": "Arial",
"size": 20,
"color": "rgb(0, 0, 0)"
},
# "tickangle": "auto",
"tickformat": "",
"showexponent": "all",
"exponentformat": "B",
"ticklen": 5,
"tickwidth": 1,
"tickcolor": "#000000",
"ticks": "outside",
"showline": True,
"mirror": False,
"showgrid": False,
"zerolinecolor": "rgb(0, 0, 0)",
"zerolinewidth": 1,
"zeroline": False,
"anchor": "y",
"side": "bottom",
"tick0": 0,
"dtick": 100,
},
"yaxis1": {
"type": "linear",
"color": "#000000",
"title": "Intensity",
"titlefont": {
"family": "Arial",
"size": 24,
"color": "#000000"
},
"nticks": 0,
"tickprefix": "",
"ticksuffix": "",
"showticklabels": True,
"tickfont": {
"family": "Arial",
"size": 20,
"color": "rgb(0, 0, 0)"
},
# "tickangle": "auto",
"tickformat": "",
"showexponent": "all",
"exponentformat": "B",
# 'separatethousands' : True,
"ticklen": 5,
"tickwidth": 1,
"tickcolor": "#000000",
"ticks": "outside",
"showline": True,
"mirror": False,
"showgrid": False,
"zerolinecolor": "rgb(0, 0, 0)",
"zerolinewidth": 1,
"zeroline": False,
"anchor": "x",
"side": "left",
"tick0": 0,
"dtick": 20000000,
},
"legend": {
"bgcolor": "#fff",
"bordercolor": "#444",
"borderwidth": 0,
"font": {
"family": "Arial",
"size": 20,
"color": "#000000"
},
"orientation": "v",
"traceorder": "normal",
"x": 1.02,
"xanchor": "left",
"y": 1,
"yanchor": "auto",
},
}
self.test_styles = [
("lines", (200, 200, 200), "solid", 0.8, None, None),
("sticks", (200, 0, 0), "solid", 0.8, None, (200, 300)),
("points", (0, 0, 200), "solid", 0.8, None, None),
("label.sticks", (0, 0, 200), "dot", 0.8, None, None),
("triangle.big", (200, 0, 200), "solid", 0.8, None, None),
("triangle.small", (200, 0, 0), "solid", 0.8, None, None),
("label.triangle.MS_precision", (0, 200, 0), "dash", 0.8, None,
None),
("label.spline", (0, 200, 0), "dash", 0.3, None, None),
("label.triangle.small", (0, 200, 0), "solid", 0.8, None, None),
("label.linear.bottom", (0, 200, 100), "solid", 0.8, self.layout,
None),
]
self.pf = Factory()
self.file_name = os.path.join(os.path.dirname(self.path),
"test_plot.html")
def test_new_plot(self):
self.pf.new_plot(MS_precision="100e-6", title="test")
self.assertEqual(self.pf.MS_precisions[0], "100e-6")
self.assertEqual(self.pf.titles[0], "test")
self.pf.new_plot()
self.assertEqual(len(self.pf.plots), 2)
self.assertEqual(self.pf.MS_precisions[1], "5e-6")
self.assertEqual(self.pf.titles[1], None)
self.pf = Factory()
def test_add_plots(self):
for plotnumber, plot in enumerate(self.test_styles):
self.pf.new_plot()
style, color, dash, opacity, layout, mz_range = plot
split_style = style.split(".")
if split_style[0] == "label":
self.pf.add(
self.spec.highest_peaks(100),
color=(200, 200, 200),
style="lines",
name="datapoints",
title="test spec plot",
plot_num=plotnumber,
mz_range=mz_range,
)
label_list = []
for peak in self.spec.highest_peaks(100):
label_list.append((peak[0], 100, "spline_top", "label"))
self.pf.add(
label_list,
color=color,
style=style,
name="Label",
opacity=opacity,
dash=dash,
title="test spec plot",
plot_num=plotnumber,
mz_range=mz_range,
)
self.assertEqual(len(self.pf.plots[plotnumber]), 2)
else:
peak_list = self.spec.highest_peaks(100)
self.pf.add(
peak_list,
color=color,
style=style,
name="Label",
opacity=opacity,
dash=dash,
title="test spec plot",
plot_num=plotnumber,
mz_range=mz_range,
)
self.assertEqual(
self.pf.plots[plotnumber][-1]["line"]["color"],
"rgba({0},{1},{2},{3})".format(color[0], color[1], color[2],
opacity),
)
self.assertEqual(self.pf.plots[plotnumber][-1]["line"]["dash"],
dash)
if "label" in style:
if "spline" in style:
mode = "lines+markers+text"
else:
mode = "text+lines"
elif style == "points":
mode = "markers"
else:
mode = "lines"
self.assertEqual(self.pf.plots[plotnumber][-1]["mode"], mode)
if mz_range is not None:
self.assertLessEqual(self.pf.x_max[plotnumber], mz_range[1])
self.assertEqual(len(self.pf.plots), len(self.test_styles))
def test_save_plot(self):
self.pf.add(
self.spec.highest_peaks(100),
color=(200, 200, 200),
style="sticks",
name="datapoints",
)
self.pf.save(filename=self.file_name, layout=self.layout)
self.assertTrue(os.path.exists(self.file_name))
def tearDown(self):
if os.path.exists(self.file_name):
os.remove(self.file_name)
class PlotTest(unittest.TestCase):
'''
'''
def setUp(self):
self.paths = test_file_paths.paths
self.path = self.paths[2]
self.Run = pymzml.run.Reader(self.path)
self.spec = self.Run[6]
self.layout = {
'font' : {
'family' : 'Arial',
'size' : 20,
'color' : '#000000',
},
'autosize' : False,
'width' : 1700,
'height' : 700,
'margin' : {
'l' : 100,
'r' : 80,
't' : 100,
'b' : 60,
},
# 'separatethousands' : False,
# 'autoexpand':True,
'xaxis1' : {
'type' : 'linear',
'color' : '#000000',
'title' : '<i>m/z</i>',
'titlefont' : {
'family' : 'Arial',
'size' : 24,
'color' : '#000000',
},
'tickmode' : 'auto',
'nticks' : 0,
'tickprefix' : '',
'ticksuffix' : '',
'showticklabels' : True,
'tickfont' : {
'family' : 'Arial',
'size' : 20,
'color' : 'rgb(0, 0, 0)',
},
'tickangle' : 'auto',
'tickformat' : '',
'showexponent' : 'all',
'exponentformat' : 'B',
'ticklen' : 5,
'tickwidth' : 1,
'tickcolor' : '#000000',
'ticks' : 'outside',
'showline' : True,
'mirror' : False,
'showgrid' : False,
'zerolinecolor' : 'rgb(0, 0, 0)',
'zerolinewidth' : 1,
'zeroline' : False,
'anchor' : 'y',
'side' : 'bottom',
'tick0' : 0,
'dtick' : 100,
},
'yaxis1' : {
'type' : 'linear',
'color' : '#000000',
'title' : 'Intensity',
'titlefont' : {
'family' : 'Arial',
'size' : 24,
'color' : '#000000',
},
'nticks' : 0,
'tickprefix' : '',
'ticksuffix' : '',
'showticklabels' : True,
'tickfont' : {
'family' : 'Arial',
'size' : 20,
'color' : 'rgb(0, 0, 0)',
},
'tickangle' : 'auto',
'tickformat' : '',
'showexponent' : 'all',
'exponentformat' : 'B',
# 'separatethousands' : True,
'ticklen' : 5,
'tickwidth' : 1,
'tickcolor' : '#000000',
'ticks' : 'outside',
'showline' : True,
'mirror' : False,
'showgrid' : False,
'zerolinecolor' : 'rgb(0, 0, 0)',
'zerolinewidth' : 1,
'zeroline' : False,
'anchor' : 'x',
'side' : 'left',
'tick0' : 0,
'dtick' : 20000000,
},
'legend' : {
'bgcolor' : '#fff',
'bordercolor' : '#444',
'borderwidth' : 0,
'font' : {
'family' : 'Arial',
'size' : 20,
'color' : '#000000',
},
'orientation' : 'v',
'traceorder' : 'normal',
'x' : 1.02,
'xanchor' : 'left',
'y' : 1,
'yanchor' : 'auto',
},
}
self.test_styles = [
(
'lines', (200,200,200), 'solid', 0.8, None, None
),
(
'sticks', (200,0,0), 'solid', 0.8, None, (200, 300)
),
(
'points', (0,0,200), 'solid', 0.8, None, None
),
(
'label.sticks', (0,0,200), 'dot', 0.8, None, None
),
(
'triangle.big', (200,0,200), 'solid', 0.8, None, None
),
(
'triangle.small', (200,0,0), 'solid', 0.8, None, None
),
(
'label.triangle.MS_precision', (0,200,0), 'dash', 0.8, None, None
),
(
'label.spline', (0,200,0), 'dash', 0.3, None, None
),
(
'label.triangle.small', (0,200,0), 'solid', 0.8, None, None
),
(
'label.linear.bottom', (0,200,100), 'solid', 0.8, self.layout, None
),
]
self.pf = Factory()
self.file_name = os.path.join(
os.path.dirname(self.path),
'test_plot.html'
)
def test_new_plot(self):
self.pf.new_plot(
MS_precision='100e-6',
title="test",
)
self.assertEqual(self.pf.MS_precisions[0],'100e-6')
self.assertEqual(self.pf.titles[0],'test')
self.pf.new_plot()
self.assertEqual(len(self.pf.plots), 2)
self.assertEqual(self.pf.MS_precisions[1],'5e-6')
self.assertEqual(self.pf.titles[1],None)
self.pf = Factory()
def test_add_plots(self):
for plotnumber, plot in enumerate(self.test_styles):
self.pf.new_plot()
style, color, dash, opacity, layout, mz_range = plot
split_style = style.split('.')
if split_style[0] == 'label':
self.pf.add(
self.spec.highest_peaks(100),
color = (200,200,200),
style = 'lines',
name = 'datapoints',
title = 'test spec plot',
plot_num = plotnumber,
mz_range = mz_range
)
label_list = []
for peak in self.spec.highest_peaks(100):
label_list.append((
peak[0],
100,
'spline_top',
'label',
))
self.pf.add(
label_list,
color = color,
style = style,
name = 'Label',
opacity = opacity,
dash = dash,
title = 'test spec plot',
plot_num = plotnumber,
mz_range = mz_range
)
self.assertEqual(len(self.pf.plots[plotnumber]),2)
else:
peak_list = self.spec.highest_peaks(100)
self.pf.add(
peak_list,
color = color,
style = style,
name = 'Label',
opacity = opacity,
dash = dash,
title = 'test spec plot',
plot_num = plotnumber,
mz_range = mz_range
)
self.assertEqual(
self.pf.plots[plotnumber][-1]['line']['color'],
'rgba({0}, {1}, {2}, {3})'.format(
color[0],
color[1],
color[2],
opacity
),
)
self.assertEqual(self.pf.plots[plotnumber][-1]['line']['dash'], dash)
if 'label' in style:
if 'spline' in style:
mode = 'lines+markers+text'
else:
mode = 'text+lines'
elif style == 'points':
mode = 'markers'
else:
mode = 'lines'
self.assertEqual(self.pf.plots[plotnumber][-1]['mode'], mode)
if mz_range is not None:
self.assertLessEqual(
self.pf.x_max[plotnumber],
mz_range[1]
)
self.assertEqual(len(self.pf.plots), len(self.test_styles))
def test_save_plot(self):
self.pf.add(self.spec.highest_peaks(100), color=(200,200,200), style='sticks', name='datapoints')
self.pf.save(filename=self.file_name, layout=self.layout)
self.assertTrue(os.path.exists(self.file_name))
def tearDown(self):
if os.path.exists(self.file_name):
os.remove(self.file_name)
def main():
peak_props = {
"inosine": {
"trivial_name": "inosine",
"chemical_formula": "+C(10)H(12)N(4)O(5)",
"charge": 2,
"scan_start_time": 0,
"peak_width": 30, # seconds
"peak_function": "gauss_tail",
"peak_params": {
"sigma": 3
},
"peak_scaling_factor": 1e6,
},
"+C(9)H(12)N(2)O(6)": {
"trivial_name": "pseudouridine",
"charge": 2,
"scan_start_time": 30,
"peak_width": 30, # seconds
"peak_function": "gauss_tail",
"peak_scaling_factor": 2e6,
"peak_params": {
"sigma": 3
},
},
"+C(10)H(13)N(5)O(7)": {
"trivial_name": "spiroiminodihydantoin",
"charge": 2,
"scan_start_time": 60,
"peak_width": 30, # seconds
"peak_function": "gauss_tail",
"peak_params": {
"sigma": 3
},
"peak_scaling_factor": 3e6,
}
}
mzml_params = {
"gradient_length": 30,
"min_intensity": 1,
}
fragmentor = NucleosideFragmentor()
noise_injector = UniformNoiseInjector()
noise_injector = UniformNoiseInjector(dropout=0.0,
ppm_noise=0,
intensity_noise=0)
noise_injector = JamssNoiseInjector()
file = NamedTemporaryFile("wb")
mzml_path = write_mzml(file, peak_props, fragmentor, noise_injector,
mzml_params)
reader = pymzml.run.Reader(mzml_path)
tic_tuples = []
for pos, spec in enumerate(reader):
if spec.ms_level == 1:
scan_time, scan_unit = spec.scan_time
if scan_unit == "second":
scan_time /= 60
tic_tuples.append((scan_time, spec.TIC))
pf = Factory()
pf.new_plot()
pf.add(tic_tuples, color=(0, 0, 0), style="lines", title="TIC")
pf.save(
"example_chromatogram.html",
layout={
"xaxis": {
"title": "Retention time [minutes]"
},
"yaxis": {
"title": "TIC"
},
},
)