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#!/usr/bin/env python3.4
# encoding: utf-8
"""
Plot a test spectrum for different plotting styles
"""
import pymzml
import os
import sys
import test_file_paths
from pymzml.plot import Factory
import unittest
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)
if __name__ == "__main__":
unittest.main(verbosity=3)
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