def test_plotting_construct():
"""Test that a construct can be plotted."""
renderer = psv.GlyphRenderer()
fig, ax = plt.subplots()
construct = psv.Construct([["RibosomeEntrySite", None, None]],
renderer,
fig=fig,
ax=ax,
start_position=(0, 0),
gapsize=20,
padding=10)
fig, ax, baseline_start, baseline_end, bounds = construct.draw()
ax.plot([baseline_start[0], baseline_end[0]],
[baseline_start[1], baseline_end[1]],
color=(0, 0, 0),
linewidth=1.5,
zorder=0)
def test_plotting_interactions():
"""Test loading glyphs from SVGs with no errors/exceptions."""
renderer = psv.GlyphRenderer()
part_list = [["Promoter", None, None], ["Promoter", None, None]]
int_list = [[
part_list[0], part_list[1], 'inhibition', {
'color': (1, 0, 0),
'headheight': 13.0,
'headwidth': 14.0,
'zorder': 2,
'direction': 'forward',
'linewidth': 2.0,
'heightskew': 15.0,
'sending_length_skew': 3.0,
'receiving_length_skew': 4.0,
'distance_from_baseline': 27.0
}
]]
construct = psv.Construct(part_list, renderer, interaction_list=int_list)
fig, ax, baseline_start, baseline_end, bounds = construct.draw()
def test_plotting_glyph():
"""Test that a single glyph with parameters, style, and rotation can be plotted."""
renderer = psv.GlyphRenderer()
fig, ax = plt.subplots()
ax.set_ylim([0, 100])
ax.set_xlim([0, 100])
user_parameters = {}
user_parameters = {'arrowbody_height': 15}
cds_style = {}
cds_style = {
'cds': {
'facecolor': (0, 0, 1),
'edgecolor': (1, 1, 0),
'linewidth': 10
}
}
bounds, end_point = renderer.draw_glyph(ax,
'CDS', (50, 50),
user_parameters=user_parameters,
user_style=cds_style,
rotation=3.142 / 3)
#!/usr/bin/env python
"""
Basic example of plotting parametric SBOL Visual glyphs using the parasbolv library.
"""
import parasbolv as psv
import matplotlib.pyplot as plt
# Generate Matplotlib Figure and Axes
fig = plt.figure(figsize=(6, 6))
ax = fig.add_axes([0.0, 0.0, 1.0, 1.0], frameon=False, aspect=1)
# Generate renderer object
renderer = psv.GlyphRenderer()
# Draw Insulator
insulator_style = {}
insulator_style['insulator-inner-path'] = {'facecolor': (1, 0, 0)}
insulator_style['insulator-outer-path'] = {
'edgecolor': (0, 1, 0),
'linewidth': 5
}
bounds, end_point = renderer.draw_glyph(ax,
'Insulator', (10, 20),
user_style=insulator_style)
# Draw Ribosome Entry Site
bounds, end_point = renderer.draw_glyph(ax, 'RibosomeEntrySite', (20, 50))
# Draw CDS 1
user_parameters = {}
#!/usr/bin/env python
"""
Basic example of plotting parametric SBOL Visual glyphs using the parasbolv library.
"""
import parasbolv as psv
import matplotlib.pyplot as plt
__author__ = 'Thomas E. Gorochowski <*****@*****.**>'
__license__ = 'MIT'
__version__ = '1.0'
renderer = psv.GlyphRenderer(glyph_path='../glyphs/')
p = renderer.get_baseline_end('RibosomeEntrySite', (0.5, 40), rotation=1.0)
print(renderer.get_glyph_bounds('RibosomeEntrySite', (0.5, 40), rotation=1.0))
fig = plt.figure(figsize=(6, 6))
ax = fig.add_axes([0.0, 0.0, 1.0, 1.0], frameon=False, aspect=1)
user_parameters = {}
user_parameters['arrowbody_width'] = 50
insulator_style = {}
insulator_style['insulator-inner-path'] = {'facecolor': (1, 0, 0)}
insulator_style['insulator-outer-path'] = {
'edgecolor': (0, 1, 0),
'linewidth': 5
}
renderer.draw_glyph(ax,
'Insulator', (10, 20),
user_parameters=user_parameters,