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 render_input(string, rotation, gapsize, interaction, save, savetype, savepath, fill):
"""Renders a construct from an input string.
Parameters
----------
string: str
Input string containing construct details.
rotation: str
String containing expression of rotation
to be evaluated
gapsize: float
Size of the gap between construct parts.
interaction: str
String to be processed defining either
a single or multiple interactions.
"""
parts = parse_string(string)
part_list = format_parts(parts, renderer, fill)
if rotation != '':
rotation = safe_eval(rotation)
else:
rotation = 0.0
if interaction != '':
interaction = process_interactions(interaction, part_list)
else:
interaction = None
construct = psv.Construct(part_list, renderer, rotation=rotation, gapsize = gapsize, interaction_list = interaction)
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)
if save == 1:
filename = f'pSBOLv-cli-output.{savetype}'
if savepath != '':
filename = f'{savepath}/{filename}'
fig.savefig(filename, dpi=300)
else:
plt.show()
part_list.append([part, None, None])
part_list.append([part, {'orientation': 'reverse'}, None])
length = len(part_list)
r = length % 12
number_of_rows = int((length - r) / 12)
for n in range(number_of_rows + 1):
parts_to_draw = part_list[n * 12:((n + 1) * 12)]
if len(parts_to_draw) == 0:
break
start_position = (start_position[0], start_position[1] - 40)
construct = psv.Construct(parts_to_draw,
renderer,
fig=fig,
ax=ax,
start_position=start_position,
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)
bounds_list.append(bounds)
# Plot glyphs not on backbone
parts = list(renderer.glyphs_library.keys())
part_list = []
[part_list[0], part_list[1], 'inhibition', {
'color': (0.75, 0, 0)
}])
interaction_list.append([
part_list[2], part_list[3], 'control', {
'color': (0, 0.75, 0),
'direction': 'reverse'
}
])
# Create renderer
renderer = psv.GlyphRenderer()
# Plot Construct
construct = psv.Construct(part_list,
renderer,
interaction_list=interaction_list)
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)
# You can also manually plot interactions:
# interaction_bounds = psv.draw_interaction(ax, ((50, 15), (50, 15)), ((60, 15), (60, 15)), 'process', None)
fig.savefig('06_draw_interactions.pdf', transparent=True, dpi=300)
fig.savefig('06_draw_interactions.jpg', dpi=300)
plt.show()
gff_el[5]['style_parameters']
])
else:
if 'user_parameters' in gff_el[5]:
part_list.append(
[gff_el[1], gff_el[5]['user_parameters'], None])
else:
part_list.append(
[gff_el[1], None, gff_el[5]['style_parameters']])
return part_list
part_list = load_part_list_from_gff('./04_plot_gff.gff',
'chrom1',
type_map=gffsvgtype_map)
renderer = psv.GlyphRenderer()
construct = psv.Construct(part_list, renderer)
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)
fig.savefig('04_plot_gff.pdf', transparent=True, dpi=300)
fig.savefig('04_plot_gff.jpg', dpi=300)
plt.show()
None,
None
] )
part_list.append( ['CDS',
{'orientation':'reverse'},
None
] )
part_list.append( ['CDS',
{'orientation':'reverse'},
None
] )
# Create renderer
renderer = psv.GlyphRenderer()
# Draw construct
construct = psv.Construct(part_list, renderer)
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)
# Draw rotated construct
construct_2 = psv.Construct(part_list, renderer, fig=fig, ax=ax, start_position=(0,-30), additional_bounds_list=[bounds])
construct_2.rotation = 3.142 / -8
construct_2.update_bounds() # Update bounds to new orientation of construct
fig, ax, baseline_start, baseline_end, bounds = construct_2.draw()
ax.plot([baseline_start[0], baseline_end[0]], [baseline_start[1], baseline_end[1]], color=(0,0,0), linewidth=1.5, zorder=0)
fig.savefig('03_plot_constructs.pdf', transparent=True, dpi=300)
fig.savefig('03_plot_constructs.jpg', dpi=300)
plt.show()
