biocomputelab / parasbolv Goto Github PK

import parasbolv as psv
import matplotlib.pyplot as plt
from collections import namedtuple

Part = namedtuple('part', ['glyph_type', 'orientation',  'user_parameters', 'style_parameters'])
Interaction = namedtuple('interaction', ['starting_glyph', 'ending_glyph', 'interaction_type', 'interaction_parameters'])


part_list = []
part_list.append(Part('CDS',
                     'forward', 
                      None,
                      {'cds': {'facecolor': (1, 0.5, 0.5), 'edgecolor': (1,0,0), 'linewidth': 2}}
                      ) )

part_list.append(Part('Terminator', 'forward', None, None))
part_list.append(Part("Promoter", "forward", None, None))

part_list.append(Part('CDS',
                     'forward', 
                      None,
                      {'cds': {'facecolor': (1, 0.5, 0.5), 'edgecolor': (1,0,0), 'linewidth': 2}}
                      ) )

part_list.append(Part('Terminator', 'forward', None, None))
part_list.append(Part("Promoter", "forward", None, None))


# Create renderer
renderer = psv.GlyphRenderer()


# Create list of interactions to pass to render_part_list
interaction_list = []
interaction_list.append(Interaction(part_list[0], part_list[2], 'inhibition', {'color': (0.75,0,0)}))

# interaction_list.append(Interaction(part_list[0], part_list[1], 'inhibition', {'color': (0.75,0,0)}))
# interaction_list.append(Interaction(part_list[2], part_list[4], 'control', {'color': (0, 0.75, 0),
#                                                                             'direction':'reverse'}))


# Plot Construct
error_case = True

if error_case:
    fig, axes = plt.subplots(ncols=1, nrows=2)
    ax = axes[0]
    figure_name = "errornous_visualization.png"
else:
    fig, axes = plt.subplots(ncols=1, nrows=1)
    ax = axes
    figure_name = "intended_visualization.png"
construct = psv.Construct(part_list, renderer, interaction_list=interaction_list, fig=fig, ax=ax, start_position=(0, 0))
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, ((120, 15), (50, 0)), ((60, 0), (60, 0)), 'process', None)


plt.savefig(figure_name)
plt.show()