def plot_results(self, results, agent, obs_name, thresh=50):
plt.figure()
plt.ion()
max_val_lim = max(max(numpy.max(results[0][1][obs_name]), 101.0),
thresh)
max_time = max([result[0][-1] for result in results])
lr = matplotlib.patches.Rectangle((0, 0),
max_time,
thresh,
color='red',
alpha=0.1)
hr = matplotlib.patches.Rectangle((0, thresh),
max_time,
max_val_lim - thresh,
color='green',
alpha=0.1)
ax = plt.gca()
ax.add_patch(lr)
ax.add_patch(hr)
if thresh + 5 < max_val_lim:
plt.text(10, thresh + 5, 'High', fontsize=10)
plt.text(10, thresh - 5, 'Low')
for tspan, yobs in results:
plt.plot(tspan, yobs[obs_name])
plt.ylim(-1, max_val_lim)
plt.xlim(-100, 10100)
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent)
plt.title('Simulation results for %s' % agent_str)
dir_path = os.path.dirname(os.path.realpath(__file__))
fig_path = os.path.join(dir_path, '%s.png' % obs_name)
plt.savefig(fig_path)
return fig_path
def test_agent_bound_mixed():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), False)
a = Agent('EGFR', bound_conditions=[bc, bc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF and not bound to EGFR')
def test_agent_bound_mixed():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), False)
a = Agent('EGFR', bound_conditions=[bc, bc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF and not bound to EGFR')
def test_agent_mods3():
mc1 = ModCondition('phosphorylation', 'tyrosine', '1111')
mc2 = ModCondition('phosphorylation')
a = Agent('EGFR', mods=[mc1, mc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111 and an unknown residue')
def test_agent_mods3():
mc1 = ModCondition('phosphorylation', 'tyrosine', '1111')
mc2 = ModCondition('phosphorylation')
a = Agent('EGFR', mods=[mc1, mc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111 and an unknown residue')
def test_agent_bound_three():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), True)
bc3 = BoundCondition(Agent('GRB2'), True)
a = Agent('EGFR', bound_conditions=[bc, bc2, bc3])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF, EGFR and GRB2')
def test_agent_bound_three():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), True)
bc3 = BoundCondition(Agent('GRB2'), True)
a = Agent('EGFR', bound_conditions=[bc, bc2, bc3])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF, EGFR and GRB2')
def plot_compare_conditions(self, ts, results, agent, obs_name):
plt.figure()
plt.ion()
plt.plot(ts, results[0][:len(ts)], label='Without condition')
plt.plot(ts, results[-1][:len(ts)], label='With condition')
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent)
plt.title('Simulation results for %s' % agent_str)
plt.legend()
dir_path = os.path.dirname(os.path.realpath(__file__))
fig_path = os.path.join(dir_path, '%s.png' % obs_name)
plt.savefig(fig_path)
return fig_path
def test_agent_mod3():
mc = ModCondition('phosphorylation', 'tyrosine', '1111')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111')
def test_agent_loc():
a = Agent('BRAF', location='cytoplasm')
print(ea._assemble_agent_str(a))
assert (ea._assemble_agent_str(a) == 'BRAF in the cytoplasm')
def test_agent_mod():
mc = ModCondition('phosphorylation')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'phosphorylated EGFR')
def test_agent_activity():
a = Agent('BRAF', activity=ActivityCondition('activity', True))
print(ea._assemble_agent_str(a))
assert (ea._assemble_agent_str(a) == 'active BRAF')
def test_agent_mut_plus():
a = Agent('BRAF',
mutations=[MutCondition('600', 'V', 'E')],
location='nucleus')
print(ea._assemble_agent_str(a))
assert (ea._assemble_agent_str(a) == 'BRAF-V600E in the nucleus')
def test_agent_not_bound():
bc = BoundCondition(Agent('EGF'), False)
a = Agent('EGFR', bound_conditions=[bc])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR not bound to EGF')
def test_agent_basic():
s = ea._assemble_agent_str(Agent('EGFR'))
print(s)
assert (s == 'EGFR')
def test_agent_basic():
s = ea._assemble_agent_str(Agent('EGFR'))
print(s)
assert (s == 'EGFR')
def test_agent_loc():
a = Agent('BRAF', location='cytoplasm')
print(ea._assemble_agent_str(a))
assert(ea._assemble_agent_str(a) == 'BRAF in the cytoplasm')
def test_agent_not_bound():
bc = BoundCondition(Agent('EGF'), False)
a = Agent('EGFR', bound_conditions=[bc])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR not bound to EGF')
def test_agent_mod3():
mc = ModCondition('phosphorylation', 'tyrosine', '1111')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111')
def test_agent_mut():
a = Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')])
print(ea._assemble_agent_str(a))
assert (ea._assemble_agent_str(a) == 'BRAF-V600E')
def test_agent_mod():
mc = ModCondition('phosphorylation')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'phosphorylated EGFR')
