def species_graph(self):
graph = pygraphviz.AGraph(start=20, directed=True, rankdir="LR", labelloc='t', fontsize=50, label='EARM flux',
bgcolor='gray')
for idx, cp in enumerate(self.model.species):
species_node = 's%d' % idx
graph.add_node(species_node,
label=parse_name(self.model.species[idx]),
shape="Mrecord",
fillcolor="#ccffcc", style="filled", color="transparent",
fontsize="35",
margin="0.06,0")
for reaction in self.model.reactions_bidirectional:
reactants = set(reaction['reactants'])
products = set(reaction['products'])
# attr_reversible = {'arrowsize': 2, 'penwidth': 5}
attr_reversible = {'dir': 'both', 'arrowtail': 'empty', 'arrowsize': 1, 'penwidth': 5} if reaction[
'reversible'] else {'arrowsize': 1, 'penwidth': 5}
for s in reactants:
for p in products:
r_link(graph, s, p, **attr_reversible)
self.sp_graph = graph
return self.sp_graph
def visualization2(self, sp_to_vis=None):
if sp_to_vis:
species_ready = list(set(sp_to_vis).intersection(self.all_sp_signatures.keys()))
else:
raise Exception('list of driver species must be defined')
if not species_ready:
raise Exception('None of the input species is a driver')
for sp in species_ready:
# Setting up figure
plt.figure()
plt.subplot(313)
mon_val = OrderedDict()
signature = self.all_sp_signatures[sp]
for idx, mon in enumerate(list(set(signature))):
if mon[0] == 'C':
mon_val[self.all_comb[sp][mon] + (-1,)] = idx
else:
mon_val[self.all_comb[sp][mon]] = idx
mon_rep = [0] * len(signature)
for i, m in enumerate(signature):
if m[0] == 'C':
mon_rep[i] = mon_val[self.all_comb[sp][m] + (-1,)]
else:
mon_rep[i] = mon_val[self.all_comb[sp][m]]
# mon_rep = [mon_val[self.all_comb[sp][m]] for m in signature]
y_pos = numpy.arange(len(mon_val.keys()))
plt.scatter(self.tspan[1:], mon_rep)
plt.yticks(y_pos, mon_val.keys())
plt.ylabel('Monomials', fontsize=16)
plt.xlabel('Time(s)', fontsize=16)
plt.xlim(0, self.tspan[-1])
plt.ylim(0, max(y_pos))
plt.subplot(312)
for name in self.model.odes[sp].as_coefficients_dict():
mon = name
mon = mon.subs(self.param_values)
var_to_study = [atom for atom in mon.atoms(sympy.Symbol)]
arg_f1 = [numpy.maximum(self.mach_eps, self.y[str(va)][1:]) for va in var_to_study]
f1 = sympy.lambdify(var_to_study, mon)
mon_values = f1(*arg_f1)
mon_name = str(name).partition('__')[2]
plt.plot(self.tspan[1:], mon_values, label=mon_name)
plt.ylabel('Rate(m/sec)', fontsize=16)
plt.legend(bbox_to_anchor=(-0.1, 0.85), loc='upper right', ncol=1)
plt.subplot(311)
plt.plot(self.tspan[1:], self.y['__s%d' % sp][1:], label=parse_name(self.model.species[sp]))
plt.ylabel('Molecules', fontsize=16)
plt.legend(bbox_to_anchor=(-0.15, 0.85), loc='upper right', ncol=1)
plt.suptitle('Tropicalization' + ' ' + str(self.model.species[sp]))
# plt.show()
plt.savefig('s%d' % sp + '.png', bbox_inches='tight', dpi=400)
def species_graph(self):
graph = pygraphviz.AGraph(directed=True, rankdir="LR", labelloc='t', fontsize=50, label='EARM flux')
for idx, cp in enumerate(self.model.species):
species_node = 's%d' % idx
label = re.sub(r'% ', r'%\\l', str(cp))
label += '\\l'
rtn_product = False
rtn = False
prdt = False
all_reactants = []
for rctn in self.model.reactions:
if rctn['reverse'][0] is False:
all_reactants.append(rctn['reactants'])
all_reactants_flat = list(set([item for sublist in all_reactants for item in sublist]))
all_products = []
for rctn in self.model.reactions:
if rctn['reverse'][0] is False:
all_products.append(rctn['products'])
all_products_flat = list(set([item for sublist in all_products for item in sublist]))
if idx in all_reactants_flat:
rtn = True
if idx in all_products_flat:
prdt = True
if rtn and prdt:
rtn_product = True
if rtn_product:
color = "Cyan"
elif rtn:
color = "#FF00F6"
elif prdt:
color = "#90EE90"
else:
pass
graph.add_node(species_node,
label=parse_name(self.model.species[idx]),
shape="Mrecord",
fillcolor=color, style="filled", color="transparent",
fontsize="35",
margin="0.06,0")
for reaction in self.model.reactions:
reactants = set(reaction['reactants'])
products = set(reaction['products'])
attr_reversible = {'arrowsize': 2, 'penwidth': 5}
for s in reactants:
for p in products:
r_link(graph, s, p, **attr_reversible)
self.sp_graph = graph
return self.sp_graph
def test_exiled(self):
"""
Tests that
:return:
"""
input_str = 'You exiled playername'
expected = ['playername']
result = parse_name(input_str)
self.assertEqual(result, expected)
def test_assist(self):
"""
:return:
"""
input_str = 'You assisted in exiling playername'
expected = ['playername']
result = parse_name(input_str)
self.assertEqual(result, expected)
def test_disrupted(self):
"""
:return:
"""
input_str = 'You disrupted playername'
expected = ['playername']
result = parse_name(input_str)
self.assertEqual(result, expected)
async def lookup_enemy(self, name):
names = parse_name(name)
users = get_users(names)
try:
for user in users['data']:
clip = create_clip(user['id'])
await self.get_channel(config.DISCORD_CHANNEL
).send(clip['data']['edit_url'])
except Exception as e:
print('Error: ', e)
def render_reactions(self):
pysb.bng.generate_equations(self.model)
graph = OrderedGraph()
ic_species = [cp for cp, parameter in self.model.initial_conditions]
for i, cp in enumerate(self.model.species):
species_node = 's%d' % i
color = "#ccffcc"
# color species with an initial condition differently
if len([s for s in ic_species if s.is_equivalent_to(cp)]):
color = "#aaffff"
graph.add_node(species_node, attr_dict=
{'label': parse_name(self.model.species[i]),
'font-size': "35",
'shape': "roundrectangle",
'background-color': color})
for i, reaction in enumerate(self.model.reactions_bidirectional):
reaction_node = 'r%d' % i
graph.add_node(reaction_node, attr_dict=
{'label': reaction_node,
'font-size': "35",
'shape': "roundrectangle",
'background-color': "#D3D3D3"})
reactants = set(reaction['reactants'])
products = set(reaction['products'])
modifiers = reactants & products
reactants = reactants - modifiers
products = products - modifiers
attr_reversible = {'source-arrow-shape': 'DIAMOND', 'target-arrow-shape': 'ARROW',
'source-arrow-fill': 'hollow', 'width': 3} if reaction['reversible'] else {
'source-arrow-shape': 'NONE', 'width': 6, 'target-arrow-shape': 'ARROW'}
for s in reactants:
r_link_reactions(graph, s, i, **attr_reversible)
for s in products:
r_link_reactions(graph, s, i, _flip=True, **attr_reversible)
for s in modifiers:
r_link_reactions(graph, s, i, arrowhead="odiamond")
self.graph = graph
return self.graph
def render_species(self):
pysb.bng.generate_equations(self.model)
graph = OrderedGraph()
for idx, cp in enumerate(self.model.species):
species_node = 's%d' % idx
graph.add_node(species_node,
{'label': parse_name(self.model.species[idx]),
'font-size': "35",
'shape': "roundrectangle",
'background-color': "#ccffcc"})
for reaction in self.model.reactions_bidirectional:
reactants = set(reaction['reactants'])
products = set(reaction['products'])
attr_reversible = {'source-arrow-shape': 'DIAMOND', 'target-arrow-shape': 'ARROW',
'source-arrow-fill': 'hollow', 'width': 3} if reaction['reversible'] else {
'source-arrow-shape': 'NONE', 'width': 6, 'target-arrow-shape': 'ARROW'}
for s in reactants:
for p in products:
r_link_species(graph, s, p, **attr_reversible)
self.graph = graph
return self.graph
def species_graph(self):
graph = OrderedGraph(ankdir="LR")
for idx, cp in enumerate(self.model.species):
species_node = 's%d' % idx
graph.add_node(species_node,
label=parse_name(self.model.species[idx]),
shape="Mrecord",
fillcolor="#ccffcc", style="filled", color="transparent",
fontsize="35",
margin="0.06,0", start="1990-01-01", end="1993-01-01")
for reaction in self.model.reactions_bidirectional:
reactants = set(reaction['reactants'])
products = set(reaction['products'])
attr_reversible = {'dir': 'both', 'arrowtail': 'empty', 'arrowsize': 2, 'penwidth': 5} if reaction[
'reversible'] else {'arrowsize': 2, 'penwidth': 5}
for s in reactants:
for p in products:
r_link(graph, s, p, **attr_reversible)
self.sp_graph = graph
print(graph.edges(data=True))
return self.sp_graph
def visualization(self, driver_species=None):
# TODO increase figure size when there are too many monomials
tropical_system = self.tropical_eqs
if driver_species:
species_ready = list(set(driver_species).intersection(self.tro_species.keys()))
else:
raise Exception('list of driver species must be defined')
if not species_ready:
raise Exception('None of the input species is a driver')
colors = sns.color_palette("Set2", max([len(ode.as_coeff_add()[1]) for ode in self.model.odes]))
sep = len(self.tspan) / 1
for sp in species_ready:
si_flux = 0
plt.figure()
plt.subplot(313)
monomials = []
monomials_inf = self.mon_names[sp]
for idx, name in enumerate(self.tro_species[sp].keys()):
m_value = self.tro_species[sp][name]
x_concentration = numpy.nonzero(m_value)[0]
monomials.append(name)
si_flux += 1
x_points = [self.tspan[x] for x in x_concentration]
prueba_y = numpy.repeat(2 * si_flux, len(x_concentration))
if monomials_inf[sympy.sympify(name)] > 0:
plt.scatter(
x_points[::int(math.ceil(len(self.tspan) / sep))],
prueba_y[::int(math.ceil(len(self.tspan) / sep))],
color=colors[idx], marker=r'$\uparrow$',
s=numpy.array([200] * len(x_concentration))[
::int(math.ceil(len(self.tspan) / sep))])
if monomials_inf[sympy.sympify(name)] < 0:
plt.scatter(
x_points[::int(math.ceil(len(self.tspan) / sep))],
prueba_y[::int(math.ceil(len(self.tspan) / sep))],
color=colors[idx], marker=r'$\downarrow$',
s=numpy.array([200] * len(x_concentration))[
::int(math.ceil(len(self.tspan) / sep))])
y_pos = numpy.arange(2, 2 * si_flux + 4, 2)
plt.yticks(y_pos, monomials, fontsize=12)
plt.ylabel('Monomials', fontsize=16)
plt.xlabel('Time (s)', fontsize=16)
plt.xlim(0, self.tspan[-1])
plt.ylim(0, max(y_pos))
plt.subplot(312)
mons = tropical_system[sp].as_coefficients_dict().items()
mons_matrix = numpy.zeros((len(mons), len(self.tspan[1:])), dtype=float)
for q, name in enumerate(self.tro_species[sp].keys()):
j = sympy.sympify(name)
for par in self.param_values:
j = j.subs(par, self.param_values[par])
var_to_study = [atom for atom in j.atoms(sympy.Symbol)] # Variables of monomial
arg_f1 = [numpy.maximum(self.mach_eps, self.y[str(va)][1:]) for va in var_to_study]
f1 = sympy.lambdify(var_to_study, j,
modules=dict(Heaviside=self._heaviside_num, log=numpy.log, Abs=numpy.abs))
mon_values = f1(*arg_f1)
mon_name = name.partition('__')[2]
plt.plot(self.tspan[1:], mon_values, label=mon_name, color=colors[q])
mons_matrix[q] = mon_values
plt.ylabel('Rate(m/sec)', fontsize=16)
plt.legend(bbox_to_anchor=(-0.1, 0.85), loc='upper right', ncol=1)
plt.subplot(311)
plt.plot(self.tspan[1:], self.y['__s%d' % sp][1:], label=parse_name(self.model.species[sp]))
plt.ylabel('Molecules', fontsize=16)
plt.legend(bbox_to_anchor=(-0.15, 0.85), loc='upper right', ncol=1)
plt.suptitle('Tropicalization' + ' ' + str(self.model.species[sp]))
plt.savefig('s%d' % sp + '.png', bbox_inches='tight', dpi=400)
# plt.ylim(0, len(monomials)+1)
return
