def parameter_signatures(par, model, tspan, type_sign='production'):
"""
:param par: parameter file path or vector of parameters
:param model: PySB model
:param tspan: time span
:return: tropical signatures of input parameters
"""
try:
if isinstance(par, str):
parames = hf.read_pars(par)
else:
parames = par
drivers = run_tropical(model, tspan, parameters=parames, type_sign=type_sign, sp_visualize=None)
return drivers
except:
print(par)
print("".join(traceback.format_exception(*sys.exc_info())))
raise Exception("".join(traceback.format_exception(*sys.exc_info())))
def display_all_species(cluster_parameters):
"""Saves figures of all species for each cluster of parameters
keyword arguments:
cluster_parameters -- list of files, where each file contains the clustered parameters
"""
for cl in cluster_parameters:
directory = '/home/oscar/Documents/tropical_project/' + cl
if not os.path.exists(directory):
os.makedirs(directory)
for sp in range(len(model.species)):
plt.figure()
for idx, par in enumerate(cluster_parameters[cl]):
params = hf.read_pars(par)
solver.run(params)
y = solver.y.T
plt.plot(solver.tspan, y[sp])
plt.title(str(model.species[sp]))
plt.savefig(directory + '/' + str(model.species[sp]) + '.jpg', format='jpg', bbox_inches='tight', dpi=400)
plt.close()
return
from earm.lopez_embedded import model from max_plus_consumption_production import run_tropical import numpy as np import os import helper_functions as hf directory = os.path.dirname(__file__) parameters_path = os.path.join(directory, "parameters_5000") all_parameters = hf.listdir_fullpath(parameters_path) parameters = hf.read_pars(all_parameters[0]) t = np.linspace(0, 20000, 100) run_tropical(model, t, parameters, diff_par=1, type_sign='consumption', sp_visualize=[6])
def signal_signature(self, param_values, diff_par=1, type_sign='production', sp_to_visualize=None):
if param_values is not None:
if type(param_values) is str:
param_values = hf.read_pars(param_values)
# accept vector of parameter values as an argument
if len(param_values) != len(self.model.parameters):
print(param_values)
raise Exception("param_values must be the same length as model.parameters")
if not isinstance(param_values, numpy.ndarray):
param_values = numpy.array(param_values)
else:
# create parameter vector from the values in the model
param_values = numpy.array([p.value for p in self.model.parameters])
# convert model parameters into dictionary
param_values = dict((p.name, param_values[i]) for i, p in enumerate(self.model.parameters))
y = self.sim.run(param_values=param_values).dataframe
# Dictionary whose keys are species and values are the monomial signatures
all_signatures = {}
if type_sign == 'production':
mon_type = 'products'
elif type_sign == 'consumption':
mon_type = 'reactants'
else:
raise Exception("type sign must be 'production' or 'consumption'")
for sp in self.eqs_for_tropicalization:
# reaction terms
monomials = []
for term in self.model.reactions_bidirectional:
if sp in term['reactants'] and term['reversible'] is True:
monomials.append((-1) * term['rate'])
elif sp in term[mon_type]:
monomials.append(term['rate'])
# Dictionary whose keys are the symbolic monomials and the values are the simulation results
mons_dict = {}
for mon_p in monomials:
mon_p_values = mon_p.subs(param_values)
var_prod = [atom for atom in mon_p_values.atoms(sympy.Symbol)] # Variables of monomial
arg_prod = [numpy.maximum(self.mach_eps, y[str(va)]) for va in var_prod]
f_prod = sympy.lambdify(var_prod, mon_p_values)
prod_values = f_prod(*arg_prod)
mons_dict[mon_p] = prod_values
# Dataframe whose rownames are the monomials and the columns contain their values at each time point
mons_df = pd.DataFrame(mons_dict).T
signature_species = mons_df.apply(self.choose_max2, args=(diff_par, self.all_comb[sp], type_sign))
all_signatures[sp] = list(signature_species)
# self.all_sp_signatures = all_signatures
if sp_to_visualize:
self.visualization2(y, all_signatures, param_values, sp_to_visualize)
return all_signatures
def display_observables(params_estimated):
"""Save a figure of the observables with different parameter values and their distributions
keyword arguments:
params_estimated -- list of parameter sets
"""
fig, axApop = plt.subplots(figsize=(7, 7))
# Construct matrix of experimental data and variance columns of interest
exp_obs_norm = exp_data[data_names].view(float).reshape(len(exp_data), -1).T
var_norm = exp_data[var_names].view(float).reshape(len(exp_data), -1).T
std_norm = var_norm ** 0.5
obs_names_disp = obs_names + ['aSmac']
totals = obs_totals + [momp_obs_total]
cparp_info = [0] * len(params_estimated)
cparp_info_fraction = [0] * len(params_estimated)
# Plot experimental data and simulation on the same axes
colors = ('r', 'b')
obs_range = [0, 1]
for exp, exp_err, obs, c in zip([exp_obs_norm[1]], [std_norm[1]], [obs_range[1]], [colors[1]]):
for idx, par in enumerate(params_estimated):
params = hf.read_pars(par)
# params[62] -= params[62] * 0.89
solver.run(params)
sim_obs = solver.yobs[obs_names_disp].view(float).reshape(len(solver.yobs), -1)
sim_obs_norm = (sim_obs / totals).T
cparp_info[idx] = curve_fit(sig_apop, solver.tspan, sim_obs_norm[1], p0=[100, 100, 100])[0]
cparp_info_fraction[idx] = sim_obs_norm[1][-1]
# axApop.plot(solver.tspan, sim_obs_norm[obs], color=c, alpha=0.5)
axApop.plot(solver.tspan, sim_obs_norm[2], color='g', alpha=0.4)
# axApop.plot(solver.tspan, sim_obs_norm[obs], color=c, alpha=0.5, label=obs_names[obs] + ' sim')
# axApop.plot(solver.tspan, sim_obs_norm[obs], color=c, alpha=0.5, label=obs_names[obs] + ' sim')
axApop.plot(solver.tspan, sim_obs_norm[2], color='g', alpha=0.4, label='aSmac' + ' sim')
axApop.vlines(momp_data[0], -0.05, 1.05, color='k', linestyle=':', label='aSmac' + ' data')
# axApop.plot(exp_data['Time'], exp, color='k', marker='.', linestyle=':', label=obs_names[obs]+' data')
# axApop.errorbar(exp_data['Time'], exp, yerr=exp_err, ecolor='k',
# elinewidth=0.5, capsize=0, fmt=None)
plt.xticks(rotation=-30)
plt.xlabel('Time')
plt.ylabel('Fraction')
fig.tight_layout()
divider = make_axes_locatable(axApop)
axHistx = divider.append_axes("top", 1.2, pad=0.3, sharex=axApop)
axHisty = divider.append_axes("right", 1.2, pad=0.3, sharey=axApop)
# make some labels invisible
plt.setp(axHistx.get_xticklabels() + axHisty.get_yticklabels(),
visible=False)
# now determine nice limits by hand:
binwidth = 0.11
binwidthx = 600
xymax = np.max([np.max(np.fabs(solver.tspan)), np.max(np.fabs(1))])
lim = (int(xymax / binwidth) + 1) * binwidth
weightsx = np.ones_like(column(cparp_info, 1)) / len(column(cparp_info, 1))
weightsy = np.ones_like(cparp_info_fraction) / len(cparp_info_fraction)
axHisty.hist(cparp_info_fraction, orientation='horizontal', bins=np.arange(0, 1.01 + binwidth, binwidth),
weights=weightsy)
axHistx.hist(column(cparp_info, 1), bins=np.arange(min(solver.tspan), max(solver.tspan) + binwidthx, binwidthx),
weights=weightsx)
# axHistx.axis["bottom"].major_ticklabels.set_visible(False)
for tl in axHistx.get_xticklabels():
tl.set_visible(False)
axHistx.set_yticks([0, 0.5, 1])
# axHisty.axis["left"].major_ticklabels.set_visible(False)
for tl in axHisty.get_yticklabels():
tl.set_visible(False)
axHisty.set_xticks([0, 0.5, 1])
axApop.legend(loc=0)
fig.savefig('/home/oscar/Documents/tropical_project/all_parameters_earm.png', format='png', dpi=400)
return
else:
parameter_ic.name == 'Bcl2_0'
sd = cv
return lognormal(mean, sd, size)
parameters_ic = {idx: p for idx, p in enumerate(model.parameters) if p in model.parameters_initial_conditions()[1:]}
samples = 100
pso_pars = hf.listdir_fullpath('/home/oscar/Documents/tropical_project/parameters_5000')
all_pars_ic = np.zeros((len(pso_pars), len(model.parameters)))
for idx, pa in enumerate(pso_pars):
pso_pars[idx] = hf.read_pars(pa)
repeated_parameter_values = np.repeat(pso_pars, samples, axis=0)
for idx, par in parameters_ic.items():
repeated_parameter_values[:, idx] = sample_lognormal(par, size=samples*len(pso_pars))
def parameter_signatures(par, model, tspan):
"""
:param par: parameter file path or vector of parameters
:param model: PySB model
:param tspan: time span
:return: tropical signatures of input parameters