def run(self, simu_path, pool_folder, eval_results_path):
"""
"""
nparams = len(pool_folder)
plog = self.get_param_from_log(simu_path)
nsimu = int(plog['nsimu'])
param_name = plog["parameter to explore name"]
param = self.get_param(pool_folder)
kt_plate = []
logger.info("Running processes on each pool")
for i, simudir in enumerate(sorted(pool_folder)):
logger.info(color("Running processes on pool called: %s" % os.path.split(simudir)[-1], 'BOLD'))
p = Process(results_path=simudir)
resu = p.evaluate(name="Mitotic Plate", draw=False, verbose=False)
kt_plate.append(resu)
# Configure and plot the graph
logger.info("Plotting results")
timelapse = np.arange(0, plog['duration'], plog['dt'])
plot_data = {}
plot_data['title'] = "Mitotic plate formation with %s variable" % param_name
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time (second)'}
plot_data['yaxis'] = {'label': 'Dispersion measure (relative to the spindle length)', 'axis': []}
plot_data['error'] = False
plot_data['legend'] = True
# plot_data['limit_y_min'] = 0
# Draw parameters box
plot_data["params_box"] = [{'name': "Name", 'data': plog["name"]},
{'name': "Simulations number", 'data': nsimu},
]
# User matplotlib to get color gradient
cm = plt.get_cmap('gist_rainbow')
for i, resu in enumerate(kt_plate):
plot_color = cm(1. * i / nparams)
plot_data['yaxis']['axis'].append({'data': resu['dispersion'],
'color': plot_color,
'legend': "%s" % resu['params'][param_name]
})
dic_plot(plot_data, os.path.join(eval_results_path, "Mitotic_Plate_Formation.svg"))
# Now we gonna plote plate formation according to parameter explored
plot_data['yaxis'] = {'label': 'Dispersion measure (relative to the spindle length)', 'axis': []}
plot_data['xaxis'] = {'data': [], 'label': param_name}
plot_data['legend'] = False
plot_data["params_box"].append({'name': 'Infos', 'data': 'Dispersion measure is the mean to the last 30 sec before anaphase trigger'})
yaxisparam = []
xaxisparam = []
for i, resu in enumerate(kt_plate):
plot_color = cm(1. * i / nparams)
# Compute mean plate rate see on last 30 second before anaphase
start = (param['t_A'] - 30) / param['dt']
stop = (param['t_A']) / param['dt']
# Remove nan value
disp = resu['dispersion'][start:stop]
disp = disp[~np.isnan(disp)]
yaxisparam.append(disp.mean())
xaxisparam.append(resu['params'][param_name])
plot_data['xaxis']['data'] = np.array(xaxisparam)
plot_data['yaxis']['axis'].append({'data': np.array(yaxisparam),
'color': 'blue',
})
dic_plot(plot_data, os.path.join(eval_results_path, "Mitotic_Plate_Formation2.svg"))
return kt_plate
def run(self, simu_path, raw_path, eval_results_path, draw=True, verbose=True):
"""
"""
# Create eval_results_path if it does not exist
if not os.path.isdir(eval_results_path):
os.makedirs(eval_results_path)
params = self.get_params(simu_path)
meta_infos = self.get_simus_params(simu_path)
num_steps = meta_infos.num_steps
nsimu = int(self.get_nsimu(simu_path))
name = self.get_name(simu_path)
ana_onset = int(params["t_A"])
chromo_attach = {'monotelic': np.zeros((nsimu, num_steps)),
'syntelic': np.zeros((nsimu, num_steps)),
'unattached': np.zeros((nsimu, num_steps)),
'amphitelic': np.zeros((nsimu, num_steps)),
'merotelic-cut': np.zeros((nsimu, num_steps)),
'merotelic-amphi': np.zeros((nsimu, num_steps)),
'merotelic-synte': np.zeros((nsimu, num_steps)),
}
if verbose:
logger.info("Loading data from simulations files")
for i, (simu_id, meta) in enumerate(self.iter_simulations(raw_path,
nsimu=nsimu,
print_progress=verbose)):
results = meta.evaluate(name="Chromosome Attachment", verbose=False)
for attach_name, value in results.items():
chromo_attach[attach_name][i] = value
logger.disabled = False
if not draw:
return chromo_attach
# Configure and plot the graph
if verbose:
logger.info("Plotting results")
timelapse = meta_infos.timelapse
plot_data = {}
plot_data['title'] = "Chromosome attachment rate"
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time'}
plot_data['yaxis'] = {'label': 'Chromosome rate', 'axis': []}
plot_data['error'] = False
# Draw parameters box
plot_data["params_box"] = [{'name': "Name", 'data': name},
{'name': "Simulations number", 'data': nsimu},
]
# Add annotation about anaphase onset
plot_data["annotations"] = []
plot_data["annotations"].append({'s': 'Anaphase onset: %i' % ana_onset,
'xy': (ana_onset, 0),
'xytext': (0,50),
'textcoords': 'offset points',
'ha': 'center',
'va': 'bottom',
'bbox': dict(boxstyle='round,pad=0.2',
fc='yellow',
alpha=0.3),
'arrowprops': dict(arrowstyle='->',
# connectionstyle='arc3,rad=0.5',
color='black')
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['monotelic'].mean(axis=0),
'color': 'cyan',
'legend': 'Monotelic',
'error': chromo_attach['monotelic'].std(axis=0)
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['unattached'].mean(axis=0),
'color': 'blue',
'legend': 'Unattached',
'error': chromo_attach['unattached'].std(axis=0)
})
# plot_data['yaxis']['axis'].append({'data': chromo_attach['amphitelic'].mean(axis=0),
# 'color': 'green',
# 'legend': 'Amphitelic',
# 'error': chromo_attach['amphitelic'].std(axis=0)
# })
plot_data['yaxis']['axis'].append({'data': chromo_attach['syntelic'].mean(axis=0),
'color': 'yellow',
'legend': 'Syntelic',
'error': chromo_attach['syntelic'].std(axis=0)
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['merotelic-cut'].mean(axis=0),
'color': 'orange',
'legend': 'Balanced Merotelic',
'error': chromo_attach['merotelic-cut'].std(axis=0)
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['merotelic-amphi'].mean(axis=0),
'color': 'red',
'legend': 'Mero-Amphitelic',
'error': chromo_attach['merotelic-amphi'].std(axis=0)
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['merotelic-synte'].mean(axis=0),
'color': 'purple',
'legend': 'Mero-Syntelic',
'error': chromo_attach['merotelic-synte'].std(axis=0)
})
dic_plot(plot_data, os.path.join(eval_results_path, "Chromosome_Attachment.svg"))
# Now plot with logarithmic xaxis
plot_data['xaxis']['label'] = 'Time (Logarithmic scale)'
plot_data['logx'] = True
dic_plot(plot_data, os.path.join(eval_results_path, "Chromosome_Attachment_logarithmic.svg"))
# Draw same plot but without all merotelic type : we merge them
plot_data['logx'] = False
plot_data['yaxis']['axis'] = plot_data['yaxis']['axis'][0:4]
mero = chromo_attach['merotelic-cut'] + chromo_attach['merotelic-synte'] + chromo_attach['merotelic-amphi']
plot_data['yaxis']['axis'].append({'data': mero.mean(axis=0),
'color': 'red',
'legend': 'Merotelic',
'error': mero.std(axis=0)
})
dic_plot(plot_data, os.path.join(eval_results_path, "Chromosome_Attachment_Merge_Mero.svg"))
# Now plot with logarithmic xaxis
plot_data['xaxis']['label'] = 'Time (Logarithmic scale)'
plot_data['logx'] = True
dic_plot(plot_data, os.path.join(eval_results_path, "Chromosome_Attachment_Merge_Mero_logarithmic.svg"))
return chromo_attach
def run(self, KD, draw=False):
"""
"""
N = int(KD.params["N"])
ana_onset = int(KD.params["t_A"])
timelapse = np.arange(0, KD.duration, KD.dt)
trajectories = {'spbR': KD.spbR.traj,
'spbL': KD.spbL.traj,
'chromosomes': [],
}
# Retrieve kinetochores trajectories
for ch in KD.chromosomes:
traj = [ch.cen_A.traj,
ch.cen_B.traj]
trajectories['chromosomes'].append(traj)
if not draw:
return trajectories
# Draw attachment state with matplotlib
timelapse = np.arange(0, KD.duration, KD.dt)
plot_data = {}
plot_data['title'] = "Chromosome kinetochores trajectories"
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time'}
plot_data['yaxis'] = {'label': 'Relative position to SPB axes center', 'axis': []}
plot_data['logx'] = False
plot_data['legend'] = False
# Add annotation about anaphase onset
plot_data["annotations"] = []
plot_data["annotations"].append({'s': 'Anaphase onset: %i' % ana_onset,
'xy': (ana_onset, -2),
'xytext': (0, 20),
'textcoords': 'offset points',
'ha': 'center',
'va': 'bottom',
'bbox': dict(boxstyle='round,pad=0.2',
fc='yellow',
alpha=0.3),
'arrowprops': dict(arrowstyle='->',
# connectionstyle='arc3,rad=0.5',
color='black')
})
plot_data['yaxis']['axis'].append({'data': trajectories['spbR'],
'color': 'black',
'plot_args': {'ls': '-',
'lw': 3}
})
plot_data['yaxis']['axis'].append({'data': trajectories['spbL'],
'color': 'black',
'plot_args': {'ls': '-',
'lw': 3}
})
# User matplotlib to get color gradient
cm = plt.get_cmap('gist_rainbow')
for i, ch in enumerate(trajectories['chromosomes']):
color = cm(1. * i / N)
plot_data['yaxis']['axis'].append({'data': ch[0],
'color': color,
})
plot_data['yaxis']['axis'].append({'data': ch[1],
'color': color,
})
dic_plot(plot_data)
return trajectories
def run(self, KD, draw=False):
"""
"""
N = int(KD.params["N"])
ana_onset = int(KD.params["t_A"])
timelapse = np.arange(0, KD.duration, KD.dt)
num_steps = KD.duration / KD.dt
kt_traj_step = num_steps / 20
spindle_length = abs(KD.spbR.traj - KD.spbL.traj)
# Dispersion is size of the segment made by extrem Kt scaled
# by spindle size
kt_plate = {'dispersion': None,
'kt_trajs': [],
'plate_shape_right': np.zeros((N , num_steps), dtype="float"),
'plate_shape_left': np.zeros((N , num_steps), dtype="float")
}
max_kt = np.zeros((N * 2, num_steps), dtype="float")
min_kt = np.zeros((N * 2, num_steps), dtype="float")
kt_trajs = []
for i, ch in enumerate(KD.chromosomes):
id1 = (i * 2) - 1
id2 = (i * 2)
max_kt[id1] = ch.cen_A.traj
max_kt[id2] = ch.cen_B.traj
min_kt[id1] = ch.cen_A.traj
min_kt[id2] = ch.cen_B.traj
kt_trajs.append(ch.cen_A.traj / spindle_length)
kt_trajs.append(ch.cen_B.traj / spindle_length)
if ch.cen_A.traj.mean() < ch.cen_B.traj.mean():
kt_plate['plate_shape_left'][i] = ch.cen_A.traj
kt_plate['plate_shape_right'][i] = ch.cen_B.traj
else:
kt_plate['plate_shape_right'][i] = ch.cen_A.traj
kt_plate['plate_shape_left'][i] = ch.cen_B.traj
kt_plate['plate_shape_left'] = kt_plate['plate_shape_left'].std(axis=0)
kt_plate['plate_shape_right'] = kt_plate['plate_shape_right'].std(axis=0)
max_kt_distance = max_kt.max(axis=0)
min_kt_distance = min_kt.min(axis=0)
kt_plate['dispersion'] = (abs(max_kt_distance - min_kt_distance) /
spindle_length)
# Scale kt trajectories
for kt in kt_trajs:
kt = kt + kt_plate['dispersion']
# Lighten array
light_traj = np.zeros(num_steps, dtype='float')
light_traj[::kt_traj_step] = 1
light_traj *= kt
light_traj[light_traj == 0] = np.nan
kt_plate['kt_trajs'].append(light_traj)
if not draw:
return kt_plate
# Draw attachment state with matplotlib
timelapse = np.arange(0, KD.duration, KD.dt)
plot_data = {}
plot_data['title'] = "Centromeres dispersion variation"
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time (second)'}
plot_data['yaxis'] = {'label': "Dispersion measure (relative to the spindle length)", 'axis': []}
plot_data['logx'] = False
plot_data['legend'] = False
plot_data['limit_y_min'] = 0
# Draw parameters box
plot_data["params_box"] = [{'name': "Lenght Dependance factor", 'data': KD.params["ldep"]},
]
# Add annotation about anaphase onset
plot_data["annotations"] = []
plot_data["annotations"].append({'s': 'Anaphase onset: %i' % ana_onset,
'xy': (ana_onset, 0),
'xytext': (0, 20),
'textcoords': 'offset points',
'ha': 'center',
'va': 'bottom',
'bbox': dict(boxstyle='round,pad=0.2',
fc='yellow',
alpha=0.3),
'arrowprops': dict(arrowstyle='->',
# connectionstyle='arc3,rad=0.5',
color='black')
})
plot_data['yaxis']['axis'].append({'data': kt_plate['dispersion'],
'color': 'blue',
'plot_args' : {'lw': 2}
})
dic_plot(plot_data)
# User matplotlib to get color gradient
cm = plt.get_cmap('gist_rainbow')
for j, kt in enumerate(kt_plate['kt_trajs']):
if j%2 == 0:
color = cm(1. * j / (N))
plot_data['yaxis']['axis'].append({'data': kt,
'color': color,
'plot_args' : {'marker': 'o'}
})
dic_plot(plot_data)
# Plot the plate shape
plot_data['title'] = "Mitotic plate formation"
plot_data['yaxis'] = {'label': "Centromeres position variance", 'axis': []}
del plot_data['limit_y_min']
plot_data['yaxis']['axis'].append({'data': kt_plate['plate_shape_right'],
'color': 'blue',
'legend': 'Right kinetochores'
})
plot_data['yaxis']['axis'].append({'data': kt_plate['plate_shape_left'],
'color': 'red',
'legend': 'Left kinetochores'
})
dic_plot(plot_data)
return kt_plate
def run(self, simu_path, raw_path, eval_results_path, draw=True, verbose=True):
"""
"""
# Create eval_results_path if it does not exist
if not os.path.isdir(eval_results_path):
os.makedirs(eval_results_path)
params = self.get_params(simu_path)
meta_infos = self.get_simus_params(simu_path)
num_steps = meta_infos.num_steps
nsimu = int(self.get_nsimu(simu_path))
name = self.get_name(simu_path)
ana_onset = int(params["t_A"])
N = int(params["N"])
Mk = int(params["Mk"])
attach_state = {'correct_attached': np.zeros((nsimu, num_steps)),
'incorrect_attached': np.zeros((nsimu, num_steps)),
'unattached': np.zeros((nsimu, num_steps))
}
if verbose:
logger.info("Loading data from simulations files")
for i, (simu_id, meta) in enumerate(self.iter_simulations(raw_path,
nsimu=nsimu,
print_progress=verbose)):
results = meta.evaluate(name="Kineto Attachment", verbose=False)
attach_state['correct_attached'][i] = results['correct_attached']
attach_state['incorrect_attached'][i] = results['incorrect_attached']
attach_state['unattached'][i] = results['unattached']
logger.disabled = False
# Mean data
logger.info("Processing data")
correct_attached = attach_state['correct_attached'].mean(axis=0)
correct_attached_std = attach_state['correct_attached'].std(axis=0)
incorrect_attached = attach_state['incorrect_attached'].mean(axis=0)
incorrect_attached_std = attach_state['incorrect_attached'].std(axis=0)
unattached = attach_state['unattached'].mean(axis=0)
unattached_std = attach_state['unattached'].std(axis=0)
if not draw:
return attach_state
# Configure and plot the graph
if verbose:
logger.info("Plotting results")
timelapse = meta_infos.timelapse
plot_data = {}
plot_data['title'] = """Kinetochores attachment rate"""
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time'}
plot_data['yaxis'] = {'label': 'Attachment rate', 'axis': []}
# Draw parameters box
plot_data["params_box"] = [{'name': "Name", 'data': name},
{'name': "Simulations number", 'data': nsimu},
{'name': "Chromosome number", 'data': '%i' % N},
{'name': "Plug site per kinetochore", 'data': '%i' % Mk}
]
# Add annotation about anaphase onset
plot_data["annotations"] = []
plot_data["annotations"].append({'s': 'Anaphase onset: %i' % ana_onset,
'xy': (ana_onset, 0),
'xytext': (0,50),
'textcoords': 'offset points',
'ha': 'center',
'va': 'bottom',
'bbox': dict(boxstyle='round,pad=0.2',
fc='yellow',
alpha=0.3),
'arrowprops': dict(arrowstyle='->',
# connectionstyle='arc3,rad=0.5',
color='black')
})
correct_attached_axis = {'data': correct_attached,
'color': 'green',
'legend': 'Correct attached kinetochore',
'error': correct_attached_std,
}
incorrect_attached_axis = {'data': incorrect_attached,
'color': 'red',
'legend': 'Incorrect attached kinetochore',
'error': incorrect_attached_std,
}
unattached_axis = {'data': unattached,
'color': 'blue',
'legend': 'Unattached kinetochore',
'error': unattached_std,
}
plot_data['yaxis']['axis'].append(correct_attached_axis)
plot_data['yaxis']['axis'].append(incorrect_attached_axis)
plot_data['yaxis']['axis'].append(unattached_axis)
dic_plot(plot_data, os.path.join(eval_results_path, "Kineto_Attachment.svg"))
# Now plot with log xaxis
plot_data['xaxis']['label'] = 'Time (Logarithmic scale)'
plot_data['logx'] = True
dic_plot(plot_data, os.path.join(eval_results_path, "Kineto_Attachment_logarithmic.svg"))
return attach_state
def run(self, simu_path, raw_path, eval_results_path, draw=True, verbose=True):
"""
"""
# Create eval_results_path if it does not exist
if not os.path.isdir(eval_results_path):
os.makedirs(eval_results_path)
params = self.get_params(simu_path)
meta_infos = self.get_simus_params(simu_path)
num_steps = meta_infos.num_steps
nsimu = int(self.get_nsimu(simu_path))
name = self.get_name(simu_path)
ana_onset = int(params["t_A"])
kt_plate = {'dispersion': np.zeros((nsimu, num_steps)),
'plate_shape_right': np.zeros((nsimu, num_steps)),
'plate_shape_left': np.zeros((nsimu, num_steps)),
'params': params
}
if verbose:
logger.info("Loading data from simulations files")
for i, (simu_id, meta) in enumerate(self.iter_simulations(raw_path,
nsimu=nsimu,
print_progress=verbose)):
results = meta.evaluate(name="Mitotic Plate", verbose=False)
kt_plate['dispersion'][i] = results['dispersion']
kt_plate['plate_shape_left'][i] = results['plate_shape_left']
kt_plate['plate_shape_right'][i] = results['plate_shape_right']
logger.disabled = False
kt_plate['dispersion_std'] = kt_plate['dispersion'].std(axis=0)
kt_plate['dispersion'] = kt_plate['dispersion'].mean(axis=0)
kt_plate['plate_shape_right'] = kt_plate['plate_shape_right'].mean(axis=0)
kt_plate['plate_shape_right_std'] = kt_plate['plate_shape_right'].std(axis=0)
kt_plate['plate_shape_left'] = kt_plate['plate_shape_left'].mean(axis=0)
kt_plate['plate_shape_left_std'] = kt_plate['plate_shape_left'].std(axis=0)
if not draw:
return kt_plate
# Configure and plot the graph
if verbose:
logger.info("Plotting results")
timelapse = meta_infos.timelapse
plot_data = {}
plot_data['title'] = "Centromeres dispersion variation"
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time (second)'}
plot_data['yaxis'] = {'label': 'Dispersion measure (relative to the spindle length)', 'axis': []}
plot_data['error'] = True
plot_data['legend'] = False
plot_data['limit_y_min'] = 0
# Draw parameters box
plot_data["params_box"] = [{'name': "Name", 'data': name},
{'name': "Simulations number", 'data': nsimu},
{'name': "Lenght Dependance factor", 'data': params["ldep"]}
]
# Add annotation about anaphase onset
plot_data["annotations"] = []
plot_data["annotations"].append({'s': 'Anaphase onset: %i' % ana_onset,
'xy': (ana_onset, 0),
'xytext': (0,50),
'textcoords': 'offset points',
'ha': 'center',
'va': 'bottom',
'bbox': dict(boxstyle='round,pad=0.2',
fc='yellow',
alpha=0.3),
'arrowprops': dict(arrowstyle='->',
# connectionstyle='arc3,rad=0.5',
color='black')
})
plot_data['yaxis']['axis'].append({'data': kt_plate['dispersion'],
'color': 'blue',
'error': kt_plate['dispersion_std']
})
dic_plot(plot_data, os.path.join(eval_results_path, "Mitotic_Plate_Formation.svg"))
# Plot the plate shape
plot_data['title'] = "Mitotic plate formation"
plot_data['yaxis'] = {'label': "Centromeres position variance", 'axis': []}
del plot_data['limit_y_min']
plot_data['legend'] = True
plot_data['yaxis']['axis'].append({'data': kt_plate['plate_shape_right'],
'color': 'blue',
'legend': 'Right kinetochores',
'error': kt_plate['plate_shape_right_std']
})
plot_data['yaxis']['axis'].append({'data': kt_plate['plate_shape_left'],
'color': 'red',
'legend': 'Left kinetochores',
'error': kt_plate['plate_shape_left_std']
})
dic_plot(plot_data, os.path.join(eval_results_path, "Mitotic_Plate_Formation2.svg"))
return kt_plate
def run(self, simu_path, raw_path, eval_results_path, draw=True, verbose=True):
"""
"""
# Create eval_results_path if it does not exist
if not os.path.isdir(eval_results_path):
os.makedirs(eval_results_path)
params = self.get_params(simu_path)
meta_infos = self.get_simus_params(simu_path)
num_steps = meta_infos.num_steps
nsimu = int(self.get_nsimu(simu_path))
name = self.get_name(simu_path)
ana_onset = int(params["t_A"])
N = int(params["N"])
trajectories = {'spbR': np.zeros((nsimu, num_steps), dtype=float),
'spbL': np.zeros((nsimu, num_steps), dtype=float),
'chromosomes': [],
}
for i in range(N):
cen_traj = [np.zeros((nsimu, num_steps), dtype=float),
np.zeros((nsimu, num_steps), dtype=float)]
trajectories['chromosomes'].append(cen_traj)
if verbose:
logger.info("Loading data from simulations files")
for i, (simu_id, meta) in enumerate(self.iter_simulations(raw_path,
nsimu=nsimu,
print_progress=verbose)):
results = meta.evaluate(name="Kinetochores Trajectories", verbose=False)
trajectories['spbR'][i] = results['spbR']
trajectories['spbL'][i] = results['spbL']
for j, ch in enumerate(results['chromosomes']):
trajectories["chromosomes"][j][0][i] = ch[0]
trajectories["chromosomes"][j][1][i] = ch[1]
logger.disabled = False
if not draw:
return trajectories
# Configure and plot the graph
if verbose:
logger.info("Plotting results")
timelapse = meta_infos.timelapse
plot_data = {}
plot_data['title'] = "Chromosome kinetochores trajectories"
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time'}
plot_data['yaxis'] = {'label': 'Relative position to SPB axes center', 'axis': []}
plot_data['error'] = False
plot_data['legend'] = False
# Draw parameters box
plot_data["params_box"] = [{'name': "Name", 'data': name},
{'name': "Simulations number", 'data': nsimu},
]
# Add annotation about anaphase onset
plot_data["annotations"] = []
plot_data["annotations"].append({'s': 'Anaphase onset: %i' % ana_onset,
'xy': (ana_onset, -2.5),
'xytext': (0, 20),
'textcoords': 'offset points',
'ha': 'center',
'va': 'bottom',
'bbox': dict(boxstyle='round,pad=0.2',
fc='yellow',
alpha=0.3),
'arrowprops': dict(arrowstyle='->',
# connectionstyle='arc3,rad=0.5',
color='black')
})
plot_data['yaxis']['axis'].append({'data': trajectories['spbR'].mean(axis=0),
'color': 'black',
'error': trajectories['spbR'].std(axis=0)
})
plot_data['yaxis']['axis'].append({'data': trajectories['spbL'].mean(axis=0),
'color': 'black',
'error': trajectories['spbL'].std(axis=0)
})
# User matplotlib to get color gradient
cm = plt.get_cmap('gist_rainbow')
for i, ch in enumerate(trajectories['chromosomes']):
color = cm(1.*i/N)
plot_data['yaxis']['axis'].append({'data': ch[0].mean(axis=0),
'color': color,
'error': ch[0].std(axis=0)
})
plot_data['yaxis']['axis'].append({'data': ch[1].mean(axis=0),
'color': color,
'error': ch[1].std(axis=0)
})
dic_plot(plot_data, os.path.join(eval_results_path, "Kt_Trajectories.svg"))
return trajectories
def run(self, KD, draw=False):
"""
"""
num_steps = KD.spbR.traj.size
N = int(KD.params['N'])
Mk = int(KD.params['Mk'])
ana_onset = int(KD.params["t_A"])
value_max = N * Mk * 2
chromo_attach = {'monotelic': np.zeros(num_steps),
'syntelic': np.zeros(num_steps),
'unattached': np.zeros(num_steps),
'amphitelic': np.zeros(num_steps),
'merotelic-cut': np.zeros(num_steps),
'merotelic-amphi': np.zeros(num_steps),
'merotelic-synte': np.zeros(num_steps),
}
for ch in KD.chromosomes:
iterator = enumerate(zip(ch.correct_history, ch.erroneous_history))
for i, (correct, incorrect) in iterator:
# Kt A n° correct attachments
ac = correct[0]
# Kt B n° correct attachments
bc = correct[1]
# Kt A n° incorrect attachments
ai = incorrect[0]
# Kt B n° incorrect attachments
bi = incorrect[1]
if ac + bc + ai + bi == 0:
# The actual chromosome is unattached (so easy...)
chromo_attach['unattached'][i] += 1
elif (ac + ai + bi == 0 and bc > 0) or \
(bc + bi + ai == 0 and ac > 0):
# The actual chromosome is monotelic
chromo_attach['monotelic'][i] += 1
elif ai + bi == 0 and ac > 0 and bc > 0:
# The actual chromosome is amphitelic
chromo_attach['amphitelic'][i] += 1
elif (ac == 0 and ai > 0) or (bc == 0 and bi > 0):
# The actual chromosome is syntelic
chromo_attach['syntelic'][i] += 1
# It should remain here, only merotelic chromosomes.
# Let's check it
elif ai > 0 or bi > 0:
# Welcome to the merotelic world !
if ac == ai or bc == bi:
chromo_attach['merotelic-cut'][i] += 1
elif ac < ai or bc < bi:
chromo_attach['merotelic-synte'][i] += 1
elif ac > ai or bc > bi:
chromo_attach['merotelic-amphi'][i] += 1
else:
# The code should never run here unless we got errors !
logger.error("Problem in attachment rate algorithm (second level condition")
return False
else:
# The code should never run here unless we got errors !
logger.error("Problem in attachment rate algorithm (first level condition")
return False
# Normalize values on 1
for state in chromo_attach:
chromo_attach[state] = chromo_attach[state] / N
if draw:
# Draw attachment state with matplotlib
timelapse = np.arange(0, KD.duration, KD.dt)
plot_data = {}
plot_data['title'] = "Chromosome attachment rate"
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time'}
plot_data['yaxis'] = {'label': 'Attachment rate', 'axis': []}
plot_data['logx'] = True
# Add annotation about anaphase onset
plot_data["annotations"] = []
plot_data["annotations"].append({'s': 'Anaphase onset: %i' % ana_onset,
'xy': (ana_onset, 0),
'xytext': (0,50),
'textcoords': 'offset points',
'ha': 'center',
'va': 'bottom',
'bbox': dict(boxstyle='round,pad=0.2',
fc='yellow',
alpha=0.3),
'arrowprops': dict(arrowstyle='->',
# connectionstyle='arc3,rad=0.5',
color='black')
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['monotelic'],
'color': 'cyan',
'legend': 'Monotelic'
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['unattached'],
'color': 'blue',
'legend': 'Unattached'
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['amphitelic'],
'color': 'green',
'legend': 'Amphitelic'
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['syntelic'],
'color': 'yellow',
'legend': 'Syntelic'
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['merotelic-cut'],
'color': 'orange',
'legend': 'Balanced Merotelic'
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['merotelic-amphi'],
'color': 'red',
'legend': 'Mero-Amphitelic'
})
plot_data['yaxis']['axis'].append({'data': chromo_attach['merotelic-synte'],
'color': 'purple',
'legend': 'Mero-Syntelic'
})
dic_plot(plot_data)
return chromo_attach
def run(self, KD, draw=False):
"""
"""
num_steps = KD.spbR.traj.size
N = int(KD.params['N'])
Mk = int(KD.params['Mk'])
value_max = N * Mk * 2
kt_attach = {'correct_attached': np.zeros(num_steps, dtype='float'),
'incorrect_attached': np.zeros(num_steps, dtype='float'),
'unattached': np.zeros(num_steps, dtype='float')
}
for ch in KD.chromosomes:
ch_incorrect = np.array(ch.erroneous_history).sum(1)
ch_correct = np.array(ch.correct_history).sum(1)
kt_attach['correct_attached'] += ch_correct
kt_attach['incorrect_attached'] += ch_incorrect
kt_attach['unattached'] = np.ones(num_steps, dtype='float') * value_max
kt_attach['unattached'] -= kt_attach['correct_attached']
kt_attach['unattached'] -= kt_attach['incorrect_attached']
# Scale values on 1
kt_attach['correct_attached'] /= value_max
kt_attach['incorrect_attached'] /= value_max
kt_attach['unattached'] /= value_max
if draw:
# Draw attachment state with matplotlib
timelapse = np.arange(0, KD.duration, KD.dt)
plot_data = {}
plot_data['title'] = "Kinetochores attachment rate"
plot_data['xaxis'] = {'data': timelapse, 'label': 'Time'}
plot_data['yaxis'] = {'label': 'Attachment rate', 'axis': []}
# Draw parameters box
correct_attached_axis = {'data': kt_attach['correct_attached'],
'color': 'green',
'legend': 'Correct attached kinetochore'}
incorrect_attached_axis = {'data': kt_attach['incorrect_attached'],
'color': 'red',
'legend': 'Incorrect attached kinetochore'}
unattached_axis = {'data': kt_attach['unattached'],
'color': 'blue',
'legend': 'Unattached kinetochore'}
plot_data['yaxis']['axis'].append(correct_attached_axis)
plot_data['yaxis']['axis'].append(incorrect_attached_axis)
plot_data['yaxis']['axis'].append(unattached_axis)
dic_plot(plot_data)
return kt_attach