def main():
_simulations = load.structured()
_simulations = filtering.by_time_points_amount(_simulations, TIME_POINTS)
_simulations = filtering.by_categories(
_simulations,
_is_single_cell=False,
_is_heterogeneity=True,
_is_low_connectivity=False,
_is_causality=False,
_is_dominant_passive=False,
_is_fibrin=False
)
_simulations = filtering.by_pair_distance(_simulations, _distance=PAIR_DISTANCE)
_simulations = filtering.by_heterogeneity(_simulations, _std=STD)
print('Total simulations:', len(_simulations))
_fiber_densities = compute_fiber_densities(_simulations)
_window_distances_communicating = [[] for _i in OFFSETS_X]
_window_distances_non_communicating = [[] for _i in OFFSETS_X]
# window distances loop
for _window_distance_index, _window_distance in enumerate(OFFSETS_X):
print('Window distance:', _window_distance)
# communicating loop
for _simulation in tqdm(_simulations, desc='Communicating loop'):
_left_cell_fiber_densities = _fiber_densities[(_simulation, _window_distance, 'left_cell')]
_right_cell_fiber_densities = _fiber_densities[(_simulation, _window_distance, 'right_cell')]
_correlation = compute_lib.correlation(
compute_lib.derivative(_left_cell_fiber_densities, _n=DERIVATIVE),
compute_lib.derivative(_right_cell_fiber_densities, _n=DERIVATIVE)
)
_window_distances_communicating[_window_distance_index].append(_correlation)
# non-communicating loop
_simulations_indices = range(len(_simulations))
for _simulation_1_index in tqdm(_simulations_indices, desc='Non-communicating pairs loop'):
_simulation_1 = _simulations[_simulation_1_index]
for _simulation_2_index in _simulations_indices[_simulation_1_index + 1:]:
_simulation_2 = _simulations[_simulation_2_index]
for _simulation_1_cell_id, _simulation_2_cell_id in product(['left_cell', 'right_cell'],
['left_cell', 'right_cell']):
_simulation_1_fiber_densities = \
_fiber_densities[(_simulation_1, _window_distance, _simulation_1_cell_id)]
_simulation_2_fiber_densities = \
_fiber_densities[(_simulation_2, _window_distance, _simulation_2_cell_id)]
_correlation = compute_lib.correlation(
compute_lib.derivative(_simulation_1_fiber_densities, _n=DERIVATIVE),
compute_lib.derivative(_simulation_2_fiber_densities, _n=DERIVATIVE)
)
_window_distances_non_communicating[_window_distance_index].append(_correlation)
# rank sums
print('Wilcoxon rank-sum tests between communicating and non-communicating:',
ranksums(_window_distances_communicating[_window_distance_index],
_window_distances_non_communicating[_window_distance_index]))
# plot
_data = []
_colors_array = config.colors(2)
for _communicating, _communicating_text, _pair_distances, _color in \
zip([True, False], ['Communicating', 'Non-communicating'],
[_window_distances_communicating, _window_distances_non_communicating],
_colors_array):
_y = []
_x = []
for _window_distance_index, _window_distance in enumerate(OFFSETS_X):
_y += _pair_distances[_window_distance_index]
_x += [_window_distance for _i in _pair_distances[_window_distance_index]]
_data.append(
go.Box(
y=_y,
x=_x,
name=_communicating_text,
boxpoints='all' if _communicating else False,
jitter=1,
pointpos=0,
line={
'width': 1
},
fillcolor='white',
marker={
'size': 10,
'color': _color
},
opacity=0.7
)
)
_fig = go.Figure(
data=_data,
layout={
'xaxis': {
'title': 'Window distance (cell diameter)',
'zeroline': False,
'tickmode': 'array',
'tickvals': OFFSETS_X,
'type': 'category'
},
'yaxis': {
'title': 'Correlation',
'range': [-1, 1],
'zeroline': False,
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
},
'boxmode': 'group',
'legend': {
'xanchor': 'right',
'yanchor': 'top',
'bordercolor': 'black',
'borderwidth': 2
}
}
)
save.to_html(
_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot'
)
def main(_type='alpha',
_low_connectivity=False,
_plots=None,
_plot_types=None):
if _plots is None:
_plots = ['same', 'different']
if _plot_types is None:
_plot_types = ['stacked_bar', 'box', 'bar']
_same_arrays = []
_different_arrays = []
_same_highest = []
_different_highest = []
if _type == 'alpha':
_alphas = ALPHAS
_betas = [BETA] * len(ALPHAS)
_names = _alphas
elif _type == 'beta':
_alphas = [ALPHA] * len(BETAS)
_betas = BETAS
_names = _betas
else:
raise Exception(
'No such type. Only \'alpha\' or \'beta\' are acceptable.')
for _alpha, _beta in zip(_alphas, _betas):
print('Alpha:', _alpha, 'beta:', _beta)
_, _same_time_lags_arrays, _different_time_lags_arrays, _same_time_lags_highest, \
_different_time_lags_highest = same_inner_correlation_vs_different_inner_correlation_cross_correlation.compute_fiber_densities(
_alpha=_alpha, _beta=_beta, _low_connectivity=_low_connectivity)
_same_arrays.append(_same_time_lags_arrays[TIME_LAG_INDEX])
_different_arrays.append(_different_time_lags_arrays[TIME_LAG_INDEX])
_same_highest.append(_same_time_lags_highest)
_different_highest.append(_different_time_lags_highest)
if _plots is not None:
# stacked bar plot
if 'stacked_bar' in _plot_types:
for _name, _sums in zip(['same', 'different'],
[_same_highest, _different_highest]):
if _name in _plots:
_y_arrays = [[], [], []]
for _type_sums in _sums:
_left_wins, _none_wins, _right_wins = 0, 0, 0
for _time_lag, _type_sum in zip(
same_inner_correlation_vs_different_inner_correlation_cross_correlation
.TIME_LAGS, _type_sums):
if _time_lag > 0:
_left_wins += _type_sum
elif _time_lag < 0:
_right_wins += _type_sum
else:
_none_wins += _type_sum
_total = sum(_type_sums)
_y_arrays[0].append(_left_wins / _total)
_y_arrays[1].append(_none_wins / _total)
_y_arrays[2].append(_right_wins / _total)
_colors_array = config.colors(3)
_fig = go.Figure(data=[
go.Bar(x=_names,
y=_y_array,
name=_name,
marker={'color': _color}) for _name, _y_array,
_color in zip(['Leader', 'None', 'Follower'],
_y_arrays, _colors_array)
],
layout={
'xaxis': {
'title': _type.capitalize(),
'zeroline': False,
'tickmode': 'array',
'tickvals': _names,
'type': 'category'
},
'yaxis': {
'title':
'Highest correlation fraction',
'range': [0, 1.1],
'zeroline': False,
'tickmode': 'array',
'tickvals': [0, 0.5, 1]
},
'barmode': 'stack',
'legend': {
'xanchor': 'right',
'yanchor': 'top',
'bordercolor': 'black',
'borderwidth': 2
},
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS,
save.get_module_name()),
_filename='plot_stacked_bar_' + _type +
'_low_con_' + str(_low_connectivity) + '_' +
_name)
# box plot
if 'box' in _plot_types:
for _name, _arrays in zip(['same', 'different'],
[_same_arrays, _different_arrays]):
if _name in _plots:
_fig = go.Figure(
data=[
go.Box(y=_y,
name=_name,
boxpoints=False,
line={'width': 1},
marker={
'size': 10,
'color': '#2e82bf'
},
showlegend=False)
for _y, _name in zip(_arrays, _names)
],
layout={
'xaxis': {
'title': _type.capitalize(),
'zeroline': False,
'tickmode': 'array',
'tickvals': _names,
'type': 'category'
},
'yaxis': {
'title':
'Inner correlation' if _name == 'same' else
'Different network correlation',
'range': [-1, 1.1],
'zeroline':
False,
'tickmode':
'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
}
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS,
save.get_module_name()),
_filename='plot_box_' + _type + '_low_con_' +
str(_low_connectivity) + '_' + _name)
# bar plot
if 'bar' in _plot_types:
for _name, _sums in zip(['same', 'different'],
[_same_highest, _different_highest]):
if _name in _plots:
_fig = go.Figure(data=go.Bar(
x=_names,
y=[
_type_sums[TIME_LAG_INDEX] / sum(_type_sums)
for _type_sums in _sums
],
marker={'color': '#2e82bf'}),
layout={
'xaxis': {
'title': _type.capitalize(),
'zeroline': False,
'tickmode': 'array',
'tickvals': _names,
'type': 'category'
},
'yaxis': {
'title': 'Lag ' + str(TIME_LAG) +
' highest correlation fraction',
'range': [0, 1.1],
'zeroline': False,
'tickmode': 'array',
'tickvals': [0, 0.5, 1]
}
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS,
save.get_module_name()),
_filename='plot_bar_' + _type + '_low_con_' +
str(_low_connectivity) + '_' + _name)
def main():
_simulations = load.structured()
_simulations = filtering.by_time_points_amount(
_simulations, _time_points=SIMULATIONS_TIME_POINTS)
_simulations = filtering.by_categories(_simulations,
_is_single_cell=False,
_is_heterogeneity=True,
_is_low_connectivity=False,
_is_causality=False,
_is_dominant_passive=False,
_is_fibrin=False)
_simulations = filtering.by_heterogeneity(_simulations, _std=STD)
_simulations = filtering.by_pair_distances(_simulations,
_distances=PAIR_DISTANCE)
print('Total simulations:', len(_simulations))
_fiber_densities = compute_fiber_densities(_simulations)
_x_arrays = [[] for _i in PAIR_DISTANCE]
_y_arrays = [[] for _i in PAIR_DISTANCE]
for _distance_index, _distance in enumerate(PAIR_DISTANCE):
_distance_simulations = filtering.by_pair_distance(_simulations,
_distance=_distance)
print('Distance:', _distance, 'Total simulations:',
len(_distance_simulations))
for _simulation in tqdm(_distance_simulations,
desc='Simulations loop'):
for _direction in ['inside', 'outside']:
_left_cell_fiber_densities = _fiber_densities[(_simulation,
'left_cell',
_direction)]
_right_cell_fiber_densities = _fiber_densities[(_simulation,
'right_cell',
_direction)]
_correlation = compute_lib.correlation(
compute_lib.derivative(_left_cell_fiber_densities,
_n=DERIVATIVE),
compute_lib.derivative(_right_cell_fiber_densities,
_n=DERIVATIVE))
if _direction == 'inside':
_x_arrays[_distance_index].append(_correlation)
else:
_y_arrays[_distance_index].append(_correlation)
print('Wilcoxon of insides minus outsides around the zero:')
print(
wilcoxon(
np.array(_x_arrays[_distance_index]) -
np.array(_y_arrays[_distance_index])))
# 2d plots
_colors_array = config.colors(4)
_legendgroup_array = ['group_1', 'group_1', 'group_2', 'group_2']
_fig = go.Figure(data=[
go.Scatter(x=_x,
y=_y,
name='Dist. ' + str(_distance),
mode='markers',
marker={
'size': 10,
'color': _color
},
legendgroup=_legendgroup)
for _x, _y, _distance, _color, _legendgroup in zip(
_x_arrays, _y_arrays, PAIR_DISTANCE, _colors_array,
_legendgroup_array)
],
layout={
'xaxis': {
'title': 'Inner correlation',
'zeroline': False,
'range': [-1.1, 1.2],
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
},
'yaxis': {
'title': 'Outer correlation',
'zeroline': False,
'range': [-1.1, 1.2],
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
},
'legend': {
'x': 0.1,
'y': 1,
'xanchor': 'left',
'yanchor': 'top',
'bordercolor': 'black',
'borderwidth': 2,
'bgcolor': 'white',
'orientation': 'h'
},
'shapes': [{
'type': 'line',
'x0': -1,
'y0': -1,
'x1': -1,
'y1': 1,
'line': {
'color': 'black',
'width': 2
}
}, {
'type': 'line',
'x0': -1,
'y0': -1,
'x1': 1,
'y1': -1,
'line': {
'color': 'black',
'width': 2
}
}, {
'type': 'line',
'x0': -1,
'y0': -1,
'x1': 1,
'y1': 1,
'line': {
'color': 'red',
'width': 2
}
}]
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot')
for _x, _y, _distance, _color in zip(_x_arrays, _y_arrays, PAIR_DISTANCE,
_colors_array):
_fig = go.Figure(data=go.Scatter(x=_x,
y=_y,
name='Dist. ' + str(_distance),
mode='markers',
marker={
'size': 10,
'color': _color
},
showlegend=True),
layout={
'xaxis': {
'title': 'Inner correlation',
'zeroline': False,
'range': [-1.1, 1.2],
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
},
'yaxis': {
'title': 'Outer correlation',
'zeroline': False,
'range': [-1.1, 1.2],
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
},
'legend': {
'xanchor': 'left',
'x': 0.1,
'yanchor': 'top',
'bordercolor': 'black',
'borderwidth': 2,
'bgcolor': 'white'
},
'shapes': [{
'type': 'line',
'x0': -1,
'y0': -1,
'x1': -1,
'y1': 1,
'line': {
'color': 'black',
'width': 2
}
}, {
'type': 'line',
'x0': -1,
'y0': -1,
'x1': 1,
'y1': -1,
'line': {
'color': 'black',
'width': 2
}
}, {
'type': 'line',
'x0': -1,
'y0': -1,
'x1': 1,
'y1': 1,
'line': {
'color': 'red',
'width': 2
}
}]
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot_distance_' + str(_distance))
# box plot
_box_y_arrays = [[] for _i in PAIR_DISTANCE]
for _x_array, _y_array, _distance_index in zip(_x_arrays, _y_arrays,
range(len(PAIR_DISTANCE))):
for _x, _y in zip(_x_array, _y_array):
_point_distance = compute_lib.distance_from_a_point_to_a_line(
_line=[-1, -1, 1, 1], _point=[_x, _y])
if _x > _y:
_box_y_arrays[_distance_index].append(_point_distance)
else:
_box_y_arrays[_distance_index].append(-_point_distance)
_fig = go.Figure(data=[
go.Box(y=_y,
name=str(_distance),
boxpoints='all',
jitter=1,
pointpos=0,
line={'width': 1},
fillcolor='white',
marker={
'size': 10,
'color': _color
},
showlegend=False) for _y, _distance, _color in zip(
_box_y_arrays, PAIR_DISTANCE, _colors_array)
],
layout={
'xaxis': {
'title': 'Pair distance (cell diameter)',
'zeroline': False,
'tickmode': 'array',
'tickvals': PAIR_DISTANCE,
'type': 'category'
},
'yaxis': {
'title': 'Inner minus outer correlation',
'zeroline': False,
'tickmode': 'array',
'tickvals': [-0.2, 0, 0.2, 0.4]
}
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot_box')
def main(_low_connectivity=False):
_names_array, _x_array, _y_array = compute_cell_pairs(_low_connectivity)
# plot
_colors_array = config.colors(3)
_fig = go.Figure(data=[
go.Scatter(x=_x,
y=[np.mean(_array) for _array in _y],
name=_name,
error_y={
'type': 'data',
'array': [np.std(_array) for _array in _y],
'thickness': 1,
'color': _color
},
mode='markers',
marker={
'size': 15,
'color': _color
},
opacity=0.7) for _x, _y, _name, _color in zip(
_x_array, _y_array, _names_array, _colors_array)
],
layout={
'xaxis': {
'title': 'Window distance (cell diameter)',
'zeroline': False
},
'yaxis': {
'title': 'Fiber density (z-score)',
'range': [-1.7, 13],
'zeroline': False,
'tickmode': 'array',
'tickvals': [0, 4, 8, 12]
},
'legend': {
'xanchor': 'right',
'yanchor': 'top',
'bordercolor': 'black',
'borderwidth': 2
},
'shapes': [{
'type': 'line',
'x0': -0.2,
'y0': -1.5,
'x1': 3.4,
'y1': -1.5,
'line': {
'color': 'black',
'width': 2
}
}, {
'type': 'line',
'x0': -0.2,
'y0': -1.5,
'x1': -0.2,
'y1': 13,
'line': {
'color': 'black',
'width': 2
}
}]
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot_low_con_' + str(_low_connectivity))
def main(_low_connectivity=False):
_simulations = load.structured()
_simulations = filtering.by_time_points_amount(
_simulations, TIME_POINT[_low_connectivity])
_simulations = filtering.by_categories(
_simulations,
_is_single_cell=False,
_is_heterogeneity=True,
_is_low_connectivity=_low_connectivity,
_is_causality=False,
_is_dominant_passive=False,
_is_fibrin=False)
_simulations = filtering.by_heterogeneity(_simulations, _std=STD)
_simulations = filtering.by_pair_distances(_simulations,
_distances=PAIR_DISTANCE)
print('Total simulations:', len(_simulations))
_fiber_densities = compute_fiber_densities(_simulations, _low_connectivity)
_y_arrays = [[] for _i in PAIR_DISTANCE]
for _distance_index, _distance in enumerate(PAIR_DISTANCE):
_distance_simulations = filtering.by_pair_distance(_simulations,
_distance=_distance)
print('Distance:', _distance, 'Total simulations:',
len(_distance_simulations))
_higher_same_counter = 0
for _same_index in tqdm(range(len(_distance_simulations)),
desc='Main loop'):
_same_simulation = _distance_simulations[_same_index]
_same_left_cell_fiber_densities = _fiber_densities[(
_same_simulation, 'left_cell')]
_same_right_cell_fiber_densities = _fiber_densities[(
_same_simulation, 'right_cell')]
_same_correlation = compute_lib.correlation(
compute_lib.derivative(_same_left_cell_fiber_densities,
_n=DERIVATIVE),
compute_lib.derivative(_same_right_cell_fiber_densities,
_n=DERIVATIVE))
for _different_index in range(len(_distance_simulations)):
if _same_index != _different_index:
_different_simulation = _distance_simulations[
_different_index]
for _same_cell_id, _different_cell_id in product(
['left_cell', 'right_cell'],
['left_cell', 'right_cell']):
_same_fiber_densities = \
_fiber_densities[(_same_simulation, _same_cell_id)]
_different_fiber_densities = \
_fiber_densities[(_different_simulation, _different_cell_id)]
_different_correlation = compute_lib.correlation(
compute_lib.derivative(_same_fiber_densities,
_n=DERIVATIVE),
compute_lib.derivative(_different_fiber_densities,
_n=DERIVATIVE))
_point_distance = compute_lib.distance_from_a_point_to_a_line(
_line=[-1, -1, 1, 1],
_point=[_same_correlation, _different_correlation])
if _same_correlation > _different_correlation:
_y_arrays[_distance_index].append(_point_distance)
_higher_same_counter += 1
else:
_y_arrays[_distance_index].append(-_point_distance)
print('Total points:', len(_y_arrays[_distance_index]))
print('Wilcoxon around the zero:')
print(wilcoxon(_y_arrays[_distance_index]))
print('Higher same amount:',
_higher_same_counter / len(_y_arrays[_distance_index]))
# plot
_colors_array = config.colors(4)
_fig = go.Figure(data=[
go.Box(y=_y,
name=str(_distance),
boxpoints=False,
line={'width': 1},
marker={
'size': 10,
'color': _color
},
showlegend=False) for _y, _distance, _color in zip(
_y_arrays, PAIR_DISTANCE, _colors_array)
],
layout={
'xaxis': {
'title': 'Pair distance (cell diameter)',
'zeroline': False,
'tickmode': 'array',
'tickvals': PAIR_DISTANCE,
'type': 'category'
},
'yaxis': {
'title': 'Same minus different correlation',
'range': [-1, 1.1],
'zeroline': False,
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
}
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot')
def main():
_simulations = load.structured()
_simulations = filtering.by_time_points_amount(
_simulations, _time_points=SIMULATIONS_TIME_POINTS)
_simulations = filtering.by_categories(_simulations,
_is_single_cell=False,
_is_heterogeneity=False,
_is_low_connectivity=False,
_is_causality=False,
_is_dominant_passive=False,
_is_fibrin=False)
_simulations = filtering.by_pair_distance(_simulations,
_distance=PAIR_DISTANCE)
print('Total simulations:', len(_simulations))
_fiber_densities = compute_fiber_densities(_simulations)
_kpss_y_arrays = [[] for _i in DERIVATIVES]
_adf_y_arrays = [[] for _i in DERIVATIVES]
for _simulation in tqdm(_simulations, desc='Simulations loop'):
for _cell_id in ['left_cell', 'right_cell']:
_cell_fiber_densities = _fiber_densities[(_simulation, _cell_id)]
for _derivative_index, _derivative in enumerate(DERIVATIVES):
_cell_fiber_densities_derivative = compute_lib.derivative(
_cell_fiber_densities, _n=_derivative)
with warnings.catch_warnings():
warnings.simplefilter('ignore',
category=InterpolationWarning)
_, _kpss_p_value, _, _ = kpss(
_cell_fiber_densities_derivative, nlags='legacy')
_kpss_y_arrays[_derivative_index].append(_kpss_p_value)
_, _adf_p_value, _, _, _, _ = adfuller(
_cell_fiber_densities_derivative)
_adf_y_arrays[_derivative_index].append(_adf_p_value)
# print results
print('KPSS:')
for _derivative_index, _derivative in enumerate(DERIVATIVES):
_stationary_count = len([
_value for _value in _kpss_y_arrays[_derivative_index]
if _value > 0.05
])
print(
'Derivative:', _derivative, 'Stationary:',
str(_stationary_count / len(_kpss_y_arrays[_derivative_index]) *
100) + '%')
print('ADF:')
for _derivative_index, _derivative in enumerate(DERIVATIVES):
_stationary_count = len([
_value for _value in _adf_y_arrays[_derivative_index]
if _value < 0.05
])
print(
'Derivative:', _derivative, 'Stationary:',
str(_stationary_count / len(_adf_y_arrays[_derivative_index]) *
100) + '%')
# plot
_colors_array = config.colors(3)
for _test_name, _y_title, _y_tickvals, _p_value_line, _y_arrays in \
zip(
['kpss', 'adf'],
['KPSS test p-value', 'ADF test p-value'],
[[0.05, 0.1], [0.05, 1]],
[0.05, 0.05],
[_kpss_y_arrays, _adf_y_arrays]
):
_fig = go.Figure(data=[
go.Box(y=_y,
name=_derivative,
boxpoints='all',
jitter=1,
pointpos=0,
line={'width': 1},
fillcolor='white',
marker={
'size': 10,
'color': _color
},
opacity=0.7,
showlegend=False) for _y, _derivative, _color in zip(
_y_arrays, DERIVATIVES_TEXT, _colors_array)
],
layout={
'xaxis': {
'title': 'Fiber density derivative',
'zeroline': False
},
'yaxis': {
'title': _y_title,
'zeroline': False,
'tickmode': 'array',
'tickvals': _y_tickvals
},
'shapes': [{
'type': 'line',
'x0': DERIVATIVES[0] - 0.75,
'y0': _p_value_line,
'x1': DERIVATIVES[-1] + 0.75,
'y1': _p_value_line,
'line': {
'color': 'red',
'width': 2,
'dash': 'dash'
}
}]
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot_' + _test_name)
def main():
_simulations = load.structured()
_simulations = filtering.by_time_points_amount(_simulations,
_time_points=TIME_POINTS)
_simulations = filtering.by_categories(_simulations,
_is_single_cell=True,
_is_heterogeneity=False,
_is_low_connectivity=False,
_is_causality=False,
_is_dominant_passive=False,
_is_fibrin=False)
print('Total simulations:', len(_simulations))
_fiber_densities = compute_simulations_fiber_densities(_simulations)
_y_arrays = [[] for _i in DERIVATIVES]
for _index_1 in tqdm(range(len(_simulations)), desc='Simulations loop'):
_simulation_1 = _simulations[_index_1]
_cell_1_fiber_densities = \
[_fiber_densities[(_simulation_1, _direction)] for _direction in ['left', 'right', 'up', 'down']]
_cell_1_fiber_densities = np.mean(_cell_1_fiber_densities, axis=0)
for _index_2 in range(_index_1 + 1, len(_simulations)):
_simulation_2 = _simulations[_index_2]
_cell_2_fiber_densities = \
[_fiber_densities[(_simulation_2, _direction)] for _direction in ['left', 'right', 'up', 'down']]
_cell_2_fiber_densities = np.mean(_cell_2_fiber_densities, axis=0)
for _derivative_index, _derivative in enumerate(DERIVATIVES):
_y_arrays[_derivative_index].append(
compute_lib.correlation(
compute_lib.derivative(_cell_1_fiber_densities,
_n=_derivative),
compute_lib.derivative(_cell_2_fiber_densities,
_n=_derivative)))
print('Total points:', len(_y_arrays[0]))
print('Wilcoxon around the zero')
for _y_array, _derivative in zip(_y_arrays, DERIVATIVES):
print('Derivative:', _derivative, wilcoxon(_y_array))
# plot
_colors_array = config.colors(3)
_fig = go.Figure(data=[
go.Box(y=_y,
name=_derivative,
boxpoints='all',
jitter=1,
pointpos=0,
line={'width': 1},
fillcolor='white',
marker={
'size': 10,
'color': _color
},
opacity=0.7,
showlegend=False) for _y, _derivative, _color in zip(
_y_arrays, DERIVATIVES_TEXT, _colors_array)
],
layout={
'xaxis': {
'title': 'Fiber density derivative',
'zeroline': False
},
'yaxis': {
'title': 'Correlation',
'range': [-1, 1],
'zeroline': False,
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
}
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot')
def main():
_simulations = load.structured()
_simulations = filtering.by_time_points_amount(_simulations, TIME_POINT)
_simulations = filtering.by_categories(
_simulations,
_is_single_cell=False,
_is_heterogeneity=None,
_is_low_connectivity=False,
_is_causality=False,
_is_dominant_passive=False,
_is_fibrin=False
)
_simulations = filtering.by_heterogeneities(_simulations, _stds=STDS)
_simulations = filtering.by_pair_distance(_simulations, _distance=PAIR_DISTANCE)
print('Total simulations:', len(_simulations))
_fiber_densities = compute_fiber_densities(_simulations)
# stds loop
_std_communicating = [[] for _i in STDS]
_std_non_communicating = [[] for _i in STDS]
for _std_index, _std in enumerate(STDS):
print('Std:', _std)
_simulations_std = filtering.by_heterogeneity(_simulations, _std=_std)
print('Total simulations:', len(_simulations_std))
# communicating loop
for _simulation in tqdm(_simulations_std, desc='Communicating pairs loop'):
_left_cell_fiber_densities = _fiber_densities[(_simulation, 'left_cell')]
_right_cell_fiber_densities = _fiber_densities[(_simulation, 'right_cell')]
_correlation = compute_lib.correlation(
compute_lib.derivative(_left_cell_fiber_densities, _n=DERIVATIVE),
compute_lib.derivative(_right_cell_fiber_densities, _n=DERIVATIVE)
)
_std_communicating[_std_index].append(_correlation)
# non-communicating loop
_simulations_indices = range(len(_simulations_std))
for _simulation_1_index in tqdm(_simulations_indices, desc='Non-communicating pairs loop'):
_simulation_1 = _simulations_std[_simulation_1_index]
for _simulation_2_index in _simulations_indices[_simulation_1_index + 1:]:
_simulation_2 = _simulations_std[_simulation_2_index]
for _simulation_1_cell_id, _simulation_2_cell_id in product(['left_cell', 'right_cell'],
['left_cell', 'right_cell']):
_simulation_1_fiber_densities = _fiber_densities[(_simulation_1, _simulation_1_cell_id)]
_simulation_2_fiber_densities = _fiber_densities[(_simulation_2, _simulation_2_cell_id)]
_correlation = compute_lib.correlation(
compute_lib.derivative(_simulation_1_fiber_densities, _n=DERIVATIVE),
compute_lib.derivative(_simulation_2_fiber_densities, _n=DERIVATIVE)
)
_std_non_communicating[_std_index].append(_correlation)
print('Wilcoxon rank-sum test:', ranksums(_std_communicating[_std_index], _std_non_communicating[_std_index]))
# histogram plot, once with and once without the legend
_colors_array = config.colors(len(STDS))
for _show_legend in [True, False]:
_fig = go.Figure(
data=[
*[
go.Histogram(
x=_non_communicating,
name='STD ' + str(_std),
marker={
'color': _color
},
nbinsx=10,
histnorm='probability',
showlegend=_show_legend
) for _std, _non_communicating, _color in zip(STDS, _std_non_communicating, _colors_array)
],
*[
go.Scatter(
x=_communicating,
y=[0.5 - 0.02 * _std_index for _i in range(len(_communicating))],
mode='text',
text='●',
textfont={
'color': _color,
'size': 15
},
showlegend=False
) for _std_index, _communicating, _color in zip(range(len(STDS)), _std_communicating, _colors_array)
]
],
layout={
'xaxis': {
'title': 'Correlation',
'zeroline': False
},
'yaxis': {
'title': 'Fraction',
'zeroline': False
},
'legend': {
'xanchor': 'right',
'yanchor': 'top',
'bordercolor': 'black',
'borderwidth': 2
},
'bargap': 0.1
}
)
save.to_html(
_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot_legend_' + str(_show_legend)
)
def main(_directions=None):
if _directions is None:
_directions = ['inside', 'outside']
_simulations = load.structured()
_simulations = filtering.by_time_points_amount(
_simulations, _time_points=SIMULATIONS_TIME_POINTS)
_simulations = filtering.by_categories(_simulations,
_is_single_cell=False,
_is_heterogeneity=False,
_is_low_connectivity=False,
_is_causality=False,
_is_dominant_passive=False,
_is_fibrin=False)
_simulations = filtering.by_pair_distance(_simulations,
_distance=PAIR_DISTANCE)
print('Total simulations:', len(_simulations))
_fiber_densities = compute_fiber_densities(_simulations, _directions)
for _direction in _directions:
_y_arrays = [[] for _i in DERIVATIVES]
for _simulation in tqdm(_simulations, desc='Simulations loop'):
_left_cell_fiber_densities = _fiber_densities[(_simulation,
'left_cell',
_direction)]
_right_cell_fiber_densities = _fiber_densities[(_simulation,
'right_cell',
_direction)]
for _derivative_index, _derivative in enumerate(DERIVATIVES):
_y_arrays[_derivative_index].append(
compute_lib.correlation(
compute_lib.derivative(_left_cell_fiber_densities,
_n=_derivative),
compute_lib.derivative(_right_cell_fiber_densities,
_n=_derivative)))
print('Direction:', _direction)
print('Total pairs:', len(_y_arrays[0]))
print('Wilcoxon around the zero')
for _y_array, _derivative in zip(_y_arrays, DERIVATIVES):
print('Derivative:', _derivative, wilcoxon(_y_array))
# plot
_y_title = 'Inner correlation' if _direction == 'inside' else 'Outer correlation'
_colors_array = config.colors(3)
_fig = go.Figure(data=[
go.Box(y=_y,
name=_derivative,
boxpoints='all',
jitter=1,
pointpos=0,
line={'width': 1},
fillcolor='white',
marker={
'size': 10,
'color': _color
},
opacity=0.7,
showlegend=False) for _y, _derivative, _color in zip(
_y_arrays, DERIVATIVES_TEXT, _colors_array)
],
layout={
'xaxis': {
'title': 'Fiber density derivative',
'zeroline': False
},
'yaxis': {
'title': _y_title,
'range': [-1, 1],
'zeroline': False,
'tickmode': 'array',
'tickvals': [-1, -0.5, 0, 0.5, 1]
}
})
save.to_html(_fig=_fig,
_path=os.path.join(paths.PLOTS, save.get_module_name()),
_filename='plot_direction_' + _direction)