def create_plots(info_path):
output_dir = os.path.join(os.path.dirname(info_path), 'plots')
if not os.path.exists(output_dir):
os.mkdir(output_dir)
prior_prob_omega_less_than = 0.0887
psi_results, omega_results, tau_results = parse_results(info_path)
cfg_to_psi = {}
cfg_to_psi_prob = {}
for cfg, psi in psi_results.iteritems():
cfg_to_psi[cfg] = psi.mode
cfg_to_psi_prob[cfg] = psi.prob
cfg_to_omega = {}
cfg_to_omega_prob = {}
cfg_to_omega_true_ests = {}
cfg_to_omega_true_ests_glm = {}
for cfg, omega in omega_results.iteritems():
cfg_to_omega[cfg] = omega.median
cfg_to_omega_prob[cfg] = omega.prob
cfg_to_omega_true_ests[cfg] = {'x': omega.true, 'y': omega.median}
cfg_to_omega_true_ests_glm[cfg] = {'x': omega.true, 'y': omega.mode_glm}
cfg_to_num_excluded = {}
cfg_to_num_excluded_glm = {}
cfg_to_prob_of_exclusion = {}
cfg_to_prob_of_exclusion_glm = {}
cfg_to_prob_of_bf_ex = {}
cfg_to_prob_of_bf_ex_glm = {}
bf_10_exclusion_prob = None
for cfg, tau in tau_results.iteritems():
cfg_to_num_excluded[cfg] = tau.num_excluded
cfg_to_num_excluded_glm[cfg] = tau.num_excluded_glm
cfg_to_prob_of_exclusion[cfg] = tau.prob_of_exclusion
cfg_to_prob_of_exclusion_glm[cfg] = tau.prob_of_exclusion_glm
cfg_to_prob_of_bf_ex[cfg] = tau.prob_of_bf_exclusion
cfg_to_prob_of_bf_ex_glm[cfg] = tau.prob_of_bf_exclusion_glm
if not bf_10_exclusion_prob:
bf_10_exclusion_prob = tau.bf_10_exclusion_prob
psi_plot = PowerPlotGrid(observed_config_to_estimates = cfg_to_psi,
variable = 'psi',
num_columns = 2,
x_title = r'Estimated number of divergence events, $\hat{\Psi}$',
y_title = 'Density',
width = 14.0,
height = 2.8,
auto_height = False,
auto_adjust_margins = False,
margin_left = 0.025,
margin_bottom = 0.1,
margin_right = 1,
margin_top = 0.835,
padding_between_horizontal = 0.5)
fig = psi_plot.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 8.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-psi-mode-6.pdf'))
psi_plot.width = 10.0
fig = psi_plot.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 12.0,
x_tick_label_size = 8.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-psi-mode-4.pdf'))
omega_prob_plot = ProbabilityPowerPlotGrid(
observed_config_to_estimates = cfg_to_omega_prob,
variable = 'omega',
div_model_prior = 'psi',
bayes_factor = 10,
bayes_factor_prob = prior_prob_omega_less_than,
num_columns = 2,
x_title = (r'Posterior probability of one divergence, '
r'$p(\Omega < 0.01 \, | \, B_{{\epsilon}}(S*))$'),
y_title = 'Density',
width = 14.0,
height = 2.8,
auto_height = False,
auto_adjust_margins = False,
margin_left = 0.025,
margin_bottom = 0.1,
margin_right = 1,
margin_top = 0.835,
padding_between_horizontal = 0.5)
fig = omega_prob_plot.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-omega-prob-6.pdf'))
omega_prob_plot.width = 10.0
fig = omega_prob_plot.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 10.0,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-omega-prob-4.pdf'))
omega_prob_plot.label_offset = 6
omega_prob_plot.width = 14.0
fig = omega_prob_plot.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
add_column_labels = False,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-omega-prob-6-panel.pdf'))
omega_prob_plot.label_offset = 4
omega_prob_plot.width = 10.0
fig = omega_prob_plot.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
add_column_labels = False,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 10.0,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-omega-prob-4-panel.pdf'))
omega_accuracy_plot = AccuracyPowerPlotGrid(
observed_config_to_estimates = cfg_to_omega_true_ests,
num_columns = 2,
x_title = r'True variance of divergence times, $\Omega$',
y_title = r'$\hat{\Omega}$',
width = 14.0,
height = 2.8,
auto_height = False,
auto_adjust_margins = False,
margin_left = 0.025,
margin_bottom = 0.1,
margin_right = 1,
margin_top = 0.825,
padding_between_horizontal = 0.5)
fig = omega_accuracy_plot.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 10.0,
share_x = False,
share_y = False)
fig.savefig(os.path.join(output_dir, 'power-accuracy-omega-median-6.pdf'))
omega_accuracy_plot.width = 10.0
fig = omega_accuracy_plot.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 10.0,
x_tick_label_size = 10.0,
share_x = False,
share_y = False)
fig.savefig(os.path.join(output_dir, 'power-accuracy-omega-median-4.pdf'))
omega_accuracy_plot_glm = AccuracyPowerPlotGrid(
observed_config_to_estimates = cfg_to_omega_true_ests_glm,
num_columns = 2,
x_title = r'True variance of divergence times, $\Omega$',
y_title = r'$\hat{\Omega}$',
width = 14.0,
height = 2.8,
auto_height = False,
auto_adjust_margins = False,
margin_left = 0.025,
margin_bottom = 0.1,
margin_right = 1,
margin_top = 0.825,
padding_between_horizontal = 0.5)
fig = omega_accuracy_plot_glm.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 10.0,
share_x = False,
share_y = False)
fig.savefig(os.path.join(output_dir, 'power-accuracy-omega-mode-glm-6.pdf'))
omega_accuracy_plot_glm.width = 10.0
fig = omega_accuracy_plot_glm.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 10.0,
x_tick_label_size = 10.0,
share_x = False,
share_y = False)
fig.savefig(os.path.join(output_dir, 'power-accuracy-omega-mode-glm-4.pdf'))
omega_accuracy_plot_glm.label_offset = 6
omega_accuracy_plot_glm.width = 14.0
fig = omega_accuracy_plot_glm.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
add_column_labels = False,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 10.0,
share_x = False,
share_y = False)
fig.savefig(os.path.join(output_dir, 'power-accuracy-omega-mode-glm-6-panel.pdf'))
omega_accuracy_plot_glm.label_offset = 4
omega_accuracy_plot_glm.width = 10.0
fig = omega_accuracy_plot_glm.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
add_column_labels = False,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 10.0,
x_tick_label_size = 10.0,
share_x = False,
share_y = False)
fig.savefig(os.path.join(output_dir, 'power-accuracy-omega-mode-glm-4-panel.pdf'))
ex_prob_plot = ProbabilityPowerPlotGrid(
observed_config_to_estimates = cfg_to_prob_of_exclusion,
variable = 'tau_exclusion',
div_model_prior = 'psi',
bayes_factor = 10,
bayes_factor_prob = bf_10_exclusion_prob,
draw_bayes_factor_line = False,
cfg_to_prob_of_bf_exclusion = cfg_to_prob_of_bf_ex,
num_columns = 2,
x_title = (r'Posterior probability of excluding true parameters, $p(\mathbf{\tau} \, \notin \, '
r'M \, | \, B_{\epsilon}(S*))$'),
y_title = 'Density',
width = 14.0,
height = 2.8,
auto_height = False,
auto_adjust_margins = False,
margin_left = 0.025,
margin_bottom = 0.1,
margin_right = 1,
margin_top = 0.835,
padding_between_horizontal = 0.5)
fig = ex_prob_plot.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-prob-exclusion-6.pdf'))
ex_prob_plot.width = 10.0
fig = ex_prob_plot.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 10.0,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-prob-exclusion-4.pdf'))
ex_prob_plot.label_offset = 6
ex_prob_plot.width = 14.0
fig = ex_prob_plot.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
add_column_labels = False,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-prob-exclusion-6-panel.pdf'))
ex_prob_plot.label_offset = 4
ex_prob_plot.width = 10.0
fig = ex_prob_plot.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
add_column_labels = False,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 10.0,
x_tick_label_size = 10.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-prob-exclusion-4-panel.pdf'))
ex_plot = PowerPlotGrid(
observed_config_to_estimates = cfg_to_num_excluded,
variable = 'tau_exclusion',
num_columns = 2,
x_title = r'Number of true $\tau$ excluded',
y_title = 'Density',
width = 14.0,
height = 2.8,
auto_height = False,
auto_adjust_margins = False,
margin_left = 0.025,
margin_bottom = 0.1,
margin_right = 1,
margin_top = 0.835,
padding_between_horizontal = 0.5)
fig = ex_plot.create_column_grid(
subplot_indices_to_exclude = [],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
x_tick_label_size = 8.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-num-excluded-6.pdf'))
ex_plot.width = 10.0
fig = ex_plot.create_column_grid(
subplot_indices_to_exclude = [1,3],
x_title_size = 14.0,
y_title_size = 14.0,
column_label_size = 16.0,
column_label_offset = 0.14,
right_text_size = 12.0,
x_tick_label_size = 8.0,
share_x = True,
share_y = True)
fig.savefig(os.path.join(output_dir, 'power-num-excluded-4.pdf'))
