def _theta_plot_default(self):
"""Create plot of theta parameters."""
# We plot both the thetas and the samples from the posterior; if the
# latter are not defined, the corresponding ArrayPlotData names
# should be set to an empty list, so that they are not displayed
theta = self.model.theta
theta_len = theta.shape[0]
# create the plot data
if not self.theta_plot_data:
self.theta_plot_data = ArrayPlotData()
self._update_plot_data()
# create the plot
theta_plot = Plot(self.theta_plot_data)
for idx in range(theta_len):
# candle plot summarizing samples over the posterior
theta_plot.candle_plot((_w_idx('index', idx),
_w_idx('min', idx),
_w_idx('barmin', idx),
_w_idx('avg', idx),
_w_idx('barmax', idx),
_w_idx('max', idx)),
color = get_annotator_color(idx),
bar_line_color = "black",
stem_color = "blue",
center_color = "red",
center_width = 2)
# plot of raw samples
theta_plot.plot((_w_idx('ysamples', idx),
_w_idx('xsamples', idx)),
type='scatter',
color='black',
marker='dot',
line_width=0.5,
marker_size=1)
# plot current parameters
theta_plot.plot((_w_idx('y', idx), _w_idx('x', idx)),
type='scatter',
color=get_annotator_color(idx),
marker='plus',
marker_size=8,
line_width=2)
# adjust axis bounds
theta_plot.range2d = self._compute_range2d()
# remove horizontal grid and axis
theta_plot.underlays = [theta_plot.x_grid, theta_plot.y_axis]
# create new horizontal axis
label_list = [str(i) for i in range(theta_len)]
label_axis = LabelAxis(
theta_plot,
orientation = 'bottom',
positions = range(1, theta_len+1),
labels = label_list,
label_rotation = 0
)
# use a FixedScale tick generator with a resolution of 1
label_axis.tick_generator = ScalesTickGenerator(scale=FixedScale(1.))
theta_plot.index_axis = label_axis
theta_plot.underlays.append(label_axis)
theta_plot.padding = 25
theta_plot.padding_left = 40
theta_plot.aspect_ratio = 1.0
container = VPlotContainer()
container.add(theta_plot)
container.bgcolor = 0xFFFFFF
self.decorate_plot(container, theta)
self._set_title(theta_plot)
return container
def _theta_plot_default(self):
"""Create plot of theta parameters."""
# We plot both the thetas and the samples from the posterior; if the
# latter are not defined, the corresponding ArrayPlotData names
# should be set to an empty list, so that they are not displayed
theta = self.model.theta
theta_len = theta.shape[0]
# create the plot data
if not self.theta_plot_data:
self.theta_plot_data = ArrayPlotData()
self._update_plot_data()
# create the plot
theta_plot = Plot(self.theta_plot_data)
for idx in range(theta_len):
# candle plot summarizing samples over the posterior
theta_plot.candle_plot((_w_idx('index', idx),
_w_idx('min', idx),
_w_idx('barmin', idx),
_w_idx('avg', idx),
_w_idx('barmax', idx),
_w_idx('max', idx)),
color = get_annotator_color(idx),
bar_line_color = "black",
stem_color = "blue",
center_color = "red",
center_width = 2)
# plot of raw samples
theta_plot.plot((_w_idx('ysamples', idx),
_w_idx('xsamples', idx)),
type='scatter',
color='black',
marker='dot',
line_width=0.5,
marker_size=1)
# plot current parameters
theta_plot.plot((_w_idx('y', idx), _w_idx('x', idx)),
type='scatter',
color=get_annotator_color(idx),
marker='plus',
marker_size=8,
line_width=2)
# adjust axis bounds
theta_plot.range2d = self._compute_range2d()
# remove horizontal grid and axis
theta_plot.underlays = [theta_plot.x_grid, theta_plot.y_axis]
# create new horizontal axis
label_list = [str(i) for i in range(theta_len)]
label_axis = LabelAxis(
theta_plot,
orientation = 'bottom',
positions = list(range(1, theta_len+1)),
labels = label_list,
label_rotation = 0
)
# use a FixedScale tick generator with a resolution of 1
label_axis.tick_generator = ScalesTickGenerator(scale=FixedScale(1.))
theta_plot.index_axis = label_axis
theta_plot.underlays.append(label_axis)
theta_plot.padding = 25
theta_plot.padding_left = 40
theta_plot.aspect_ratio = 1.0
container = VPlotContainer()
container.add(theta_plot)
container.bgcolor = 0xFFFFFF
self.decorate_plot(container, theta)
self._set_title(theta_plot)
return container
def _theta_plot_default(self):
theta = self.theta
nannotators = theta.shape[0]
samples = self.theta_samples
# plot data object
plot_data = ArrayPlotData()
# create the plot
plot = Plot(plot_data)
# --- plot theta as vertical dashed lines
# add vertical lines extremes
plot_data.set_data('line_extr', [0., 1.])
for k in range(nannotators):
name = self._theta_name(k)
plot_data.set_data(name, [theta[k], theta[k]])
plots = {}
for k in range(nannotators):
name = self._theta_name(k)
line_plot = plot.plot(
(name, 'line_extr'),
line_width = 2.,
color = get_annotator_color(k),
line_style = 'dash',
name = name
)
plots[name] = line_plot
# --- plot samples as distributions
if samples is not None:
bins = np.linspace(0., 1., 100)
max_hist = 0.
for k in range(nannotators):
name = self._theta_name(k) + '_distr_'
hist, x = np.histogram(samples[:,k], bins=bins)
hist = hist / float(hist.sum())
max_hist = max(max_hist, hist.max())
# make "bars" out of histogram values
y = np.concatenate(([0], np.repeat(hist, 2), [0]))
plot_data.set_data(name+'x', np.repeat(x, 2))
plot_data.set_data(name+'y', y)
for k in range(nannotators):
name = self._theta_name(k) + '_distr_'
plot.plot((name+'x', name+'y'),
line_width = 2.,
color = get_annotator_color(k)
)
# --- adjust plot appearance
plot.aspect_ratio = 1.6 if is_display_small() else 1.7
plot.padding = [20,0,10,40]
# adjust axis bounds
x_low, x_high = theta.min(), theta.max()
y_low, y_high = 0., 1.
if samples is not None:
x_high = max(x_high, samples.max())
x_low = min(x_low, samples.min())
y_high = max_hist
plot.range2d = DataRange2D(
low = (max(x_low-0.05, 0.), y_low),
high = (min(x_high*1.1, 1.), min(y_high*1.1, 1.))
)
# label axes
plot.value_axis.title = 'Probability'
plot.index_axis.title = 'Theta'
# add legend
legend = Legend(component=plot, plots=plots,
align="ul", padding=5)
legend.tools.append(LegendTool(legend, drag_button="left"))
plot.overlays.append(legend)
container = VPlotContainer()
container.add(plot)
container.bgcolor = 0xFFFFFF
self.decorate_plot(container, theta)
self._set_title(plot)
return container
def _theta_plot_default(self):
theta = self.theta
nannotators = theta.shape[0]
samples = self.theta_samples
# plot data object
plot_data = ArrayPlotData()
# create the plot
plot = Plot(plot_data)
# --- plot theta as vertical dashed lines
# add vertical lines extremes
plot_data.set_data('line_extr', [0., 1.])
for k in range(nannotators):
name = self._theta_name(k)
plot_data.set_data(name, [theta[k], theta[k]])
plots = {}
for k in range(nannotators):
name = self._theta_name(k)
line_plot = plot.plot(
(name, 'line_extr'),
line_width = 2.,
color = get_annotator_color(k),
line_style = 'dash',
name = name
)
plots[name] = line_plot
# --- plot samples as distributions
if samples is not None:
bins = np.linspace(0., 1., 100)
max_hist = 0.
for k in range(nannotators):
name = self._theta_name(k) + '_distr_'
hist, x = np.histogram(samples[:,k], bins=bins)
hist = hist / float(hist.sum())
max_hist = max(max_hist, hist.max())
# make "bars" out of histogram values
y = np.concatenate(([0], np.repeat(hist, 2), [0]))
plot_data.set_data(name+'x', np.repeat(x, 2))
plot_data.set_data(name+'y', y)
for k in range(nannotators):
name = self._theta_name(k) + '_distr_'
plot.plot((name+'x', name+'y'),
line_width = 2.,
color = get_annotator_color(k)
)
# --- adjust plot appearance
plot.aspect_ratio = 1.6 if is_display_small() else 1.7
plot.padding = [20,0,10,40]
# adjust axis bounds
x_low, x_high = theta.min(), theta.max()
y_low, y_high = 0., 1.
if samples is not None:
x_high = max(x_high, samples.max())
x_low = min(x_low, samples.min())
y_high = max_hist
plot.range2d = DataRange2D(
low = (max(x_low-0.05, 0.), y_low),
high = (min(x_high*1.1, 1.), min(y_high*1.1, 1.))
)
# label axes
plot.value_axis.title = 'Probability'
plot.index_axis.title = 'Theta'
# add legend
legend = Legend(component=plot, plots=plots,
align="ul", padding=5)
legend.tools.append(LegendTool(legend, drag_button="left"))
plot.overlays.append(legend)
container = VPlotContainer()
container.add(plot)
container.bgcolor = 0xFFFFFF
self.decorate_plot(container, theta)
self._set_title(plot)
return container
