def __init__(self, data, model=None, all_models=None, axes_style={},
data_style={}, init_style={}, best_style={}, **kwargs):
# Dropdown menu of all subclasses of Model, incl. user-defined.
self.models_menu = Dropdown()
# Dropbox API is very different between IPy 2.x and 3.x.
if IPY2:
if all_models is None:
all_models = dict([(m.__name__, m) for m in Model.__subclasses__()])
self.models_menu.values = all_models
else:
if all_models is None:
all_models = [(m.__name__, m) for m in Model.__subclasses__()]
self.models_menu.options = all_models
self.models_menu.on_trait_change(self._on_model_value_change,
'value')
# Button to trigger fitting.
self.fit_button = Button(description='Fit')
self.fit_button.on_click(self._on_fit_button_click)
# Button to trigger guessing.
self.guess_button = Button(description='Auto-Guess')
self.guess_button.on_click(self._on_guess_button_click)
# Parameter widgets are not built here. They are (re-)built when
# the model is (re-)set.
super(NotebookFitter, self).__init__(data, model, axes_style,
data_style, init_style,
best_style, **kwargs)
def make_plot(self, b):
controller = self.controller
b.description = 'Creating plot... Please Wait.'
b.disabled = True
try:
b.pvals = controller.pvals.copy()
if b.plot_type.value == 'Design Space (interactive)':
self.make_interactive_plot(b)
elif b.plot_type.value == 'Design Space':
self.make_static_plot(b)
elif b.plot_type.value == 'Stability':
self.make_stability_plot(b)
elif b.plot_type.value == 'Eigenvalues':
self.make_eigenvalue_plot(b)
else:
self.make_function_plot(b)
except Exception as e:
close_button = Button(description="Close")
error_message = '<div width="200px" style="float:center; text-align:center;">'
error_message += '<b>An error occured while plotting</b></div>'
error_window = Popup(children=[HTML(value=error_message),close_button])
close_button.window = error_window
close_button.on_click(lambda x: x.window.close())
if old_ipython is False:
error_window.box_style='danger'
close_button.float = 'center'
error_window.width='250px'
error_window.height='150px'
display(error_window)
b.description = 'Add Plot'
b.disabled = False
else:
b.description = 'Add Plot'
b.disabled = False
def update_log_gains(self):
controller = self.controller
case = self.case
if case.ssystem.solution is None:
self.log_gains.children = []
return
table = HTML()
html_str = '<div><table>\n<caption>Logarithmic gains and parameter sensitivities for Case ' + case.case_number + ' (' + case.signature + '). </caption>\n'
html_str += '<tr ><th rowspan="2" align=center style="padding:0 15px 0 15px;"> Dependent<br> Variables </th>'
html_str += '<th colspan="' + str(len(case.independent_variables)) + '" align=center style="padding:0 15px 0 15px;"> Independent Variables and Parameters</th></tr><tr align=center>'
for xi in case.independent_variables:
html_str += '<td><b>{0}</b></td>'.format(xi)
html_str += '</tr>\n'
for xd in case.dependent_variables:
html_str += '<tr><td align=center style="padding:0 15px 0 15px;"><b>{0}</b></td>'.format(xd)
for xi in case.independent_variables:
html_str += '<td align=center style="padding:0 15px 0 15px;">{0}</td>'.format(str(case.ssystem.log_gain(xd, xi)))
html_str += '</tr>\n'
html_str += '</table></div><br>'
save_button = Button(description='Save Log-Gain Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
table.value = html_str
self.log_gains.children = [HTML(value='<br>'),
save_button,
table]
return
def update_global_tolerances(self):
controller = self.controller
case = self.case
pvals = self.pvals
if pvals is None:
self.tolerances_table.children = []
return
if case.is_valid(p_bounds=pvals) is False:
self.tolerances_table.children = []
return
table = HTML()
html_str = '<div><table>\n<caption>Global tolerances determined for Case ' + case.case_number + ' (' + case.signature + ') showing fold-difference to a large qualitative change{0}. </caption>\n'.format(' in log-coordinates' if self.log_coordinates is True else '')
html_str += '<tr ><th align=center rowspan=2 style="padding:0 15px 0 15px;"> Parameters </th><th colspan=2> Tolerance </th></tr>'
html_str += '<tr><td style="padding:0 15px 0 15px;"><b> Lower bound</b></td><td style="padding:0 15px 0 15px;"><b> Upper bound</b></td></tr>'
tolerances = case.measure_tolerance(pvals, log_out=self.log_coordinates)
for xi in sorted(pvals.keys()):
lower_th = 1e-15 if self.log_coordinates is False else -15
upper_th = 1e15 if self.log_coordinates is False else 15
lower, upper = tolerances[xi]
html_str += '<tr><td style="padding:0 15px 0 15px;"><b>{0}</b></td><td style="padding:0 15px 0 15px;">{1}</td><td style="padding:0 15px 0 15px;">{2}</td></tr>'.format(
xi,
lower if lower > lower_th else '-∞',
upper if upper < upper_th else '∞')
html_str += '</table><caption>'
html_str += 'Note: Global tolerance calculated based on the following values for the parameters: '
html_str += '; '.join([i + ' = ' + str(pvals[i]) for i in sorted(pvals.keys())]) + '.'
html_str += '</caption></div>'
table.value = html_str
save_button = Button(description='Save Global Tolerance Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
self.tolerances_table.children = [HTML(value='<br>'),
save_button,
table]
return
def update_bounding_box(self):
controller = self.controller
case = self.case
pvals = self.pvals
if case.is_valid(p_bounds=pvals) is False:
self.bounding_box_table.children = []
return
if case.is_cyclical is True:
self.bounding_box_table.children = []
return
table = HTML()
html_str = '<div><table>\n<caption>Bounding box determined for Case ' + case.case_number + ' (' + case.signature + '){0}. </caption>\n'.format(' in log-coordinates' if self.log_coordinates is True else '')
html_str += '<tr ><th align=center rowspan=2 style="padding:0 15px 0 15px;"> Parameters </th><th colspan=2> Tolerance </th></tr>'
html_str += '<tr><td style="padding:0 15px 0 15px;"><b> Lower bound</b></td><td style="padding:0 15px 0 15px;"><b> Upper bound</b></td></tr>'
tolerances = case.bounding_box(log_out=self.log_coordinates)
for xi in sorted(tolerances.keys()):
lower_th = 1e-15 if self.log_coordinates is False else -15
upper_th = 1e15 if self.log_coordinates is False else 15
lower, upper = tolerances[xi]
html_str += '<tr><td style="padding:0 15px 0 15px;"><b>{0}</b></td><td style="padding:0 15px 0 15px;">{1}</td><td style="padding:0 15px 0 15px;">{2}</td></tr>'.format(
xi,
lower if lower > lower_th else '-∞',
upper if upper < upper_th else '∞')
html_str += '</table></div>'
table.value = html_str
save_button = Button(description='Save Bounding Box Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
self.bounding_box_table.children = [HTML(value='<br>'),
save_button,
table]
return
def save_figure_widget(self, image_data, title='', caption = '', pvals=None, colors=None):
image_widget = Image()
image_widget.value = image_data
children = [i for i in self.figures_widget.children]
html_str = '<b>Figure '+str(len(children)+1)+'. '+title+'</b>' + caption
html_widget = HTML(value=html_str)
restore_pvals = Button(description='Restore Parameter Values')
restore_pvals.pvals = pvals
if pvals is None:
restore_pvals.visible = False
if old_ipython is True:
image_widget = Image()
image_widget.value = image_data
tab_widget = VBox(children=[image_widget, html_widget])
if colors is not None:
html_widgets = self.colorbar_tabs(colors)
tab_widget.description='Figure'
tab_widget = Tab(children=[tab_widget]+html_widgets)
else:
image_widget = self._image_widget_new(image_data, colors=colors)
tab_widget = VBox(children=[image_widget, html_widget])
restore_pvals.on_click(self.restore_figure_pvals)
if old_ipython is True:
wi = Popup(children=[tab_widget, restore_pvals])
else:
contents = VBox(children=[tab_widget, restore_pvals])
contents.width = '100%'
wi = Popup(children=[contents])
wi.border = '1px solid black'
children.append(wi)
self.figures_widget.children = children
if colors is not None:
if old_ipython is True:
tab_widget.set_title(0, 'Figure')
tab_widget.set_title(1, 'Colorbar')
def make_interactive_plot(self, b):
controller = self.controller
if str(b.ylabel.value) == 'None':
return
button = Button(description='Stop interactive plot')
button.on_click(self.remove_plot)
button.name = 'Interactive Plot (' + str(np.random.randint(0, 1000)) + ')'
image_widget = Image()
popup_widget = Popup(children=[image_widget])
image_widget.width='100%'
rangex, rangey = self.axes_ranges(b)
interactive_plot = controller.ds.draw_2D_slice_notebook(controller.pvals, str(b.xlabel.value),
str(b.ylabel.value),
rangex, rangey,
{i:[1e-5, 1e5] for i in
controller.pvals},
intersections=[1],
image_container=image_widget)
wi = VBox(description=button.name,
children=[interactive_plot,
button,
popup_widget])
controller.options.update({'xaxis':str(b.xlabel.value),
'yaxis':str(b.ylabel.value),
'x_range':rangex,
'y_range':rangey})
controller.update_child(button.name, wi)
def __init__(self,
data,
model=None,
all_models=None,
axes_style={},
data_style={},
init_style={},
best_style={},
**kwargs):
# Dropdown menu of all subclasses of Model, incl. user-defined.
self.models_menu = Dropdown()
# Dropbox API is very different between IPy 2.x and 3.x.
if IPY2:
if all_models is None:
all_models = {m.__name__: m for m in Model.__subclasses__()}
self.models_menu.values = all_models
else:
if all_models is None:
all_models = [(m.__name__, m) for m in Model.__subclasses__()]
self.models_menu.options = all_models
self.models_menu.on_trait_change(self._on_model_value_change, 'value')
# Button to trigger fitting.
self.fit_button = Button(description='Fit')
self.fit_button.on_click(self._on_fit_button_click)
# Button to trigger guessing.
self.guess_button = Button(description='Auto-Guess')
self.guess_button.on_click(self._on_guess_button_click)
# Parameter widgets are not built here. They are (re-)built when
# the model is (re-)set.
super(NotebookFitter,
self).__init__(data, model, axes_style, data_style, init_style,
best_style, **kwargs)
def interactive_lavalamp_pooled_inconsistent(
self,
sample_subsets=None,
feature_subsets=None,
difference_threshold=(0.001, 1.00),
colors=["red", "green", "blue", "purple", "yellow"],
savefile="",
):
from IPython.html.widgets import interact
savefile = "figures/last.lavalamp_pooled_inconsistent.pdf"
def do_interact(
sample_subset=self.default_sample_subsets,
feature_subset=self.default_feature_subsets,
difference_threshold=0.1,
color=red,
savefile=savefile,
):
for k, v in locals().iteritems():
if k == "self":
continue
sys.stdout.write("{} : {}\n".format(k, v))
assert feature_subset in self.splicing.feature_subsets.keys()
feature_ids = self.splicing.feature_subsets[feature_subset]
sample_ids = self.sample_subset_to_sample_ids(sample_subset)
color = str_to_color[color]
self.splicing.plot_lavalamp_pooled_inconsistent(sample_ids, feature_ids, difference_threshold, color=color)
plt.tight_layout()
if feature_subsets is None:
feature_subsets = Interactive.get_feature_subsets(self, ["splicing", "expression"])
if sample_subsets is None:
sample_subsets = self.default_sample_subsets
gui = interact(
do_interact,
sample_subset=sample_subsets,
feature_subset=feature_subsets,
difference_threshold=difference_threshold,
color=colors,
savefile="",
)
def save(w):
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
gui.widget.result.savefig(savefile.value, format=extension.lstrip("."))
savefile = TextWidget(description="savefile", value="figures/clustermap.pdf")
save_widget = ButtonWidget(description="save")
gui.widget.children = list(gui.widget.children) + [savefile, save_widget]
save_widget.on_click(save)
def update_constraints(self):
constraints_widget = Textarea(description='Constraints',
value = ',\n'.join(self.constraints)
)
constraints_widget.visible = self.active_constraints
button = Button(description='Done' if self.active_constraints else 'Modify constraints')
button.constraints_widget = constraints_widget
button.on_click(self.modify_constraints)
self.constraints_widget.children = [constraints_widget, button]
def edit_parameters_widget(self):
controller = self.controller
if controller.ds is None:
return
pvals_widgets = [FloatText(description=i, value=controller.pvals[i]) for i in sorted(controller.pvals.keys())]
wi = VBox(children=pvals_widgets)
button = Button(value=False, description="Done")
button.on_click(self.update_parameters)
button.pvals = pvals_widgets
button.wi = wi
edit_pvals = VBox(description="Edit Parameters", children=[wi, button])
controller.update_child("Edit Parameters", edit_pvals)
def edit_symbols_widget(self):
controller = self.controller
if controller.ds is None:
return
symbols = {i:controller.symbols[i] for i in controller.symbols if i in controller.ds.dependent_variables + controller.ds.independent_variables}
symbols.update({i:i for i in controller.ds.dependent_variables + controller.ds.independent_variables if i not in symbols})
self.symbols = symbols
symbols_widgets = [Text(description=i, value=self.symbols[i]) for i in symbols]
wi = VBox(children=symbols_widgets)
button = Button(value=False, description='Done')
button.on_click(self.update_symbols)
button.symbols = symbols_widgets
button.wi = wi
edit_symbols = VBox(description='Edit Symbols', children=[wi, button])
controller.update_child('Edit Symbols', edit_symbols)
wi.visible = True
def make_display_widget(self):
controller = self.controller
if controller.ds is None:
return
self.info = VBox()
self.constraints_widget = VBox()
self.plot = HBox()
self.log_coordinates = True
self.global_tolerance = VBox()
close_button = Button(description='Close Tab')
close_button.on_click(self.close_widget)
ss_options = ['log('+ i + ')' for i in controller.ds.dependent_variables]
self.y_dropdown = Dropdown(description='y-axis',
values=ss_options,
options=ss_options,
value=self.y_variable)
self.make_plot = Button(description='Create Plot')
self.make_plot.on_click(self.change_y_axis)
self.make_plot.yaxis = self.y_dropdown
self.make_plot.visible = True
check_box = Checkbox(description='Logarithmic coordinates',
value=self.log_coordinates)
check_box.on_trait_change(self.update_log, 'value')
self.y_dropdown.visible = False
if len(self.slice_variables) <= 3:
## self.make_plot.visible = True
if len(self.slice_variables) == 1:
self.y_dropdown.visible = True
if len(self.slice_variables) == 3:
self.y_dropdown = HTML(value='<font color="red">Warning 3D plots are experimental.</font>')
wi = VBox(children=[self.info,
self.constraints_widget,
check_box,
self.y_dropdown,
self.make_plot,
self.global_tolerance,
close_button])
if old_ipython is True:
wi.set_css('height', '400px')
else:
wi.height='400px'
wi.overflow_x = 'auto'
wi.overflow_y = 'auto'
self.update_display()
controller.update_child(self.name, wi)
def update_parameter_table(self):
controller = self.controller
case = self.case
pvals = self.pvals
if pvals is None:
self.parameter_table.children = []
return
if case.is_valid(p_bounds=pvals) is False:
self.parameter_table.children = []
return
make_nominal = Button(description='Make Nominal Parameter Set')
make_nominal.on_click(self.save_parameters)
table = HTML()
html_str = '<div><table>\n<caption>Value for the parameters automatically determined for Case ' + case.case_number + ' (' + case.signature + '). </caption>\n'
html_str += '<tr ><th align=center style="padding:0 15px 0 15px;"> Parameters </th><th> Value </th>'
for xi in sorted(pvals.keys()):
html_str += '<tr><td><b>{0}</b></td><td>{1}</td></tr>'.format(
xi,
pvals[xi])
html_str += '</table></div>'
table.value = html_str
save_button = Button(description='Save Parameter Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
self.parameter_table.children = [HTML(value='<br>'),
save_button,
table,
make_nominal
]
return
def make_options_menu(self, b):
wi = b.wi
b.visible = False
b.name.visible = False
b.load.visible = False
actions = [('Enumerate Phenotypes', self.enumerate_phenotypes_menu),
('Analyze Case', self.case_report_menu),
('Intersect Phenotypes', self.case_intersect_menu),
('Co-localize Phenotypes', self.co_localize_menu),
('Create Plot', self.create_plot_menu)]
actions_h = HTML(value='<b>Actions</b>')
options_h = HTML(value='<b>Options</b>')
options = [('Edit Symbols', self.create_edit_symbols),
('Edit Parameters', self.create_edit_parameters),
('Save Data', self.save_widget_data)]
actions_w = Tab()
options_w = []
for name, method in options:
button = Button(description=name)
button.on_click(method)
## button.version = b.version
if method is None:
button.disabled = True
options_w.append(button)
edit = Button(description='Modify System')
edit.on_click(self.modify_equations_widget)
warning = HTML()
warning.value = '<font color="red"><b>Warning! Modifying system erases saved figures and tables.</b></font>'
wi.children = [actions_h, actions_w] + [options_h] + options_w + [edit, warning]
for title, method in actions:
title, widget = method(self)
children = [i for i in actions_w.children] + [widget]
actions_w.children = children
actions_w.set_title(len(children)-1, title)
self.widget.selected_index = 1
def __init__(self, data, model=None, **kwargs):
# Dropdown menu of all subclasses of Model, incl. user-defined.
self.models_menu = Dropdown()
all_models = {m.__name__: m for m in Model.__subclasses__()}
self.models_menu.values = all_models
self.models_menu.on_trait_change(self._on_model_value_change,
'value')
# Button to trigger fitting.
self.fit_button = Button(description='Fit')
self.fit_button.on_click(self._on_fit_button_click)
# Button to trigger guessing.
self.guess_button = Button(description='Auto-Guess')
self.guess_button.on_click(self._on_guess_button_click)
# Parameter widgets are not built here. They are (re-)built when
# the model is (re-)set.
super(NotebookFitter, self).__init__(data, model, **kwargs)
def create_case_widget(self):
controller = self.controller
if controller.ds is None:
return
by_signature = Checkbox(
description='Cases indicated by signature?',
value=self.by_signature
)
case_id = Text(description='* Analysis for case:')
if 'biological_constraints' not in controller.options:
bio_constraints = ''
else:
bio_constraints = ', '.join(controller.defaults('biological_constraints'))
constraints = Textarea(description='Biological constraints:',
value=bio_constraints)
button = Button(description='Create Analysis')
button.on_click(self.create_report)
button.case_id = case_id
button.by_signature = by_signature
button.constraints = constraints
wi = VBox(children=[by_signature,
case_id,
constraints,
button])
return ('Analyze Case', wi)
def update_info(self):
title = HTML(value='<b> Cases to Co-localize </b>')
buttons = []
html_str = '<div><b>Is Valid: {0}</b></div>'.format(self.ci.is_valid())
if self.ci.is_valid() is False:
self.make_plot.disabled = True
else:
self.make_plot.disabled = False
valid = HTML(value = html_str)
html_str = '<table><caption> Auxiliary variables for ' + self.name
html_str += ' with ' + ', '.join(self.slice_variables)
html_str += ' as the slice variable{0}.</caption>'.format('s' if len(self.slice_variables) > 1 else '')
html_str += '<tr ><th rowspan="2" align=center style="padding:0 15px 0 15px;"> Slice<br> Variables </th>'
html_str += '<th colspan="' + str(len(self.cases)) + '" align=center style="padding:0 15px 0 15px;"> Cases </th></tr><tr align=center>'
for c in self.cases:
html_str += '<td style="padding:0 15px 0 15px;"><b> {0} </b></td>'.format(c.case_number)
html_str += '</tr>\n'
pset = self.ci.valid_interior_parameter_set()
for i in self.cases:
key = i.case_number
case_button = Button(description='Case ' + key)
buttons.append(case_button)
case_button.pvals = pset[key] if key in pset else None
case_button.on_click(self.open_case)
for j, xj in enumerate(self.slice_variables):
html_str += '<tr align=center><td>{0}</td>'.format(xj)
for i, c in enumerate(self.cases):
html_str += '<td>${0}_{1}</td>'.format(xj, i)
html_str += '</tr>'
html_str += '</table>'
html_str += '<caption>Case co-localization assumes that the slice variables '
html_str += 'for one case are independent from the slice variables for the other cases in the co-localization.'
html_str += 'Each auxiliary variable corresponds to a slice variable for one cases.</caption>'
save_table = Button(description='Save variable table')
save_table.on_click(self.save_table)
save_table.table_data = html_str
variables = HTML(value=html_str)
self.info.children = [title] + buttons + [valid, save_table, variables]
def create_case_widget(self):
controller = self.controller
if controller.ds is None:
return
case = self.case
self.info = VBox()
self.equations = VBox()
self.log_gains = VBox()
self.parameter_table = VBox()
self.tolerances_table = VBox()
self.bounding_box_table = VBox()
calculate_pvals = Button(description='Determine values for the parameters')
calculate_pvals.visible = False
calculate_pvals.on_click(self.identify_parameters)
if case.is_valid() is True and case.is_cyclical is False:
if self.pvals is None:
calculate_pvals.visible = True
close_button = Button(description='Close Tab')
close_button.on_click(self.close_widget)
wi = Popup(children=[self.info,
self.equations,
self.log_gains,
self.bounding_box_table,
calculate_pvals,
self.parameter_table,
self.tolerances_table,
close_button])
if ipy_old is True:
wi.set_css('height', '400px')
else:
wi.width = '700px'
self.update_display()
subtitle = self.subtitle
if subtitle != '':
subtitle = ' (' + subtitle + ')'
self.title = 'Case ' + self.case.case_number + subtitle
controller.update_child(self.title, wi)
def save_popup_widget(self):
controller = self.controller
save_button = Button(description='Save')
cancel_button = Button(description='Cancel')
name_field = Text(description='* Name', value=controller.name)
version_field = Text(description='Version',
value=controller.version)
save_button.on_click(self.save_widget_data)
save_button.name_field = name_field
save_button.version_field = version_field
cancel_button.on_click(self.cancel_save)
self.save_data = VBox(description='Save Data',
children=[VBox(children=[
HTML(value='<center width="100%"><b>Are you sure you want to save?</b></center>'),
name_field,
version_field,
HBox(children=[
save_button,
cancel_button])])])
self.save_data.box_style = 'warning'
self.save_data.overflow_x = 'auto'
self.save_data.overflow_y = 'auto'
self.save_data.width = '100vh'
return self.save_data
def colocalization_widget(self):
controller = self.controller
cases = Textarea(description='* Cases to co-localize:')
by_signature = Checkbox(description='Cases indicated by signature?',
value=self.by_signature)
slice_variables = Textarea(description='* Slice variables:')
if 'biological_constraints' not in controller.options:
bio_constraints = ''
else:
bio_constraints = ', '.join(controller.defaults('biological_constraints'))
constraints = Textarea(description='Biological constraints:',
value=bio_constraints)
button = Button(description='Create Co-Localization')
button.on_click(self.make_colocalization)
button.cases = cases
button.by_signature = by_signature
button.slice_variables = slice_variables
button.constraints = constraints
wi = VBox(children=[cases,
by_signature,
slice_variables,
constraints,
button])
return ('Co-localizations', wi)
def create_plot_widget(self):
controller = self.controller
options = self.controller.options
if controller.ds is None:
return
xaxis = controller.defaults('xaxis')
if xaxis is None:
xaxis = controller.ds.independent_variables[0]
yaxis = controller.defaults('yaxis')
if yaxis is None:
yaxis = controller.ds.independent_variables[1]
center = controller.defaults('center_axes')
range_x = controller.defaults('range_x')
range_y = controller.defaults('range_y')
xlabel = Dropdown(
description='* X-Axis',
values=controller.ds.independent_variables,
options=controller.ds.independent_variables,
value=xaxis)
ylabel = Dropdown(
description='* Y-Axis',
values=['None'] + controller.ds.independent_variables,
options=['None'] + controller.ds.independent_variables,
value=yaxis)
xmin = FloatText(description='* X-Min',
value=range_x[0])
xmax = FloatText(description='* X-Max',
value=range_x[1])
ymin = FloatText(description='* Y-Min',
value=range_y[0])
ymax = FloatText(description='* Y-Max',
value=range_y[1])
center_axes = Checkbox(description='Center Axes',
value=center)
boundaries = Checkbox(description='Draw Boundaries',
value=False)
plot_type = Dropdown(description='* Plot Type',
values=self.widget_types,
options=self.widget_types,
value='Design Space (interactive)')
title_widget = Text(description='Title')
caption_widget = Textarea(description='Caption')
included = controller.defaults('included_cases')
if included is None:
included = []
if isinstance(included, list) is False:
included = [included]
included_widget = Textarea(description='Only Cases',
value=', '.join(included))
wi = VBox(children=[xlabel, ylabel, plot_type,
xmin, xmax, ymin, ymax,
center_axes, boundaries,
title_widget, caption_widget,
included_widget])
for i in [xlabel, ylabel, plot_type]:
i.on_trait_change(self.update_field, 'value')
plot_type.widget_container = wi
button = Button(value=False, description='Add Plot')
button.on_click(self.make_plot)
button.xlabel = xlabel
button.ylabel = ylabel
button.xmin = xmin
button.xmax = xmax
button.ymin = ymin
button.ymax = ymax
button.center_axes = center_axes
button.boundaries = boundaries
button.plot_type = plot_type
button.title = title_widget
button.caption = caption_widget
button.included = included_widget
button.wi = wi
self.title = title_widget
self.caption = caption_widget
self.boundaries = boundaries
self.plot_type = plot_type
self.xlabel = xlabel
self.ylabel = ylabel
self.ymin = ymin
self.ymax = ymax
self.xmin = xmin
self.xmax = xmax
add_plot = VBox(description='Add Plot',
children=[wi,
self.plot_data,
button])
self.update_plot_widget('value', 'Design Space (Interactive)')
return ('Create Plot', add_plot)
class NotebookFitter(BaseFitter):
__doc__ = _COMMON_DOC + """
If IPython is available, it uses the IPython notebook's rich display
to fit data interactively in a web-based GUI. The Parameters are
represented in a web-based form that is kept in sync with `current_params`.
All subclasses to Model, including user-defined ones, are shown in a
drop-down menu.
Clicking the "Fit" button updates a plot, as above, and updates the
Parameters in the form to reflect the best fit.
""" + _COMMON_EXAMPLES_DOC
def __init__(self, data, model=None, **kwargs):
# Dropdown menu of all subclasses of Model, incl. user-defined.
self.models_menu = Dropdown()
all_models = {m.__name__: m for m in Model.__subclasses__()}
self.models_menu.values = all_models
self.models_menu.on_trait_change(self._on_model_value_change,
'value')
# Button to trigger fitting.
self.fit_button = Button(description='Fit')
self.fit_button.on_click(self._on_fit_button_click)
# Button to trigger guessing.
self.guess_button = Button(description='Auto-Guess')
self.guess_button.on_click(self._on_guess_button_click)
# Parameter widgets are not built here. They are (re-)built when
# the model is (re-)set.
super(NotebookFitter, self).__init__(data, model, **kwargs)
def _repr_html_(self):
display(self.models_menu)
button_box = Box()
button_box.children = [self.fit_button, self.guess_button]
display(button_box)
button_box.add_class('hbox')
for pw in self.param_widgets:
display(pw)
self.plot()
def guess(self):
guessing_successful = super(NotebookFitter, self).guess()
self.guess_button.disabled = not guessing_successful
def _finalize_model(self, value):
first_run = not hasattr(self, 'param_widgets')
if not first_run:
# Remove all Parameter widgets, and replace them with widgets
# for the new model.
for pw in self.param_widgets:
pw.close()
self.models_menu.value = value
self.param_widgets = [ParameterWidgetGroup(p)
for _, p in self._current_params.items()]
if not first_run:
for pw in self.param_widgets:
display(pw)
def _finalize_params(self):
for pw in self.param_widgets:
pw.value = self._current_params[pw.name].value
pw.min = self._current_params[pw.name].min
pw.max = self._current_params[pw.name].max
pw.vary = self._current_params[pw.name].vary
def plot(self):
clear_output(wait=True)
super(NotebookFitter, self).plot()
def fit(self):
super(NotebookFitter, self).fit()
self.plot()
def __init__(self, domains, components, circuit=None, **kwargs):
super(CircuitBuilder, self).__init__(**kwargs)
self.button_text = "Launch CircuitBuilder"
self.description = circuit.name
def _resize_inputs(el):
el.set_css({"width": "100px"})
##### make controls
self.basic_controls = HorizontalContainer()
self.add_component_controls = HorizontalContainer()
self.add_port_controls = HorizontalContainer()
self.change_component_controls = HorizontalContainer()
self.change_port_controls = HorizontalContainer()
# 1) basic controls
self.reset_view_btn = ButtonWidget(description="Reset view")
self.reset_view_btn.on_click(self.reset_view)
self.circname = TextWidget(description="Circuit name", value=circuit.name)
self.circname.on_displayed(_resize_inputs)
self.rename_circ_btn = ButtonWidget(description="Rename")
self.rename_circ_btn.on_click(self.rename_circuit)
self.add_port_btn = ButtonWidget(description="New Port")
self.add_port_btn.on_click(self.show_add_port_controls)
self.add_comp_btn = ButtonWidget(description="New Component")
self.add_comp_btn.on_click((self.show_add_comp_controls))
# self.download_btn = ButtonWidget(description="SaveAsSVG")
# self.download_btn.on_click()
self.basic_controls.children = [
self.reset_view_btn,
self.circname,
self.rename_circ_btn,
self.add_port_btn,
self.add_comp_btn,
]
# 2) add component
self.add_comp_type = DropdownWidget(description="ComponentType")
self.add_comp_name = TextWidget(description="Component name")
self.add_comp_name.on_displayed(_resize_inputs)
self.add_comp_add = ButtonWidget(description="Add Component")
self.add_comp_add.on_click(self.add_component)
self.add_comp_back = ButtonWidget(description="Back")
self.add_comp_back.on_click(self.back)
self.add_component_controls.children = [
self.add_comp_type,
self.add_comp_name,
self.add_comp_add,
self.add_comp_back,
]
# 3) add port
self.add_port_name = TextWidget(description="Port name")
self.add_port_name.on_displayed(_resize_inputs)
self.add_port_domain = DropdownWidget(description="Domain")
self.add_port_domain.on_trait_change(self._update_port_directions, "value_name")
self.add_port_direction = DropdownWidget(description="Direction",
values={"in": "Input", "out": "Output"})
self.add_port_add = ButtonWidget(description="Add Port")
self.add_port_add.on_click(self.add_port)
self.add_port_back = ButtonWidget(description="Back")
self.add_port_back.on_click(self.back)
self.add_port_controls.children = [
self.add_port_name,
self.add_port_domain,
self.add_port_direction,
self.add_port_add,
self.add_port_back,
]
# 4) change component
self.mod_comp_name = TextWidget(description="Component name")
self.mod_comp_name.on_displayed(_resize_inputs)
self.mod_comp_rename = ButtonWidget(description="Rename")
self.mod_comp_rename.on_click(self.rename_component)
self.mod_comp_delete = ButtonWidget(description="Delete")
self.mod_comp_delete.on_click(self.delete_component)
self.mod_comp_back = ButtonWidget(description="Back")
self.mod_comp_back.on_click(self.back)
self.change_component_controls.children = [
self.mod_comp_name,
self.mod_comp_rename,
self.mod_comp_delete,
self.mod_comp_back,
]
# 5) change port
self.mod_port_name = TextWidget(description="Port name")
self.mod_port_name.on_displayed(_resize_inputs)
self.mod_port_rename = ButtonWidget(description="Rename")
self.mod_port_rename.on_click(self.rename_port)
self.mod_port_dec = ButtonWidget(description="<")
self.mod_port_inc = ButtonWidget(description=">")
self.mod_port_dec.on_click(self.dec_port_order)
self.mod_port_inc.on_click(self.inc_port_order)
self.mod_port_delete = ButtonWidget(description="Delete")
self.mod_port_delete.on_click(self.delete_port)
self.mod_port_back = ButtonWidget(description="Back")
self.mod_port_back.on_click(self.back)
self.change_port_controls.children = [
self.mod_port_name,
self.mod_port_rename,
self.mod_port_dec,
self.mod_port_inc,
self.mod_port_delete,
self.mod_port_back,
]
# has to come at end!!
self.domains = domains
self.components = components
self.circuit = circuit
self.circuit.on_trait_change(self._handle_circuit_selection, "selected_element")
self.circuit.on_trait_change(self._handle_circuit_name, "name")
self.children = [
self.basic_controls,
self.add_component_controls,
self.add_port_controls,
self.change_component_controls,
self.change_port_controls,
self.circuit
]
self.back()
class CircuitBuilder(PopupWidget):
"""
Adds additional controls to the circuit widget for
adding/removing external ports and component instances.
"""
_view_name = Unicode("CircuitBuilderView", sync=True)
circuit = Instance(klass=Circuit, sync=True)
domains = List()
_domains_by_name = Dict()
components = List()
_components_by_name = Dict()
def _components_changed(self, name, old, new):
self.add_comp_type.values = {c.name: c.name for c in new}
self._components_by_name = {c.name: c for c in new}
def _domains_changed(self, name, old, new):
self.add_port_domain.values = {d.name: d.name for d in new}
self.add_port_domain.value_name = new[0].name
self._domains_by_name = {d.name: d for d in new}
self._update_port_directions()
def __init__(self, domains, components, circuit=None, **kwargs):
super(CircuitBuilder, self).__init__(**kwargs)
self.button_text = "Launch CircuitBuilder"
self.description = circuit.name
def _resize_inputs(el):
el.set_css({"width": "100px"})
##### make controls
self.basic_controls = HorizontalContainer()
self.add_component_controls = HorizontalContainer()
self.add_port_controls = HorizontalContainer()
self.change_component_controls = HorizontalContainer()
self.change_port_controls = HorizontalContainer()
# 1) basic controls
self.reset_view_btn = ButtonWidget(description="Reset view")
self.reset_view_btn.on_click(self.reset_view)
self.circname = TextWidget(description="Circuit name", value=circuit.name)
self.circname.on_displayed(_resize_inputs)
self.rename_circ_btn = ButtonWidget(description="Rename")
self.rename_circ_btn.on_click(self.rename_circuit)
self.add_port_btn = ButtonWidget(description="New Port")
self.add_port_btn.on_click(self.show_add_port_controls)
self.add_comp_btn = ButtonWidget(description="New Component")
self.add_comp_btn.on_click((self.show_add_comp_controls))
# self.download_btn = ButtonWidget(description="SaveAsSVG")
# self.download_btn.on_click()
self.basic_controls.children = [
self.reset_view_btn,
self.circname,
self.rename_circ_btn,
self.add_port_btn,
self.add_comp_btn,
]
# 2) add component
self.add_comp_type = DropdownWidget(description="ComponentType")
self.add_comp_name = TextWidget(description="Component name")
self.add_comp_name.on_displayed(_resize_inputs)
self.add_comp_add = ButtonWidget(description="Add Component")
self.add_comp_add.on_click(self.add_component)
self.add_comp_back = ButtonWidget(description="Back")
self.add_comp_back.on_click(self.back)
self.add_component_controls.children = [
self.add_comp_type,
self.add_comp_name,
self.add_comp_add,
self.add_comp_back,
]
# 3) add port
self.add_port_name = TextWidget(description="Port name")
self.add_port_name.on_displayed(_resize_inputs)
self.add_port_domain = DropdownWidget(description="Domain")
self.add_port_domain.on_trait_change(self._update_port_directions, "value_name")
self.add_port_direction = DropdownWidget(description="Direction",
values={"in": "Input", "out": "Output"})
self.add_port_add = ButtonWidget(description="Add Port")
self.add_port_add.on_click(self.add_port)
self.add_port_back = ButtonWidget(description="Back")
self.add_port_back.on_click(self.back)
self.add_port_controls.children = [
self.add_port_name,
self.add_port_domain,
self.add_port_direction,
self.add_port_add,
self.add_port_back,
]
# 4) change component
self.mod_comp_name = TextWidget(description="Component name")
self.mod_comp_name.on_displayed(_resize_inputs)
self.mod_comp_rename = ButtonWidget(description="Rename")
self.mod_comp_rename.on_click(self.rename_component)
self.mod_comp_delete = ButtonWidget(description="Delete")
self.mod_comp_delete.on_click(self.delete_component)
self.mod_comp_back = ButtonWidget(description="Back")
self.mod_comp_back.on_click(self.back)
self.change_component_controls.children = [
self.mod_comp_name,
self.mod_comp_rename,
self.mod_comp_delete,
self.mod_comp_back,
]
# 5) change port
self.mod_port_name = TextWidget(description="Port name")
self.mod_port_name.on_displayed(_resize_inputs)
self.mod_port_rename = ButtonWidget(description="Rename")
self.mod_port_rename.on_click(self.rename_port)
self.mod_port_dec = ButtonWidget(description="<")
self.mod_port_inc = ButtonWidget(description=">")
self.mod_port_dec.on_click(self.dec_port_order)
self.mod_port_inc.on_click(self.inc_port_order)
self.mod_port_delete = ButtonWidget(description="Delete")
self.mod_port_delete.on_click(self.delete_port)
self.mod_port_back = ButtonWidget(description="Back")
self.mod_port_back.on_click(self.back)
self.change_port_controls.children = [
self.mod_port_name,
self.mod_port_rename,
self.mod_port_dec,
self.mod_port_inc,
self.mod_port_delete,
self.mod_port_back,
]
# has to come at end!!
self.domains = domains
self.components = components
self.circuit = circuit
self.circuit.on_trait_change(self._handle_circuit_selection, "selected_element")
self.circuit.on_trait_change(self._handle_circuit_name, "name")
self.children = [
self.basic_controls,
self.add_component_controls,
self.add_port_controls,
self.change_component_controls,
self.change_port_controls,
self.circuit
]
self.back()
def _handle_circuit_selection(self):
e = self.circuit.selected_element
if e:
if isinstance(e, Port) and e.is_ext:
self.back()
self.show_mod_port_controls(e)
return
elif isinstance(e, ComponentInstance):
self.back()
self.show_mod_comp_controls(e)
return
self.back()
def _handle_circuit_name(self):
self.circname.value = self.circuit.name
self.description = self.circuit.name
def reset_view(self, *_):
self.circuit.zoom = (0., 0., 1.)
def back(self, *_):
for c in [
self.add_component_controls,
self.add_port_controls,
self.change_component_controls,
self.change_port_controls,
]:
c.visible = False
self.basic_controls.visible = True
def show_mod_comp_controls(self, c):
self.basic_controls.visible = False
self.change_component_controls.visible = True
self.mod_comp_name.value = c.name
def show_mod_port_controls(self, p):
self.basic_controls.visible = False
self.change_port_controls.visible = True
self.mod_port_name.value = p.name
def show_add_port_controls(self, *_):
self.basic_controls.visible = False
self.add_port_controls.visible = True
def show_add_comp_controls(self, *_):
self.basic_controls.visible = False
self.add_component_controls.visible = True
def _update_port_directions(self):
d = self._domains_by_name.get(self.add_port_domain.value_name, False)
if isinstance(d, Domain):
self.add_port_direction.visible = d.causal
def rename_circuit(self, *_):
if len(self.circname.value):
self.circuit.name = self.circname.value
def add_component(self, *_):
ctype = self._components_by_name[self.add_comp_type.value_name]
cname = self.add_comp_name.value
if len(cname) and not cname in self.circuit.c:
new_comp = ctype.make_instance(cname)
self.circuit.component_instances = self.circuit.component_instances + [new_comp]
def add_port(self, *_):
d = self._domains_by_name[self.add_port_domain.value_name]
dir = self.add_port_direction.value_name
if not d.causal:
dir = "inout"
pname = self.add_port_name.value
if len(pname) and not pname in self.circuit.p:
newp = Port(name=pname, domain=d, direction=dir)
self.circuit.ports = self.circuit.ports + [newp]
def rename_component(self, *_):
c = self.circuit.selected_element
if not isinstance(c, ComponentInstance):
return
newname = self.mod_comp_name.value
if len(newname) and not newname in self.circuit.c:
del self.circuit.c[c.name]
c.name = newname
self.circuit.c[c.name] = c
def rename_port(self, *_):
p = self.circuit.selected_element
if not isinstance(p, Port):
return
newname = self.mod_port_name.value
if len(newname) and not newname in self.circuit.p:
del self.circuit.p[p.name]
p.name = newname
self.circuit.p[p.name] = p
def delete_component(self, *_):
c = self.circuit.selected_element
if not isinstance(c, ComponentInstance) \
or not c in self.circuit.component_instances:
return
self.circuit.component_instances = filter(lambda cc: cc is not c,
self.circuit.component_instances)
for p in c.ports:
for cc in p.connections_in + p.connections_out:
cc.remove()
self.circuit.selected_element = None
def delete_port(self, *_):
p = self.circuit.selected_element
if not isinstance(p, Port) \
or not p in self.circuit.ports:
return
self.circuit.ports = filter(lambda pp: pp is not p,
self.circuit.ports)
for c in p.connections_in + p.connections_out:
c.remove()
self.circuit.selected_element = None
def dec_port_order(self, *_):
p = self.circuit.selected_element
if not isinstance(p, Port) \
or not p in self.circuit.ports:
return
ps = list(self.circuit.ports)
ii = ps.index(p)
ps.pop(ii)
ii = max(1, ii)
self.circuit.ports = ps[:ii-1] + [p] + ps[ii-1:]
def inc_port_order(self, *_):
p = self.circuit.selected_element
if not isinstance(p, Port) \
or not p in self.circuit.ports:
return
ps = list(self.circuit.ports)
ii = ps.index(p)
ps.pop(ii)
self.circuit.ports = ps[:ii+1] + [p] + ps[ii+1:]
def increment_face(self):
if self.index + 1 >= len(self.imgs):
return self.index
else:
while str(self.index) in self.results:
print self.index
self.index += 1
return self.index
def record_result(self, smile=True):
self.results[str(self.index)] = smile
trainer = Trainer()
button_smile = ButtonWidget(description='smile')
button_no_smile = ButtonWidget(description='sad face')
def display_face(face):
clear_output()
imshow(face, cmap='gray')
axis('off')
def update_smile(b):
trainer.record_result(smile=True)
trainer.increment_face()
display_face(trainer.imgs[trainer.index])
def update_no_smile(b):
trainer.record_result(smile=False)
trainer.increment_face()
def interactive_plot_modalities_lavalamps(
self,
sample_subsets=None,
feature_subsets=None,
color=red,
x_offset=0,
use_these_modalities=True,
bootstrapped=False,
bootstrapped_kws=None,
savefile="",
):
def do_interact(
sample_subset=None,
feature_subset=None,
color=red,
x_offset=0,
use_these_modalities=True,
bootstrapped=False,
bootstrapped_kws=None,
savefile="",
):
for k, v in locals().iteritems():
if k == "self":
continue
sys.stdout.write("{} : {}\n".format(k, v))
assert feature_subset in self.splicing.feature_subsets.keys()
feature_ids = self.splicing.feature_subsets[feature_subset]
from sklearn.preprocessing import LabelEncoder
le = LabelEncoder()
n_in_this_class = len(set(le.fit_transform(self.experiment_design.data[sample_subset])))
try:
assert n_in_this_class
except:
raise RuntimeError("this sample designator is not binary")
# TODO: cast non-boolean binary ids to boolean
dtype = self.experiment_design.data[sample_subset].dtype
try:
assert dtype == "bool"
except:
raise RuntimeError("this sample designator is not boolean")
sample_ids = self.experiment_design.data[sample_subset].index[self.experiment_design.data[sample_subset]]
self.splicing.plot_modalities_lavalamps(
sample_ids,
feature_ids,
color=color,
x_offset=x_offset,
use_these_modalities=use_these_modalities,
bootstrapped=bootstrapped,
bootstrapped_kws=bootstrapped_kws,
ax=None,
)
plt.tight_layout()
if feature_subsets is None:
feature_subsets = Interactive.get_feature_subsets(self, ["splicing"])
if sample_subsets is None:
sample_subsets = self.default_sample_subsets
if bootstrapped_kws is None:
bootstrapped_kws = {}
gui = interact(
do_interact,
sample_subset=sample_subsets,
feature_subset=feature_subsets,
color=color,
x_offset=x_offset,
use_these_modalities=use_these_modalities,
bootstrapped=bootstrapped,
bootstrapped_kws=bootstrapped_kws,
savefile=savefile,
)
def save(w):
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
gui.widget.result.savefig(savefile.value, format=extension.lstrip("."))
savefile = TextWidget(description="savefile", value="figures/clustermap.pdf")
save_widget = ButtonWidget(description="save")
gui.widget.children = list(gui.widget.children) + [savefile, save_widget]
save_widget.on_click(save)
def interactive_correlations(self):
def do_interact(
data_type="expression",
sample_subset=self.default_sample_subsets,
feature_subset=self.default_feature_subset,
metric="euclidean",
method="average",
list_link="",
scale_fig_by_data=True,
fig_width="",
fig_height="",
featurewise=False,
):
for k, v in locals().iteritems():
if k == "self":
continue
sys.stdout.write("{} : {}\n".format(k, v))
if feature_subset != "custom" and list_link != "":
raise ValueError('set feature_subset to "custom" to use list_link')
if feature_subset == "custom" and list_link == "":
raise ValueError("use a custom list name please")
if feature_subset == "custom":
feature_subset = list_link
elif feature_subset not in self.default_feature_subsets[data_type]:
warnings.warn(
"This feature_subset ('{}') is not available in "
"this data type ('{}'). Falling back on all "
"features.".format(feature_subset, data_type)
)
return self.plot_correlations(
sample_subset=sample_subset,
feature_subset=feature_subset,
data_type=data_type,
scale_fig_by_data=scale_fig_by_data,
method=method,
metric=metric,
featurewise=featurewise,
)
feature_subsets = Interactive.get_feature_subsets(self, ["expression", "splicing"])
method = ("average", "weighted", "single", "complete", "ward")
metric = (
"euclidean",
"seuclidean",
"sqeuclidean",
"chebyshev",
"cosine",
"cityblock",
"mahalonobis",
"minowski",
"jaccard",
)
gui = interact(
do_interact,
data_type=("expression", "splicing"),
sample_subset=self.default_sample_subsets,
feature_subset=feature_subsets,
metric=metric,
method=method,
featurewise=False,
)
def save(w):
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
gui.widget.result.savefig(savefile.value, format=extension.lstrip("."))
savefile = TextWidget(description="savefile", value="figures/correlations.pdf")
save_widget = ButtonWidget(description="save")
gui.widget.children = list(gui.widget.children) + [savefile, save_widget]
save_widget.on_click(save)
return gui
class NotebookFitter(MPLFitter):
__doc__ = _COMMON_DOC + """
If IPython is available, it uses the IPython notebook's rich display
to fit data interactively in a web-based GUI. The Parameters are
represented in a web-based form that is kept in sync with `current_params`.
All subclasses to Model, including user-defined ones, are shown in a
drop-down menu.
Clicking the "Fit" button updates a plot, as above, and updates the
Parameters in the form to reflect the best fit.
Parameters
----------
data : array-like
model : lmfit.Model
optional initial Model to use, maybe be set or changed later
all_models : list
optional list of Models to populate drop-down menu, by default
all built-in and user-defined subclasses of Model are used
Additional Parameters
---------------------
axes_style : dictionary representing style keyword arguments to be
passed through to `Axes.set(...)`
data_style : dictionary representing style keyword arguments to be passed
through to the matplotlib `plot()` command the plots the data points
init_style : dictionary representing style keyword arguments to be passed
through to the matplotlib `plot()` command the plots the initial fit
line
best_style : dictionary representing style keyword arguments to be passed
through to the matplotlib `plot()` command the plots the best fit
line
**kwargs : independent variables or extra arguments, passed like `x=x`
""" + _COMMON_EXAMPLES_DOC
def __init__(self,
data,
model=None,
all_models=None,
axes_style={},
data_style={},
init_style={},
best_style={},
**kwargs):
# Dropdown menu of all subclasses of Model, incl. user-defined.
self.models_menu = Dropdown()
# Dropbox API is very different between IPy 2.x and 3.x.
if IPY2:
if all_models is None:
all_models = {m.__name__: m for m in Model.__subclasses__()}
self.models_menu.values = all_models
else:
if all_models is None:
all_models = [(m.__name__, m) for m in Model.__subclasses__()]
self.models_menu.options = all_models
self.models_menu.on_trait_change(self._on_model_value_change, 'value')
# Button to trigger fitting.
self.fit_button = Button(description='Fit')
self.fit_button.on_click(self._on_fit_button_click)
# Button to trigger guessing.
self.guess_button = Button(description='Auto-Guess')
self.guess_button.on_click(self._on_guess_button_click)
# Parameter widgets are not built here. They are (re-)built when
# the model is (re-)set.
super(NotebookFitter,
self).__init__(data, model, axes_style, data_style, init_style,
best_style, **kwargs)
def _repr_html_(self):
display(self.models_menu)
button_box = HBox()
button_box.children = [self.fit_button, self.guess_button]
display(button_box)
for pw in self.param_widgets:
display(pw)
self.plot()
def guess(self):
guessing_successful = super(NotebookFitter, self).guess()
self.guess_button.disabled = not guessing_successful
def _finalize_model(self, value):
first_run = not hasattr(self, 'param_widgets')
if not first_run:
# Remove all Parameter widgets, and replace them with widgets
# for the new model.
for pw in self.param_widgets:
pw.close()
self.models_menu.value = value
self.param_widgets = [
ParameterWidgetGroup(p) for _, p in self._current_params.items()
]
if not first_run:
for pw in self.param_widgets:
display(pw)
def _finalize_params(self):
for pw in self.param_widgets:
pw.value = self._current_params[pw.name].value
pw.min = self._current_params[pw.name].min
pw.max = self._current_params[pw.name].max
pw.vary = self._current_params[pw.name].vary
def plot(self):
clear_output(wait=True)
super(NotebookFitter, self).plot()
def fit(self):
super(NotebookFitter, self).fit()
self.plot()
def interactive_pca(
self,
data_types=("expression", "splicing"),
sample_subsets=None,
feature_subsets=None,
color_samples_by=None,
featurewise=False,
x_pc=(1, 10),
y_pc=(1, 10),
show_point_labels=False,
list_link="",
plot_violins=False,
scale_by_variance=True,
savefile="figures/last.pca.pdf",
):
def do_interact(
data_type="expression",
sample_subset=self.default_sample_subsets,
feature_subset=self.default_feature_subsets,
featurewise=False,
list_link="",
x_pc=1,
y_pc=2,
plot_violins=False,
show_point_labels=False,
color_samples_by=self.metadata.phenotype_col,
bokeh=False,
scale_by_variance=True,
most_variant_features=False,
std_multiplier=(0, 5.0),
):
for k, v in locals().iteritems():
if k == "self":
continue
sys.stdout.write("{} : {}\n".format(k, v))
if feature_subset != "custom" and list_link != "":
raise ValueError('Set feature_subset to "custom" to use list_link')
if feature_subset == "custom" and list_link == "":
raise ValueError("Use a custom list name please")
if feature_subset == "custom":
feature_subset = link_to_list(list_link)
elif feature_subset not in self.default_feature_subsets[data_type]:
warnings.warn(
"This feature_subset ('{}') is not available in "
"this data type ('{}'). Falling back on all "
"features.".format(feature_subset, data_type)
)
return self.plot_pca(
sample_subset=sample_subset,
data_type=data_type,
featurewise=featurewise,
x_pc=x_pc,
y_pc=y_pc,
show_point_labels=show_point_labels,
feature_subset=feature_subset,
plot_violins=plot_violins,
color_samples_by=color_samples_by,
bokeh=bokeh,
std_multiplier=std_multiplier,
scale_by_variance=scale_by_variance,
most_variant_features=most_variant_features,
)
# self.plot_study_sample_legend()
if feature_subsets is None:
feature_subsets = Interactive.get_feature_subsets(self, data_types)
if sample_subsets is None:
sample_subsets = self.default_sample_subsets
color_samples_by = self.metadata.data.columns.tolist()
gui = interact(
do_interact,
data_type=data_types,
sample_subset=sample_subsets,
feature_subset=feature_subsets + ["custom"],
featurewise=featurewise,
x_pc=x_pc,
y_pc=y_pc,
show_point_labels=show_point_labels,
list_link=list_link,
plot_violins=plot_violins,
color_samples_by=color_samples_by,
scale_by_variance=scale_by_variance,
)
def save(w):
# Make the directory if it's not already there
filename, extension = os.path.splitext(savefile.value)
self.maybe_make_directory(savefile.value)
gui.widget.result.fig_reduced.savefig(savefile.value, format=extension)
# add "violins" after the provided filename, but before the
# extension
violins_file = "{}.{}".format("_".join([filename, "violins"]), extension)
try:
gui.widget.result.fig_violins.savefig(violins_file, format=extension.lstrip("."))
except AttributeError:
pass
savefile = TextWidget(description="savefile")
save_widget = ButtonWidget(description="save")
gui.widget.children = list(gui.widget.children) + [savefile, save_widget]
save_widget.on_click(save)
return gui
def add_figure_widget(self, image_data, title='', caption = '', pvals=None, colors=None):
children = [i for i in self.unsaved.children]
if len(title) > 0:
title = title + '.'
if len(caption) > 0:
caption = ' ' + caption
html_str = '<b>'+title+'</b>' + caption
html_widget = HTML(value=html_str)
save_button = Button(description='Save Figure')
save_button.image_data = image_data
save_button.title = title
save_button.caption = caption
save_button.on_click(self.save_unsaved_figure)
save_button.pvals = pvals
save_button.colors = colors
close_button = Button(description='Remove Figure')
close_button.on_click(self.remove_unsaved_figure)
restore_pvals = Button(description='Restore Parameter Values')
restore_pvals.pvals = pvals
if pvals is None:
restore_pvals.visible = False
if old_ipython is True:
image_widget = Image()
image_widget.value = image_data
tab_widget = VBox(children=[image_widget, html_widget])
if colors is not None:
html_widgets = self.colorbar_tabs(colors)
tab_widget.description='Figure'
tab_widget = Tab(children=[tab_widget]+html_widgets)
else:
image_widget = self._image_widget_new(image_data, colors=colors)
tab_widget = VBox(children=[image_widget, html_widget])
toggle = Button(description='Hide')
restore_pvals.on_click(self.restore_figure_pvals)
if old_ipython is True:
wi = Popup(children=[close_button, save_button, tab_widget, restore_pvals])
else:
contents = VBox(children=[close_button, save_button, tab_widget, restore_pvals])
contents.width = '100%'
wi = Popup(children=[contents])
wi.border = '1px solid black'
save_button.wi = wi
close_button.wi = wi
children.append(wi)
self.unsaved.children = children
if colors is not None:
if old_ipython is True:
tab_widget.set_title(0, 'Figure')
tab_widget.set_title(1, 'Colorbar')
class DisplayColocalization(object):
def __init__(self, controller, cases, slice_variables):
setattr(self, 'controller', controller)
setattr(self, 'colocalizations_widget', None)
setattr(self, 'cases', cases)
setattr(self, 'slice_variables', slice_variables)
setattr(self, 'name', 'Co-localization: ' + ', '.join([i.case_number for i in self.cases]))
setattr(self, 'constraints', [])
setattr(self, 'active_constraints', False)
setattr(self, 'ci', dspace.CaseColocalization(cases, slice_variables))
setattr(self, 'pvals', {})
setattr(self, 'y_variable', 'log('+controller.ds.dependent_variables[0]+')')
def make_display_widget(self):
controller = self.controller
if controller.ds is None:
return
self.info = VBox()
self.constraints_widget = VBox()
self.plot = HBox()
self.log_coordinates = True
self.global_tolerance = VBox()
close_button = Button(description='Close Tab')
close_button.on_click(self.close_widget)
ss_options = ['log('+ i + ')' for i in controller.ds.dependent_variables]
self.y_dropdown = Dropdown(description='y-axis',
values=ss_options,
options=ss_options,
value=self.y_variable)
self.make_plot = Button(description='Create Plot')
self.make_plot.on_click(self.change_y_axis)
self.make_plot.yaxis = self.y_dropdown
self.make_plot.visible = True
check_box = Checkbox(description='Logarithmic coordinates',
value=self.log_coordinates)
check_box.on_trait_change(self.update_log, 'value')
self.y_dropdown.visible = False
if len(self.slice_variables) <= 3:
## self.make_plot.visible = True
if len(self.slice_variables) == 1:
self.y_dropdown.visible = True
if len(self.slice_variables) == 3:
self.y_dropdown = HTML(value='<font color="red">Warning 3D plots are experimental.</font>')
wi = VBox(children=[self.info,
self.constraints_widget,
check_box,
self.y_dropdown,
self.make_plot,
self.global_tolerance,
close_button])
if old_ipython is True:
wi.set_css('height', '400px')
else:
wi.height='400px'
wi.overflow_x = 'auto'
wi.overflow_y = 'auto'
self.update_display()
controller.update_child(self.name, wi)
def update_display(self):
self.update_info()
self.update_constraints()
self.update_global_tolerances()
def update_log(self, name, value):
controller = self.controller
self.log_coordinates = value
if value == False:
ss_old = ['log('+ i + ')' for i in controller.ds.dependent_variables]
ss_new = [i for i in controller.ds.dependent_variables]
else:
ss_old = [i for i in controller.ds.dependent_variables]
ss_new = ['log('+i+')' for i in controller.ds.dependent_variables]
ss_options = OrderedDict([(unicode(i),i) for i in ss_new])
index = ss_old.index(self.y_variable)
self.y_variable = ss_new[index]
self.y_dropdown.values = ss_options
self.y_dropdown.options = ss_options
self.y_dropdown.value = unicode(self.y_variable)
self.update_display()
def update_info(self):
title = HTML(value='<b> Cases to Co-localize </b>')
buttons = []
html_str = '<div><b>Is Valid: {0}</b></div>'.format(self.ci.is_valid())
if self.ci.is_valid() is False:
self.make_plot.disabled = True
else:
self.make_plot.disabled = False
valid = HTML(value = html_str)
html_str = '<table><caption> Auxiliary variables for ' + self.name
html_str += ' with ' + ', '.join(self.slice_variables)
html_str += ' as the slice variable{0}.</caption>'.format('s' if len(self.slice_variables) > 1 else '')
html_str += '<tr ><th rowspan="2" align=center style="padding:0 15px 0 15px;"> Slice<br> Variables </th>'
html_str += '<th colspan="' + str(len(self.cases)) + '" align=center style="padding:0 15px 0 15px;"> Cases </th></tr><tr align=center>'
for c in self.cases:
html_str += '<td style="padding:0 15px 0 15px;"><b> {0} </b></td>'.format(c.case_number)
html_str += '</tr>\n'
pset = self.ci.valid_interior_parameter_set()
for i in self.cases:
key = i.case_number
case_button = Button(description='Case ' + key)
buttons.append(case_button)
case_button.pvals = pset[key] if key in pset else None
case_button.on_click(self.open_case)
for j, xj in enumerate(self.slice_variables):
html_str += '<tr align=center><td>{0}</td>'.format(xj)
for i, c in enumerate(self.cases):
html_str += '<td>${0}_{1}</td>'.format(xj, i)
html_str += '</tr>'
html_str += '</table>'
html_str += '<caption>Case co-localization assumes that the slice variables '
html_str += 'for one case are independent from the slice variables for the other cases in the co-localization.'
html_str += 'Each auxiliary variable corresponds to a slice variable for one cases.</caption>'
save_table = Button(description='Save variable table')
save_table.on_click(self.save_table)
save_table.table_data = html_str
variables = HTML(value=html_str)
self.info.children = [title] + buttons + [valid, save_table, variables]
def update_constraints(self):
constraints_widget = Textarea(description='Constraints',
value = ',\n'.join(self.constraints)
)
constraints_widget.visible = self.active_constraints
button = Button(description='Done' if self.active_constraints else 'Modify constraints')
button.constraints_widget = constraints_widget
button.on_click(self.modify_constraints)
self.constraints_widget.children = [constraints_widget, button]
def modify_constraints(self, b):
if self.active_constraints is False:
self.active_constraints = True
else:
self.active_constraints = False
self.constraints = str(b.constraints_widget.value).split(',')
self.constraints = [i.strip() for i in self.constraints]
self.ci = dspace.CaseColocalization(self.cases,
self.slice_variables,
constraints = self.constraints)
self.update_info()
## self.update_plot()
self.update_constraints()
def update_plot(self):
controller = self.controller
ds = controller.ds
## if len(self.slice_variables) > 3:
## return
ci = self.ci
if ci.is_valid() is False:
## self.plot.children = []
self.pvals = {}
return
pset = self.ci.valid_interior_parameter_set()
self.pvals = pset[pset.keys()[0]]
pvals = self.pvals
fig = plt.figure(dpi=600, facecolor='w')
cases = [i.case_number for i in self.cases]
if len(self.slice_variables) == 1:
fig = plt.figure(figsize=[6, 3], dpi=600, facecolor='w')
ax1 = fig.add_axes([0.2, 0.3, 0.55, 0.6])
ax2 = fig.add_axes([0.2, 0.2, 0.55, 0.075])
ax3 = fig.add_axes([0.8, 0.2, 0.05, 0.7])
xaxis = self.slice_variables[0]
xvalues = [pset[i][xaxis] for i in pset]
x_range = [min(xvalues)*1e-2, max(xvalues)*1e2]
colors = ds.draw_1D_slice(ax2,
pvals, xaxis, x_range, colorbar=False, intersections=[1, 3, 5, 7])
ds.draw_1D_ss_function(ax1, self.y_variable,
pvals, xaxis, x_range, colors=colors, lw=2.)
for case_number in pset:
case = controller.ds(case_number)
pvals = pset[case_number]
yval = case.ssystem.steady_state_function(self.y_variable, pvals)
ax1.plot(np.log10(pset[case_number][xaxis]), yval,
'o', mfc=colors[case_number], mec='k', ms=5., lw=2.)
ax1.set_xticklabels('')
ax1.set_xlabel('')
ds.draw_region_colorbar(ax3, colors)
title = 'System design space showing a 1-D case co-localization'
caption = 'Different cases shown by line segments of different colors. '
caption += 'Steady state function shown on the y-axis. '
caption += 'Bottom bar shows 1D design space slice showing valid cases '
caption += 'as shown by the colorbar.'
caption += ' Figure generated with the following parameter values: '
caption += '; '.join([i + ' = ' + str(pvals[i]) for i in sorted(pvals) if i not in [xaxis]]) + '.'
elif len(self.slice_variables) == 2:
options = []
fig = plt.figure(figsize=[6, 4], dpi=600, facecolor='w')
ax = fig.add_axes([0.2, 0.2, 0.7, 0.7])
xaxis = self.slice_variables[0]
yaxis = self.slice_variables[1]
xvalues = [pset[i][xaxis] for i in pset]
yvalues = [pset[i][yaxis] for i in pset]
x_range = [min(xvalues)*1e-2, max(xvalues)*1e2]
y_range = [min(yvalues)*1e-2, max(yvalues)*1e2]
colors = ds.draw_2D_slice(ax, pvals, xaxis, yaxis,
x_range, y_range, included_cases=cases)
for case_number in pset:
case = controller.ds(case_number)
pvals = pset[case_number]
ax.plot(np.log10(pset[case_number][xaxis]), np.log10(pset[case_number][yaxis]),
'o', mfc=colors[case_number], mec='k', ms=5., lw=2.)
title = 'System design space showing a 2-D case co-localization'
caption = 'Enumerated co-localized qualitatively-distinct phenotypes represented '
caption += 'on the z-axis and identified by color. '
caption += 'Circles represent automatically determined values for each phenotype.'
caption += ' Figure generated with the following parameter values: '
caption += '; '.join([i + ' = ' + str(pvals[i]) for i in sorted(pvals) if i not in [xaxis, yaxis]]) + '.'
elif len(self.slice_variables) == 3:
options = []
fig = plt.figure(figsize=[6, 4], dpi=600, facecolor='w')
ax = fig.add_axes([0.2, 0.2, 0.7, 0.7], projection='3d')
xaxis = self.slice_variables[0]
yaxis = self.slice_variables[1]
zaxis = self.slice_variables[2]
xvalues = [pset[i][xaxis] for i in pset]
yvalues = [pset[i][yaxis] for i in pset]
zvalues = [pset[i][zaxis] for i in pset]
x_range = [min(xvalues)*1e-2, max(xvalues)*1e2]
y_range = [min(yvalues)*1e-2, max(yvalues)*1e2]
z_range = [min(zvalues)*1e-2, max(zvalues)*1e2]
colors = ds.draw_3D_slice(ax, pvals, xaxis, yaxis, zaxis,
x_range, y_range, z_range, included_cases=cases)
title = 'System design space showing a 3-D case co-localization'
caption = 'Enumerated co-localized qualitatively-distinct phenotypes represented '
caption += 'on the z-axis and identified by color. '
caption += ' Figure generated with the following parameter values: '
caption += '; '.join([i + ' = ' + str(pvals[i]) for i in sorted(pvals) if i not in [xaxis, yaxis]]) + '.'
else:
options = []
slice_variables = self.slice_variables
fig = plt.figure(figsize=[6, 3], dpi=600, facecolor='w')
ax1 = fig.add_axes([0.2, 0.2, 0.55, 0.7])
ax2 = fig.add_axes([0.8, 0.2, 0.05, 0.7])
values = {i:[pset[i][axis] for axis in slice_variables] for i in pset}
## ranges = {axis:(min(values[axis])*1e-2,max(values[axis])*1e2) for axis in slice_variables}
colors = {name:mt.cm.hsv(float(i)/float(len(cases))) for i, name in enumerate(cases)}
min_value = None
max_value = None
for case in cases:
y_values = np.log10(values[case])
min_y = min(y_values)
max_y = max(y_values)
if min_value is None:
min_value = min_y
else:
min_value = min([min_value, min_y])
if max_value is None:
max_value = max_y
else:
max_value = max([max_value, max_y])
ax1.plot(range(len(slice_variables)),
y_values,
lw=2., c=colors[case])
ax1.set_ylim([min_value-2, max_value+2])
ax1.set_xticks(range(len(slice_variables)))
ax1.set_xticklabels(['$' + controller.symbols[i] + '$' for i in slice_variables])
ds.draw_region_colorbar(ax2, colors)
ax1.set_xlim([0, len(slice_variables)-1])
title = 'Values for the slice variable for the n-D case co-localization'
caption = 'The y-axis represents value for the slice variable on the'
caption += ' x-axis for a case identified by color.'
caption += ' Figure generated with the following parameter values: '
caption += '; '.join([i + ' = ' + str(pvals[i]) for i in sorted(pvals) if i not in slice_variables]) + '.'
canvas = FigureCanvasAgg(fig)
plt.close()
buf = cStringIO.StringIO()
canvas.print_png(buf)
data = buf.getvalue()
controller.figures.add_figure(data,
title=title,
caption=caption)
def update_global_tolerances(self):
controller = self.controller
ds = controller.ds
ci = self.ci
if ci.is_valid() is False:
self.global_tolerance.children = []
return
pvals = self.ci.valid_interior_parameter_set(project=False)
if pvals is None:
self.global_tolerance.children = []
return
table = HTML()
html_str = '<div><table>\n<caption>Global tolerances determined for ' + self.name + ' showing fold-difference to a large qualitative change{0}. </caption>\n'.format(' in log-coordinates' if self.log_coordinates is True else '')
html_str += '<tr ><th align=center rowspan=2 style="padding:0 15px 0 15px;"> Parameters </th><th colspan=2> Tolerance </th></tr>'
html_str += '<tr><td style="padding:0 15px 0 15px;"><b> Lower bound</b></td><td style="padding:0 15px 0 15px;"><b> Upper bound</b></td></tr>'
tolerances = ci.measure_tolerance(pvals, log_out=self.log_coordinates)
for xi in sorted(pvals.keys()):
lower_th = 1e-15 if self.log_coordinates is False else -15
upper_th = 1e15 if self.log_coordinates is False else 15
lower, upper = tolerances[xi]
html_str += '<tr><td style="padding:0 15px 0 15px;"><b>{0}</b></td><td style="padding:0 15px 0 15px;">{1}</td><td style="padding:0 15px 0 15px;">{2}</td></tr>'.format(
xi,
lower if lower > lower_th else '-∞',
upper if upper < upper_th else '∞')
html_str += '</table><caption>'
html_str += 'Note: Global tolerance calculated based on the following values for the parameters: '
html_str += '; '.join([i + ' = ' + str(pvals[i]) for i in sorted(pvals.keys())]) + '.'
html_str += '</caption></div>'
table.value = html_str
save_button = Button(description='Save Global Tolerance Table')
save_button.table_data = html_str
save_button.on_click(self.save_table)
self.global_tolerance.children = [HTML(value='<br>'),
save_button,
table]
return
def save_table(self, b):
controller = self.controller
html_string = b.table_data
controller.tables.add_table(html_string)
controller.save_widget_data(b)
def change_y_axis(self, b):
self.y_variable = str(b.yaxis.value)
## self.plot.children = [self.plot.children[0]]
self.update_plot()
def open_case(self, b):
case_id = b.description.split(' ')[1]
c_widget = DisplayCase(self.controller,
str(case_id),
by_signature=False,
pvals=b.pvals,
subtitle='Co-localized')
c_widget.create_case_widget()
def close_widget(self, b):
controller = self.controller
controller.update_child(self.name, None)
class NotebookFitter(MPLFitter):
__doc__ = _COMMON_DOC + """
If IPython is available, it uses the IPython notebook's rich display
to fit data interactively in a web-based GUI. The Parameters are
represented in a web-based form that is kept in sync with `current_params`.
All subclasses to Model, including user-defined ones, are shown in a
drop-down menu.
Clicking the "Fit" button updates a plot, as above, and updates the
Parameters in the form to reflect the best fit.
Parameters
----------
data : array-like
model : lmfit.Model
optional initial Model to use, maybe be set or changed later
all_models : list
optional list of Models to populate drop-down menu, by default
all built-in and user-defined subclasses of Model are used
Additional Parameters
---------------------
axes_style : dictionary representing style keyword arguments to be
passed through to `Axes.set(...)`
data_style : dictionary representing style keyword arguments to be passed
through to the matplotlib `plot()` command the plots the data points
init_style : dictionary representing style keyword arguments to be passed
through to the matplotlib `plot()` command the plots the initial fit
line
best_style : dictionary representing style keyword arguments to be passed
through to the matplotlib `plot()` command the plots the best fit
line
**kwargs : independent variables or extra arguments, passed like `x=x`
""" + _COMMON_EXAMPLES_DOC
def __init__(self, data, model=None, all_models=None, axes_style={},
data_style={}, init_style={}, best_style={}, **kwargs):
# Dropdown menu of all subclasses of Model, incl. user-defined.
self.models_menu = Dropdown()
# Dropbox API is very different between IPy 2.x and 3.x.
if IPY2:
if all_models is None:
all_models = dict([(m.__name__, m) for m in Model.__subclasses__()])
self.models_menu.values = all_models
else:
if all_models is None:
all_models = [(m.__name__, m) for m in Model.__subclasses__()]
self.models_menu.options = all_models
self.models_menu.on_trait_change(self._on_model_value_change,
'value')
# Button to trigger fitting.
self.fit_button = Button(description='Fit')
self.fit_button.on_click(self._on_fit_button_click)
# Button to trigger guessing.
self.guess_button = Button(description='Auto-Guess')
self.guess_button.on_click(self._on_guess_button_click)
# Parameter widgets are not built here. They are (re-)built when
# the model is (re-)set.
super(NotebookFitter, self).__init__(data, model, axes_style,
data_style, init_style,
best_style, **kwargs)
def _repr_html_(self):
display(self.models_menu)
button_box = HBox()
button_box.children = [self.fit_button, self.guess_button]
display(button_box)
for pw in self.param_widgets:
display(pw)
self.plot()
def guess(self):
guessing_successful = super(NotebookFitter, self).guess()
self.guess_button.disabled = not guessing_successful
def _finalize_model(self, value):
first_run = not hasattr(self, 'param_widgets')
if not first_run:
# Remove all Parameter widgets, and replace them with widgets
# for the new model.
for pw in self.param_widgets:
pw.close()
self.models_menu.value = value
self.param_widgets = [ParameterWidgetGroup(p)
for _, p in self._current_params.items()]
if not first_run:
for pw in self.param_widgets:
display(pw)
def _finalize_params(self):
for pw in self.param_widgets:
pw.value = self._current_params[pw.name].value
pw.min = self._current_params[pw.name].min
pw.max = self._current_params[pw.name].max
pw.vary = self._current_params[pw.name].vary
def plot(self):
clear_output(wait=True)
super(NotebookFitter, self).plot()
def fit(self):
super(NotebookFitter, self).fit()
self.plot()
