cameo.visualization package¶

Submodules¶

cameo.visualization.escher_ext module¶

class cameo.visualization.escher_ext.NotebookBuilder(**kwargs)[source]¶

Bases: escher.plots.Builder

Attributes

allow_building_duplicate_reactions

A trait which allows any value.

and_method_in_gene_reaction_rule

A trait which allows any value.

canvas_size_and_loc

A trait which allows any value.

cofactors

A trait which allows any value.

comm

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

cross_validation_lock

A contextmanager for running a block with our cross validation lock set to True.

disabled_buttons

A trait which allows any value.

embedded_css

A trait for unicode strings.

enable_editing

A trait which allows any value.

enable_keys

A trait which allows any value.

enable_keys_with_tooltip

A trait which allows any value.

enable_search

A trait which allows any value.

enable_tooltips

A trait which allows any value.

full_screen_button

A trait which allows any value.

gene_data

A trait which allows any value.

gene_font_size

A trait which allows any value.

height

An int trait.

hide_all_labels

A trait which allows any value.

hide_secondary_metabolites

A trait which allows any value.

highlight_missing

A trait which allows any value.

identifiers_on_map

A trait which allows any value.

keys

An instance of a Python list.

layout

An instance trait which coerces a dict to an instance.

This lets the instance be specified as a dict, which is used to initialize the instance.

Also, we default to a trivial instance, even if args and kwargs is not specified.

log

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

map_json

A trait for unicode strings.

map_name

A trait for unicode strings.

marker_radius

A trait which allows any value.

menu

A trait which allows any value.

metabolite_compare_style

A trait which allows any value.

metabolite_data

A trait which allows any value.

metabolite_no_data_color

A trait which allows any value.

metabolite_no_data_size

A trait which allows any value.

metabolite_scale

A trait which allows any value.

metabolite_scale_preset

A trait which allows any value.

metabolite_styles

A trait which allows any value.

model

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

model_id

Gets the model id of this widget.

model_json

A trait for unicode strings.

model_name

A trait for unicode strings.

never_ask_before_quit

A trait which allows any value.

primary_metabolite_radius

A trait which allows any value.

reaction_compare_style

A trait which allows any value.

reaction_data

A trait which allows any value.

reaction_no_data_color

A trait which allows any value.

reaction_no_data_size

A trait which allows any value.

reaction_scale

A trait which allows any value.

reaction_scale_preset

A trait which allows any value.

reaction_styles

A trait which allows any value.

scroll_behavior

A trait which allows any value.

secondary_metabolite_radius

A trait which allows any value.

semantic_zoom

A trait which allows any value.

show_gene_reaction_rules

A trait which allows any value.

starting_reaction

A trait which allows any value.

use_3d_transform

A trait which allows any value.

zoom_to_element

A trait which allows any value.

Methods

`add_class`(className)	Adds a class to the top level element of the widget.
`add_traits`(**traits)	Dynamically add trait attributes to the Widget.
`class_own_trait_events`(name)	Get a dict of all event handlers defined on this class, not a parent.
`class_own_traits`(**metadata)	Get a dict of all the traitlets defined on this class, not a parent.
`class_trait_names`(**metadata)	Get a list of all the names of this class' traits.
`class_traits`(**metadata)	Get a `dict` of all the traits of this class.
`close`()	Close method.
`display_in_browser`(args, *kwargs)	Deprecated.
`display_in_notebook`(args, *kwargs)	Deprecated.
`get_manager_state`([drop_defaults, widgets])	Returns the full state for a widget manager for embedding
`get_state`([key, drop_defaults])	Gets the widget state, or a piece of it.
`handle_comm_opened`(comm, msg)	Static method, called when a widget is constructed.
`has_trait`(name)	Returns True if the object has a trait with the specified name.
`hold_sync`()	Hold syncing any state until the outermost context manager exits
`hold_trait_notifications`()	Context manager for bundling trait change notifications and cross validation.
`notify_change`(change)	Called when a property has changed.
`observe`(handler[, names, type])	Setup a handler to be called when a trait changes.
`on_displayed`(callback[, remove])	(Un)Register a widget displayed callback.
`on_msg`(callback[, remove])	(Un)Register a custom msg receive callback.
`on_trait_change`([handler, name, remove])	DEPRECATED: Setup a handler to be called when a trait changes.
`on_widget_constructed`(callback)	Registers a callback to be called when a widget is constructed.
`open`()	Open a comm to the frontend if one isn't already open.
`remove_class`(className)	Removes a class from the top level element of the widget.
`save_html`(filepath)	Save an HTML file containing the map.
`send`(content[, buffers])	Sends a custom msg to the widget model in the front-end.
`send_state`([key])	Sends the widget state, or a piece of it, to the front-end, if it exists.
`set_state`(sync_data)	Called when a state is received from the front-end.
`set_trait`(name, value)	Forcibly sets trait attribute, including read-only attributes.
`setup_instance`(**kwargs)	This is called before self.__init__ is called.
`trait_defaults`(names, *metadata)	Return a trait's default value or a dictionary of them
`trait_events`([name])	Get a `dict` of all the event handlers of this class.
`trait_has_value`(name)	Returns True if the specified trait has a value.
`trait_metadata`(traitname, key[, default])	Get metadata values for trait by key.
`trait_names`(**metadata)	Get a list of all the names of this class' traits.
`trait_values`(**metadata)	A `dict` of trait names and their values.
`traits`(**metadata)	Get a `dict` of all the traits of this class.
`unobserve`(handler[, names, type])	Remove a trait change handler.
`unobserve_all`([name])	Remove trait change handlers of any type for the specified name.

close_all
get_view_spec
update

update(reaction_data=None, metabolite_data=None, gene_data=None, reaction_scale=None)[source]¶

cameo.visualization.palette module¶

class cameo.visualization.palette.PaletteMapper[source]¶

Bases: object

Methods

add_palettalbe_palette
map_palette

add_palettalbe_palette(name, palette)[source]¶

map_palette(name, n=3, reverse=False)[source]¶

cameo.visualization.sympy_ext module¶

cameo.visualization.visualization module¶

cameo.visualization.visualization.graph_to_svg(g, layout=<function spring_layout>)[source]¶: return the SVG of a matplotlib figure generated from a graph

cameo.visualization.visualization.draw_knockout_result(model, map_name, simulation_method, knockouts, *args, **kwargs)[source]¶

cameo.visualization.visualization.inchi_to_svg(inchi, file=None, debug=False, three_d=False)[source]¶

Generate an SVG drawing from an InChI string.

Parameters

inchistr: An InChI string.

Returns

str: A vector graphics of the compound represented as SVG.

‘ # noqa

cameo.visualization package¶

Submodules¶

cameo.visualization.escher_ext module¶

cameo.visualization.palette module¶

cameo.visualization.sympy_ext module¶

cameo.visualization.visualization module¶

Module contents¶

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