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
cameo.visualization.palette module¶
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.
<svg version=”1.1” id=”topsvg” xmlns=”http://www.w3.org/2000/svg” xmlns:xlink=”http://www.w3.org/1999/xlink” xmlns:cml=”http://www.xml-cml.org/schema” x=”0” y=”0” width=”200px” height=”200px” viewBox=”0 0 100 100”> <title>OBDepict</title> <rect x=”0” y=”0” width=”100” height=”100” fill=”white”/> <text text-anchor=”middle” font-size=”6” fill =”black” font-family=”sans-serif” x=”50” y=”98” ></text> <g transform=”translate(0,0)”> <svg width=”100” height=”100” x=”0” y=”0” viewBox=”0 0 80 80” font-family=”sans-serif” stroke=”rgb(0,0,0)” stroke-width=”2” stroke-linecap=”round”> <text x=”36” y=”48” fill=”rgb(255,12,12)” stroke=”rgb(255,12,12)” stroke-width=”1” font-size=”16” >OH</text> <text x=”60” y=”51.68” fill=”rgb(255,12,12)” stroke=”rgb(255,12,12)” stroke-width=”1” font-size=”13” >2</text> </svg> </g> </svg>
‘ # noqa