cameo.visualization package

Submodules

cameo.visualization.escher_ext module

class cameo.visualization.escher_ext.NotebookBuilder(*args, **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(self, className)

Adds a class to the top level element of the widget.

add_traits(self, \*\*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(self)

Close method.

display_in_browser(self, \*args, \*\*kwargs)

Deprecated.

display_in_notebook(self, \*args, \*\*kwargs)

Deprecated.

get_manager_state([drop_defaults, widgets])

Returns the full state for a widget manager for embedding

get_state(self[, 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(self, name)

Returns True if the object has a trait with the specified name.

hold_sync(self)

Hold syncing any state until the outermost context manager exits

hold_trait_notifications(self)

Context manager for bundling trait change notifications and cross validation.

notify_change(self, change)

Called when a property has changed.

observe(self, handler[, names, type])

Setup a handler to be called when a trait changes.

on_displayed(self, callback[, remove])

(Un)Register a widget displayed callback.

on_msg(self, callback[, remove])

(Un)Register a custom msg receive callback.

on_trait_change(self[, 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(self)

Open a comm to the frontend if one isn’t already open.

remove_class(self, className)

Removes a class from the top level element of the widget.

save_html(self, filepath)

Save an HTML file containing the map.

send(self, content[, buffers])

Sends a custom msg to the widget model in the front-end.

send_state(self[, key])

Sends the widget state, or a piece of it, to the front-end, if it exists.

set_state(self, sync_data)

Called when a state is received from the front-end.

set_trait(self, name, value)

Forcibly sets trait attribute, including read-only attributes.

setup_instance(self, \*args, \*\*kwargs)

This is called before self.__init__ is called.

trait_events([name])

Get a dict of all the event handlers of this class.

trait_metadata(self, traitname, key[, default])

Get metadata values for trait by key.

trait_names(self, \*\*metadata)

Get a list of all the names of this class’ traits.

traits(self, \*\*metadata)

Get a dict of all the traits of this class.

unobserve(self, handler[, names, type])

Remove a trait change handler.

unobserve_all(self[, name])

Remove trait change handlers of any type for the specified name.

close_all

get_view_spec

update
update(self, 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(self, name, palette)[source]
map_palette(self, name, n=3, reverse=False)[source]

cameo.visualization.sympy_ext module

cameo.visualization.visualization module

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

cameo.visualization.visualization.graph_to_svg(g, layout=<function fruchterman_reingold_layout at 0x2ba8bfedb488>)[source]

return the SVG of a matplotlib figure generated from a graph

Module contents