booldog.io.cytoscape

Export BoolDog Boolean models to a running Cytoscape session, via the optional py4cytoscape dependency.

Attributes

_CYTOSCAPE_AVAILABLE

Functions

silence_p4c_loggers()

Raise the log level of py4cytoscape's loggers to CRITICAL.

test_cytoscape_connection()

Test if a connection to Cytoscape can be established.

booldog2cytoscape(model[, as_logic_circuit, title, ...])

Display a BoolDog Boolean model in Cytoscape.

Module Contents

booldog.io.cytoscape._CYTOSCAPE_AVAILABLE = True
booldog.io.cytoscape.silence_p4c_loggers()

Raise the log level of py4cytoscape’s loggers to CRITICAL.

Silences the informational/warning messages that py4cytoscape emits by default, so that BoolDog’s own logging output is not cluttered.

Notes

Called automatically at import time (if py4cytoscape is available).

booldog.io.cytoscape.test_cytoscape_connection()

Test if a connection to Cytoscape can be established.

Returns:

True, if a running Cytoscape instance was successfully pinged.

Return type:

bool

Raises:

  • ImportError –

    If the optional py4cytoscape dependency is not installed.

  • ConnectionError – If py4cytoscape is installed but no running Cytoscape instance could be reached.

booldog.io.cytoscape.booldog2cytoscape(model, as_logic_circuit=False, title=None, collection='Booldog Network', layout=None, style=None)

Display a BoolDog Boolean model in Cytoscape.

Parameters:

  • model (booldog:BoolDogModel) – A BoolDog object representing a Boolean network.

  • as_logic_circuit (bool) – If True, the graph is exported as a logic circuit (Boolean rules are represented as “logical” nodes (and, or, not) and edges. Otherwise, it is exported as a interaction graph. Default is False.

  • title (str or None) – The title of the Cytoscape network. Default is ‘{model_id} interaction network’ if as_logic_circuit is False and ‘{model_id} logic circuit’ else.

  • collection (str) – The name of the Cytoscape collection to add the network to. Default is “Booldog Network”.

  • layout (str or None) – The name of the Cytoscape layout to apply to the network. Default is None (no layout).

  • style (str or None) – The name of the Cytoscape visual style to apply to the network. If None, a default style will be applied. Default is None.

Returns:

suid – The SUID of the created Cytoscape network.

Return type:

int