omnipath.interactions.import_intercell_network

omnipath.interactions.import_intercell_network(include=(<InteractionDataset.OMNIPATH>, <InteractionDataset.PATHWAY_EXTRA>, <InteractionDataset.KINASE_EXTRA>, <InteractionDataset.LIGREC_EXTRA>), interactions_params=None, transmitter_params=None, receiver_params=None)[source]

Import intercellular network combining intercellular annotations and protein interactions.

First, it imports a network of protein-protein interactions. Then, it retrieves annotations about the proteins intercellular communication roles, once for the transmitter (delivering information from the expressing cell) and second, the receiver (receiving signal and relaying it towards the expressing cell) side.

These 3 queries can be customized by providing parameters which will be passed to omnipath.interactions.OmniPath.get() for the network and omnipath.requests.Intercell() for the annotations.

Finally the 3 pandas.DataFrame are combined in a way that the source proteins in each interaction annotated by the transmitter, and the target proteins by the receiver categories. If undirected interactions present (these are disabled by default) they will be duplicated, i.e. both partners can be both receiver and transmitter.

Parameters:

include (Union[str, InteractionDataset, Sequence[str], Sequence[InteractionDataset]]) – Interaction datasets to include for omnipath.interactions.AllInteractions.get().
interactions_params (Optional[Mapping[str, Any]]) – Parameters for the omnipath.interactions.AllInteractions.get().
transmitter_params (Optional[Mapping[str, Any]]) – Parameters defining the transmitter side of intercellular connections. See omnipath.interactions.AllInteractions.params() for available values.
receiver_params (Optional[Mapping[str, Any]]) – Parameters defining the receiver side of intercellular connections. See omnipath.interactions.AllInteractions.params() for available values.

Returns:

A dataframe containing information about protein-protein interactions and the inter-cellular roles of the proteins involved in those interactions.

Return type:

pandas.DataFrame