commot.tl.communication_direction
- commot.tl.communication_direction(adata, database_name=None, pathway_name=None, lr_pair=None, k=5, pos_idx=None, copy=False)
Construct spatial vector fields for inferred communication.
- Parameters
adata (
AnnData
) – The data matrix of shapen_obs
×n_var
. Rows correspond to cells or spots and columns to genes.database_name (
Optional
[str
]) – Name of the ligand-receptor database. If both pathway_name and lr_pair are None, the signaling direction of all ligand-receptor pairs is computed.pathway_name (
Optional
[str
]) – Name of the signaling pathway. If given, only the signaling direction of this signaling pathway is computed.lr_pair – A tuple of ligand-receptor pair. If given, only the signaling direction of this pair is computed.
k (
int
) – Top k senders or receivers to consider when determining the direction.pos_idx (
Optional
[ndarray
]) – The columns in.obsm['spatial']
to use. If None, all columns are used. For example, to use just the first and third columns, set pos_idx tonumpy.array([0,2],int)
.copy (
bool
) – Whether to return a copy of theanndata.AnnData
.
- Returns
adata – Vector fields describing signaling directions are added to
.obsm
, e.g., for a database named “databaseX”,.obsm['commot_sender_vf-databaseX-ligA-recA']
and.obsm['commot_receiver_vf-databaseX-ligA-recA']
describe the signaling directions of the cells as, respectively, senders and receivers through the ligand-receptor pair ligA and recA. If copy=True, return the AnnData object and return None otherwise.- Return type
anndata.AnnData