monkeybread.plot.cell_contact_embedding

monkeybread.plot.cell_contact_embedding(adata, contacts, group=None, basis='spatial', show=True, ax=None, **kwargs)

Shows embeddings of cells in contact. Can be spatial or any other basis.

Plots the results of monkeybread.calc.cell_contact(), highlighting the cells in contact.

Parameters

• adata (AnnData) – Annotated data matrix.

• contacts (Dict[str, Set[str]]) – The actual cell contacts, as calculated by monkeybread.calc.cell_contact().

• group (Optional[str] (default: None)) – Column in adata.obs to label cell contacts by.

• basis (Optional[str] (default: 'spatial')) – Coordinates in adata.obsm[X_{basis}] to use. Defaults to spatial.

• show (Optional[bool] (default: True)) – Whether to show the plot or return the Axes object.

• ax (Optional[Axes] (default: None)) – An Axes object to add the plots to.

• kwargs – Keyword arguments that will be passed to scanpy.pl.embedding().

Return type

Optional[Axes]

Returns

If show = True, returns nothing. Otherwise, returns the Axes object the plot is contained within.