spatialvi.data.NeighborhoodGraphField

class spatialvi.data.NeighborhoodGraphField(obsm_key)

AnnData obsm field for neighbor index/distance arrays.

Stores dense numpy arrays. Squidpy outputs sparse CSR matrices — this field converts them to dense on registration (documented behavior). Keys: index_neighbor and distance_neighbor (matching upstream ResolVI).

Parameters:

obsm_key (str) – Key to access the neighbor graph in adata.obsm.

__init__(obsm_key)

Methods

__init__(obsm_key)
get_data_registry()	Returns a nested dictionary which describes the mapping to the data field.
get_field_data(adata)	Returns the requested data as determined by the field.
get_summary_stats(state_registry)	Get summary stats.
register_field(adata)	Register the field.
transfer_field(state_registry, adata_target, ...)	Transfer the field.
validate_field(adata)	Validate the field.
view_state_registry(state_registry)	View the state registry.

Attributes

COLUMN_NAMES_KEY
attr_key	The key of the data field within the relevant AnnData attribute.
attr_name	The name of the AnnData attribute where the data is stored.
is_empty	Returns True if the field is empty as a function of its kwargs.
mod_key	The modality key of the data field within the MuData (if applicable).
registry_key	The key that is referenced by models via a data loader.