mantispy.tl.neighbors_local_density

mantispy.tl.neighbors_local_density#

mantispy.tl.neighbors_local_density(adata, k=15, by='Metadata_ImageNumber', key_added='Metadata_LocalDensity', copy=False)#

Mean distance to the k nearest cells in the same field of view.

Local crowding changes morphology independently of treatment. Consider regressing it out with regress_out() before attributing a change to a perturbation.

Parameters:

  • adata (AnnData) – Single-cell object carrying Metadata_Center_X and Metadata_Center_Y.

  • k (int (default: 15)) – Number of neighbors averaged over.

  • by (str (default: 'Metadata_ImageNumber')) – obs column identifying the field of view. Neighbors are searched within each field only, since coordinates from different images are not comparable.

  • key_added (str (default: 'Metadata_LocalDensity')) – obs column written.

  • copy (bool (default: False)) – Return a modified copy instead of mutating in place.

Return type:

AnnData | None

Returns:

None, or the modified copy. Writes obs[key_added], and a cell alone in its field gets NaN.

Raises:

KeyError – obs is missing Metadata_Center_X or Metadata_Center_Y.