opendvp.tl.spatial_autocorrelation

opendvp.tl.spatial_autocorrelation(adata, method='moran', x_y=('x_centroid', 'y_centroid'), k=8, threshold=10.0, island_threshold=0.1)

Compute spatial autocorrelation statistics (Moran’s I or Geary’s C) for each gene in an AnnData object.

Return type:

None

Parameters

adataAnnData

Annotated data matrix where observations are cells and variables are genes.

method{‘moran’, ‘geary’}, default ‘moran’

Spatial statistic to compute: ‘moran’ or ‘geary’.

x_ySequence[str], default (“x_centroid”, “y_centroid”)

Names of columns in adata.obs containing spatial coordinates.

kint, default 8

Number of neighbors for Moran’s I (ignored for Geary’s C).

thresholdint or float, default 10.0

Distance threshold for neighbors for Geary’s C (ignored for Moran’s I).

island_thresholdfloat, default 0.1 (10%)

If more than this fraction of samples are islands (no neighbors), raises error.

Returns:

None

Results are added to adata.var in-place.

Raises:

ValueError

If method is not ‘moran’ or ‘geary’.

RuntimeError

If too many islands are detected in Geary’s C mode.