omicverse.space.moranI

omicverse.space.moranI(adata, connectivity_key='spatial_connectivities', genes=None, transformation=True, n_perms=None, two_tailed=False, corr_method='fdr_bh', layer=None, seed=None, copy=False, auto_spatial_neighbors=False, n_neighs=6, radius=None, spatial_key='spatial')[source]

Compute Moran’s I spatial autocorrelation for gene expression.

A convenience wrapper around spatial_autocorr() with mode='moran'. Set auto_spatial_neighbors to True to build the spatial neighborhood graph automatically via spatial_neighbors() when the connectivity matrix is missing from adata.obsp.

Parameters:

  • adata – AnnData with spatial coordinates in adata.obsm and optionally a precomputed connectivity in adata.obsp.

  • connectivity_key (str (default: 'spatial_connectivities')) – Key of the spatial connectivity matrix in adata.obsp. Default: ‘spatial_connectivities’.

  • genes (default: None) – Gene names/indices to test. None tests all genes. Default: None.

  • transformation (bool (default: True)) – Row-normalise the weight matrix before scoring. Default: True.

  • n_perms (default: None) – Permutations for empirical p-values; None uses only the analytical value. Default: None.

  • two_tailed (bool (default: False)) – Two-tailed z-score test. Default: False.

  • corr_method (default: 'fdr_bh') – Multiple-testing correction ('fdr_bh', 'bonferroni', …). Default: ‘fdr_bh’.

  • layer (default: None) – Expression layer to use; None uses adata.X. Default: None.

  • seed (default: None) – Random seed for permutation reproducibility. Default: None.

  • copy (bool (default: False)) – Return the result DataFrame. Default: False.

  • auto_spatial_neighbors (bool (default: False)) – Automatically build the spatial neighborhood graph if connectivity_key is absent from adata.obsp. Default: False.

  • n_neighs (int (default: 6)) – Number of KNN neighbours used when auto_spatial_neighbors is True. Default: 6.

  • radius (default: None) – Radius for radius-based graph when auto_spatial_neighbors is True. Default: None.

  • spatial_key (str (default: 'spatial')) – Key in adata.obsm holding 2-D coordinates. Default: ‘spatial’.

Returns:

Moran’s I results with columns I, pval_norm, and optionally pval_sim, pval_z_sim, pval_adj. Also stored in adata.uns['moranI'].

Return type:

DataFrame

Examples

>>> import omicverse as ov
>>> ov.space.spatial_neighbors(adata, n_neighs=6)
>>> df = ov.space.moranI(adata)
>>> df.head()
>>> # One-liner with auto graph building
>>> df = ov.space.moranI(adata, auto_spatial_neighbors=True)