napari_prism.gr.cellular_neighborhood_enrichment

napari_prism.gr.cellular_neighborhood_enrichment#

napari_prism.gr.cellular_neighborhood_enrichment(adata, neighborhood, phenotype, label, grouping, pseudocount=0.001)#

Perform a cellular neighborhood enrichment test using OLS linear models.

Parameters:

  • adata (AnnData) – Annotated data object.

  • neighborhood (str) – Column in .obs that defines the neighborhood index or label that a cell belongs to.

  • phenotype (str) – Column in .obs that defines the cellular label to take into account. Ideally this should be the phenotype that was used to compute the given neighborhood.

  • label (str) – Column in .obs that defines the binary label defining distinct grouping groups.

  • grouping (str) – Column in .obs that defines distinct samples.

  • pseudo_count – Pseudocount to add to the log2 normalised proportions data. Defaults to 1e-3.

Return type:

dict

Returns:

Dictionary containing the p-values, adjusted p-values,

coefficients, t-values and null hypothesis rejection status. Each entry is a DataFrame with neighborhoods as rows and phenotypes as columns.

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