troutpy.tl.in_out_correlation

troutpy.tl.in_out_correlation#

troutpy.tl.in_out_correlation(sdata, extracellular_layer='segmentation_free_table', cellular_layer='table', n_neighbors=5, copy=None)#

Computes the correlation between intracellular and extracellular gene expressionusing k-nearest extracellular bins.

Parameters:

  • sdata (spatialdata.SpatialData) – A SpatialData object containing both extracellular and cellular AnnData objects.

  • extracellular_layer (str) – Key for the extracellular AnnData object in sdata.

  • cellular_layer (str) – Key for the cellular AnnData object in sdata.

  • n_neighbors (int) – Number of nearest extracellular bins to consider for aggregation.

Returns:

-correlation_results (DataFrame) A DataFrame containing correlation values for each gene, with gene names as the indexand columns [‘SpearmanR’, ‘PValue’].

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