stlearn.tl.cci.adj_pvals

stlearn.tl.cci.adj_pvals(adata, pval_adj_cutoff: float = 0.05, correct_axis: str = 'spot', adj_method: str = 'fdr_bh')[source]
Performs p-value adjustment and determination of significant spots.

Default settings of this function are already run in st.tl.cci.run.

Parameters:

  • adata (AnnData) – Must have st.tl.cci.run performed prior.

  • pval_adj_cutoff (float) – Cutoff for spot to be significant based on adjusted p-value.

  • correct_axis (str) – Either ‘spot’, ‘LR’, or None; former corrects for number of LRs tested in each spot, middle corrects for number of spots tested per LR, and latter performs no adjustment (uses p-value for significant testing)

  • adj_method (str) – Any method supported by statsmodels.stats.multitest.multipletests; https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html

Returns:

adata – Adjusts all of the LR results; warning, does not adjust celltype-celltype results from running ran st.tl.run_cci downstream.

Return type:

AnnData