Extended Data Fig. 10: Performance evaluation of SCOTIA with varied parameters using PDAC SMI and co-culture snRNA-seq datasets.
a, The number of significant LRs enriched in treated samples as a function of varying SCOTIA parameters; adjusted p < 0.05, two-sided Mann-Whitney U. b, The power (y axis) of SCOTIA with varied parameters for identifying treatment-enriched ligand-receptor (LR) interactions. Ground truth was defined with the co-culture snRNA-seq dataset. True LR interactions were defined as those exhibiting enrichment in treated tumoroids. Both ligand and receptor genes were required to display higher expression in treated compared to untreated samples, with at least one gene having a fold change >1.5. Conversely, false LR interactions were defined by enrichment in untreated samples with the same criteria. Performance was measured by sensitivity, specificity, F1 score, and precision. Reg is the entropy regularization term, the default is 1.0; Regm is the marginal relaxation term, the default is 2.0; Dist_cutoff is the distance cutoff for defining ‘adjacent’ cell clusters, the default is 50 µm.
