Extended Data Fig. 6: The permutation test strategy used in SCOTIA.
a, Pearson correlation of receptor gene expression between malignant subtypes or ligand gene expression between CAF subtypes (two-sided t test). b, Schematic of the permutation test model used for spatial molecular imaging data. The null distribution was established by randomizing cell locations within a small range (from -20 to 20 µm) while shuffling gene expression in each FOV. c, Neighborhood composition for each cell type from one example FOV with the original (left), permuted (middle) and shuffled negative control (right) data. The negative control was constructed by shuffling cell type labels without any constraints. Neighborhood cells were defined as cells within a radius of 30 µm. d, Boxplots showing the Jaccard index of the top 5% most likely interacting LRs inferred between CAF and malignant cells with varying reg (left) and regm (right) parameters, n = 16. For boxplots, the box limits denote the first and third quartiles, with the median shown in the center and whiskers covering data within 1.5× the interquartile range from the box, with diamonds representing outliers. e, The top five strongest interacting cell type pairs inferred by using cost function Eq. 6 (left) and 7 (right) (Methods). Dot size represents the number of permutation test-significant LR pairs, colored based on the average LR interaction score. Bar plot indicates the average interaction strengths of each cell type pair for the treated and untreated groups. U, untreated; T, treated; b, base 960-plex panel; a, augmented 990-plex panel. f, The top five strongest interacting cell type pairs inferred by using different permutation strategies.
