Extended Data Fig. 8: Aggregated multidimensional scaling.

a, Summary statistics of the multicellular factor analysis model (MOFAcellulaR) for snRNA-seq. In the left heatmaps, the lower panel shows the hierarchical clustering of the factor scores for the samples in the study. Patient and sample metrics data and lesion type are indicated in each row. Center panel shows the -log10(adj. p-values) of testing for associations between the factor scores and if they were MS or CTRL (Dis), lesion type (Les), Sex, Age, RIN, and technical batch (ANOVA). The upper panel shows the percentage of explained variance of each cell type expression matrix recovered by the factor. Right box plots visualize distribution of Factor 1 and 4 scores between CTRL and MS lesion types (n = 6 for CTRL, n = 6 for MS-CA, n = 4 for MS-CI). b, Summary statistics of MOFAcellular for ST data of MS samples. Left heatmaps show factor scores, associations with lesion type, sex, age, and duration, and percentage of explained variance for each spatial niche, as described in b. Right box plots visualize distribution of Factor 3 between MS lesion types (n = 8 for MS-CA, n = 4 for MS-CI). c, MDS computed on distances at the snRNA-seq cell type proportion level. d, MDS computed on distances at the ST deconvoluted cell type proportion level. e, MDS computed on distances at the snRNA-seq cell subtype proportion level. f, MDS computed on distances at the snRNA-seq MOFAcellulaR factor level. g, MDS computed on distances at the ST MOFAcellulaR factor level. h, MDS computed on distances at the aggregated distances across all levels. Color indicates CTRL and MS lesion type. Text indicates sample ID. i, Distribution of silhouette coefficient for each sample grouped by level (n = 16 for snRNA-seq prop, n = 16 for Cell state prop, n = 18 for ST prop, n = 16 for snRNA-seq MOFA, n = 12 for ST MOFA, n = 15 for total). Box plots illustrate the median (represented by the white dot), the 25th percentile (Q1), and the 75th percentile (Q3), with the ends of the black box indicating Q1 and Q3; the whiskers extend to the furthest datapoint within 1.5 times the interquartile range (IQR), specifically 1.5 * (Q3 - Q1), beyond Q3 or below Q1.