Fig. 4

Application of f-scLVM to neuronal cells. a Factor relevance and gene set augmentation for the most important 30 factors identified by f-scLVM based on REACTOME pathways. Bottom panel: Identified factors and corresponding gene set size ordered by relevance (white = low relevance; black = high relevance). Top panel: Gene set augmentation, showing the number of genes added (red) and removed (blue) by the model for each factor. b Breakdown of the cumulative factor relevance of annotated and unannotated factors (see also Additional file 2: Figure S5). c Bivariate visualization of cells using the factors muscle contraction and innate immune system. Colours correspond to cell types identified in [20]; numbers denote relative factor activities inferred by the model. d Weights for the most important genes in the muscle contraction factor, showing both genes that were pre-annotated by REACTOME (black) and genes added by the model (red)