Fig. 3

Single-cell multi-omics datasets processed and visualised using MUON. a MOFA factors estimated from simultaneous scRNA-seq and scATAC-seq profiling of PBMCs, with cells coloured by either left: coarse-grained cell type; or right: gene expression (in blue) and peak accessibility (in red). Displayed genes and peaks are selected to represent cell-type-specific variability along factor axes. b UMAP latent space for the same dataset as in a, constructed from left: principal components for individual modalities; or right: MOFA factors and WNN cell neighbourhood graph. Cells are coloured by coarse-grained cell type. c. Examples of individual feature values of protein abundance in the CITE-seq profiling of PBMCs after applying dsb normalisation. Colours correspond to the relative local density of cells with red for high density and blue for low density. d UMAP latent space for the same dataset as in c, constructed from MOFA factors (top) or WNN cell neighbourhood graph (bottom). Cells are coloured by their coarse-grained cell type or feature values (blue for gene expression, yellow for protein abundance