Fig. 5: Tri-omics integration and subclustering of PBMC data.

a Schematic representation of the integration; b UMAP visualization of all the integrated cell embeddings colored by their modality of origin; c–e UMAP visualization of scConfluence’s integrated cell embeddings plotted one modality at a time and colored by their cell type annotation of origin. The red circles highlight B cells which are already sub-annotated in scATAC and CyTOF. The blue circles highlight monocytes that are already sub-annotated in scRNA and CyTOF; f UMAP visualization of all the integrated cell embeddings colored based on inferred cluster annotations. Additional plots are provided for ATAC monocytes and RNA B cells which have been subclustered. The significance of the overlap between the marker genes obtained from scRNA and scATAC for each subcluster (Fisher’s exact test) is plotted. The dashed vertical line corresponds to FDR = 0.01. No alignment significance score is reported for cluster 6 as it only contains cells from the scATAC experiment. Source data are provided as a Source Data file; g–i Sankey diagrams displaying the comparison between cell annotations in their original publication and in our integrative analysis. Source data are provided as a Source Data file.