Fig. 3

MultiMAP integration of single-cell transcriptomics and chromatin accessibility. a MultiMAP visualization of the integration of published scATAC-seq [22] and newly generated scRNA-seq data of the mouse spleen (n = 1), colored by omic technology (left hand panel) and independent cell type annotations of each omic technology (right hand panel). b Dot plot showing the z-score of the mean log-normalized gene expression and gene activity scores of known markers of each identified joint cluster. The top dot of each row shows the cells from the scRNA-seq data, and the bottom dot represents the cells from the scATAC-seq data. c Riverplot showing correspondence between the joint clusters and the independent annotations of the scATAC-seq and scRNAseq data. d Confusion matrix of label transfer from the scRNAseq to the scATAC-seq. e MultiMAP visualization of the integration of single-cell transcriptomics and chromatin accessibility of human bone marrow and peripheral blood mononuclear cells [23] colored by omic technology (left hand panel) and by the published cell type annotation (right hand panel). f UMAP (panels in top row) and MultiMAP (panels in bottom row) visualization of the scRNA-seq and scATAC-seq data colored by cluster annotation and batch, showing the effective batch correction of both modalities using MultiMAP