Fig. 3

Myeloid cell and B cell clusters. a tSNE plots of 2,719 myeloid cells, color by relevant clusters (left) or sample type (right). b Bubble plots displaying expressions of specific genes in DCs (cluster 7), monocytes (clusters 3 and 5) and macrophages (clusters 0, 1, 2, 4, 6, 8, 9 and 10). c Violin plots displaying expressions of the selected marker genes in macrophage clusters. d Differences in pathway activity of each cell scored by GSVA. e–f Pseudotime trajectory of macrophage inferred by Monocle and showed by subcluster (e) and state (f). g Heatmap of single-cell regulon scores inferred by SCENIC. Number in brackets is the number of the target genes. g, genes. h tSNE plots of 1,485 B cells and myeloid cells, color by relevant clusters (left) or sample types (right). i Color coding for expression (gray to blue) of marker genes of plasma B cells, follicular B cells, IL7R + B cells and mast cells. j Pseudotime trajectory of B cell and mast cell state inferred by Monocle and characterized by state (left) and cell types (right). k Differences in pathway activity of each cell scored by GSVA. l Bubble plots displaying expressions of selected genes in subclusters