a, Diffusion maps highlighting inferred dpt and Alb expression (left), and a self-organizing map for mouse hepatocyte single-cell RNA-seq data9 (right; see Methods). See Fig. 2 for details. b, Heat map showing the spatial hepatocyte zonation profiles (nine zones) inferred by Halpern et al.9 using the same ordering of genes as in a. c, Pearson’s correlation coefficient of zonation profiles inferred by Halpern et al.9 and our dpt approach after discretizing dpt-inferred zonation profiles into nine equally sized bins. We found that 1,347 out of 1,684 genes (80%) above the expression cutoff exhibited a positive correlation between the two methods. d, Pearson’s correlation coefficient as a function of average normalized expression. Negative correlations are enriched at low expression, and Pearson’s correlation of zonation profiles positively correlates with expression (Spearman’s R = 0.25; n = 1,684 genes). e, t-SNE map of single-cell transcriptomes highlighting the clusters generated by RaceID3, run separately on hepatocytes (clusters 11, 14, and 17 in Fig. 1c). The map reveals a major group of hepatocyte clusters and a number of small clusters that co-express T cell-related genes, B cell-related genes or progenitor genes. f, t-SNE maps highlighting the expression of ALB, the immune cell marker gene PTPRC, the B cell marker gene IGKC, and the progenitor marker gene EPCAM. The colour bar indicates log 2 normalized expression. Co-expression of hepatocyte and immune cell markers could either indicate the presence of doublets or be due to spillover of highly expressed genes such as ALB between cells during library preparation. For the zonation analysis (Fig. 2), only cells in clusters 3, 7, 19, 4, 2, 9, 8 and 11 from the map in e were included. e, f, n = 3,040 cells. g, Immunostaining for the periportal markers CPS1, PCK1, MTHFS, and GATM from the Human Protein Atlas31. The zonation module containing each gene in the SOM (Fig. 2a) is indicated in parentheses. P, portal tracts; C, central veins. h, Pathways enriched for genes in hepatocyte central/mid modules 24 and 33 (top; n = 659 genes) and periportal modules 1 and 3 (bottom; n = 422 genes) (compare with Fig. 2a). i, Immunostaining of the central marker ENG from the Human Protein Atlas31. The zonation module in the SOM (Fig. 2b) is indicated in parentheses. j, Pathways enriched for genes in endothelial central/mid modules 1 and 3 (top; n = 422 genes) and periportal module 20 (bottom; n = 73 genes) (compare with Fig. 2b). h, j, P values in the pathway enrichment analysis were calculated using a hypergeometric model and adjusted using the Benjamini–Hochberg method (see Methods). k, Pearson’s correlation coefficient of hepatocyte zonation profiles of orthologue pairs of human and mouse genes. Mouse data are from Halpern et al.9 (n = 967 genes) l, Pearson’s correlation coefficient of endothelial cell (including MVECs and LSECs) zonation profiles of orthologue pairs of human and mouse genes (n = 977 genes). Mouse data are from Halpern et al.13. See Methods for details.