Fig. 4: Heterogeneity within the microenvironmental cell states.

a, Donut chart representing the number of cells per cell type analyzed to identify robust NMF MPs, labeled with the number of cells and MPs found in each cell type. The size of the donut represents the relative proportion of all TME cells. b, Selected TME NMF state composition of tumors assigned to each BPs. The statistical significance of TME composition between samples with assigned BP to ECM (n = 23), glial (n = 39) or NEU (n = 35) was computed using a two-sided Kruskal–Wallis test (n = 97). c, Interaction graph between malignant cell states and TME cell type abundance. Each node represents malignant cell-state (red) or TME cell type nodes (colored according to cell type as presented). The thickness and color of the edge indicate the strength of the Pearson correlation. d, Correlation heatmap for the Pearson correlation between the relative malignant cell-state proportions (rows) and relative TME cell-state abundance (columns), which show representative associations for the hypoxic environment. e, Ligand–receptor cross-talk graph. Each green circled node represents a malignant cell state versus nonmalignant cell type pair, while each squared node represents a ligand–receptor interaction; there is an edge if that cross-talk is present. The thickness and color of the edge indicate the percentage of tumors in which both malignant cell state and nonmalignant cell type are present and the cross-talk exist. Open ‘(’ and closed ‘)’ parentheses reflect multiple ligand or receptor interaction from the same family. Specifically, closed parentheses ‘)’ indicated multiple ligands interacting with the same receptor, and viceversa for closed ‘)’ parentheses, multiple receptors interacting with the same ligand. UPR, unfolded protein response.