Extended Data Fig. 7: Intra-patient and inter-site heterogeneity of T, NK and myeloid cell phenotypes.

a, T/NK cell cluster composition based on scRNA-seq, ranked by fraction of T naive/memory clusters (left) or fraction of T dysfunctional clusters (right). Panels analogous to Fig. 1g–i. b, Site-specific enrichment of coarse-grained T/NK cell clusters using GLM. Colour gradient indicates log₂ odds ratios and sizes indicate the Bonferroni-corrected -log₁₀(P value). c, Dimensionality reduction of the dissimilarity in T/NK cluster composition between pairs of samples using NMDS (Methods). Convex hulls highlight differences between samples based on the anatomic site. Size indicates the Shannon entropy in cluster composition per sample. d, Genes of interest in subsets of CD8⁺ T cells as a function of pseudotime inferred from diffusion components. e, Scaled module scores with respect to pseudotime, grouped by tumour site. f, Myeloid cell cluster composition. Ranked by fraction of cDC2 (left), M1.S1008 cells (middle) and M2.SELENOP cells (right). Panels analogous to Fig. 1g–i. g, Site-specific enrichment of coarse-grained myeloid cell clusters using GLM analogous to b. h, Dimensionality reduction of the dissimilarity in myeloid cluster composition between pairs of samples using NMDS (Methods). Convex hulls highlight differences between samples based on the anatomic site. Size indicates the Shannon entropy in cluster composition per sample.