Fig. 2

The detailed immune components across HCC tissues. A The heatmap of meta-clusters of immune cells from all samples, colored by major cell subsets and labeled with cluster frequencies on the left, detailed cluster annotation was labeled on the right. B The tSNE plot of immune cells from all samples, colored by meta-clusters. C The PCA projections of immune signatures for different tissue samples, colored by tissue sites (top). The important immune features are labeled with colored arrows (bottom). D The barplot shows the compositions of major T cell subsets for different tissue sites (top); Frequency comparisons of the ratio of CD4⁺/CD8⁺ T cells across tissue sites (bottom). E Mean expression comparisons of selected markers in CD4⁺ (top) and CD8⁺ (bottom) T cells between INT and TB tissues. F Frequency comparisons of CD4⁺ (top) and CD8.⁺ (bottom) T cell clusters between INT and TB tissues. G The heatmap shows the significance level of frequency comparison for meta-cluster across patients grouped by defined clinical features in INT tissues, colored by the signed -log₁₀(p-value). H Frequency comparisons for meta-clusters in INT tissues across patients grouped by the defined clinical features. HCC patients were divided into early-stage and advanced-stage groups according to the level of corresponding clinical parameters listed in supplemental table 5. Unpaired student’s t-test was used in (D-H), with *p < 0.05, **p < 0.01, and ***p < 0.001