Fig 1: Breast Tumors and Their Immunoenvironment Are Interwoven Entities(A–C) Spearman correlation analyses using the frequencies of (A) epithelial clusters, (B) T cell, myeloid, and epithelial clusters, and (C) T cell and myeloid clusters in all samples. Euclidean distance and average linkage were used (top). Also shown are frequencies of selected clusters in juxta-tumoral and tumor samples (bottom).(D) Spearman correlation analysis of T cell and myeloid cluster frequencies with phenotypic abnormality and individuality scores and frequencies of ERa+, CA9+, and Ki-67+ cells in tumors.(E) Heatmap of frequencies of T cell and myeloid clusters in all samples by hierarchical clustering using cosine distance and average linkage. For tumors, the subtype, grade, and three main groups, Tu1–Tu3, from Figure 5A are indicated by color.(F) Pseudo-bright-field images of immunofluorescence staining of the indicated tumor samples. Arrowheads indicate PD-1+CTLA-4+ T cells (left) or PD-L1+ TAMs (right). Scale bar, 25 µm.(G and H) Boxplots of (G) phenotypic abnormality and (H) individuality scores for tumors in tumor immune groups TIG1–TGI3.(I) Cluster frequency map for tumors in TIG2.Tumors and epithelial clusters were sorted by increasing phenotypic abnormality score. A cutoff of p = 0.01 was used in (A)–(D). Wilcoxon rank-sum test was used for (G) and (H). *p < 0.05, **p < 0.01, ***p < 0.001. See also Figure S6.