Fig. 3: Niche-phenotype mapping identifies spatial phenotypes and summarizes the phenotypic architecture of breast tumors.
From: NIPMAP: niche-phenotype mapping of multiplex histology data by community ecology
a Different cell types have phenotypes (columns) with specific associations to the different histological niches and their interfaces (rows). Shown are all phenotypes with a niche-phenotype correlation of at least 0.3 and a false discovery rate of less than 1%. b–g Niche-phenotype mapping reveals expected (b–d) and novel (e–g) niche-phenotype associations, which are visualized by overlaying phenotypic marker intensity (dot color) and tissue segmentation (background color). Cells of types other than the type indicated in each panel are not shown for clarity. b B cells are positive for HLA-DR in the tertiary lymphoid structure (TLS) niche. c Keratin-positive tumor cells are positive for HLA-DR/MHC class II in the inflammatory niche. d Keratin-positive tumor cells are positive for HLA class I at the interface of the cancer and inflammatory niches. e CD45RO intensity in macrophages is associated with the inflammatory niche. f Keratin 6 in dendritic cells is associated with the inflammatory niche. g PD-L1 intensity in neutrophils associated with the interface of cancer and inflammatory niches. Marker intensity represents Z scored marker abundance, as quantified in the original study21. Source data are provided as a Source Data file.
