Fig. 3: The SDNs surrounding individual malignant cells.
From: Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer
A Schematic overview of SDN determination. For a targeted malignant cell, its surroundings were determined based on a 40 µm distance. Malignant cells were further characterized by the compositions of their surroundings and were subjected to clustering analysis. The average surrounding composition of each malignant cell cluster was used to define SDNs. B Malignant cell clusters determined based on the approach in (A). Malignant cells within the same cluster share similar surrounding features. See also Supplementary Fig. 8C. C Dot plot of the surrounding compositions for each malignant cell cluster in (B). Each row of the dot plot represents the composition of the surroundings of a malignant cell cluster. The color and size of the dots indicate the scaled (scaled to [0, 1] by column) proportion of cell state/subtype. Only dots with scaled values ≥ 0.2 are displayed in this figure to present the major enriched cell state/subtypes. See also Supplementary Fig. 8D. D A representative example (1CB, left panel) of malignant cells colored by their SDNs. Malignant cells were indicated using cool colors, while the surrounding non-malignant cells were shown in warm colors. Other cells are shown in gray. Two representative windows were selected with corresponding protein staining. A total of 15 samples were profiled using CosMxTM SMI. Scale bars, 50 µm.
