Fig. 4: Geometric analyses and spatial statistics on the MERSCOPE human liver hepatocellular carcinoma dataset.

a Niches (or spatial domains) after geometric conversion to shapely polygons. b Geometric statistics of the niches: their occurrence, perimeter, area, roundness, and inner cell density. c Heatmap of average hop distance between niches and niches. d Localisation of TREM2 macrophages shown in the visualizer. The TREM2 and C1QC genes are shown, and cells are coloured by their gene counts for the two selected genes. e Heatmap of average hop distance between cell types and all other cell types. LRP1, CEBP, and TREM2 macrophages show a high proximity. f Heatmap of average hop distance between cell types and niches. The macrophage subpopulations show heterogeneous localisation with respect to the niches. LRP1, CEBP, and TREM2 macrophages are enriched in the necrosis niche. g Network plot summarising the distance metrics of c, e, f. Each node of the network corresponds either to a niche (hexagon) or a cell type (circle). The lower the mean distance between the two nodes, the higher the weight of the edge between these two nodes. A high node-node proximity is shown by a dark edge. Overall, it provides an overview of the colocalisation of cell types and niches in the tumour environment.