Comprehensive scanning of different clustering resolutions from 0.1 to 1.2 (an interval of 0.05) for each of the four samples. The resolution parameter is used in the graph optimisation procedure to find the optimal number of cell communities (clusters)—a higher resolution leads to more clusters. Cluster partitioning is visualised hierarchically from low resolution (top) to high resolution (bottom), where each row and colour corresponds to the result from one resolution (visualised by Clustree). Branching and merging of cells and clusters are shown by horizontal and vertical arrows when moving from one resolution to the next. CI represents connectivity index, a measure of differences in heterogeneity due to separating or grouping spots that are similar (nearest neighbour). CI values of controls (2709 and 2029) are higher than Palbociclib (1171 and 1431), indicating the reduced heterogenity in samples under drug treatments.