Extended Data Fig. 10: Milo differentially abundant neighborhoods analysis. Related to methods.
(a) Log fold change of Milo neighborhoods for Tot1 cells at day 6 post transfer, with positive (blue) values higher in aPD1 treated vs control mice. Neighborhoods are separated by cell state by the consensus of cells’ annotations from our atlas. (b) UMAP 2D projection of the differentially abundant neighborhoods. (c) Log fold change (top-left), 2D projection (bottom-left) and differentially expressed genes of Milo neighborhood groups for Tot1 cells at day 6 post transfer, with positive (blue) values higher in aPD1 treated vs control mice.
