Figure 1. Locally homogenous neighborhoods enable sensitive cell type identification.

a, Strategy for inferring locally homogenous neighborhoods by pruning knn-networks. Links are removed if the transcript levels in a neighboring cell are not explained by a local background model. Thickness of links represents the likelihood of belonging to the same cell state. b, Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) representation²¹ of mouse hematopoietic progenitor single-cell RNA-seq data¹⁰ highlighting clusters inferred by Louvain clustering on the pruned knn-network (k=10 and α=10). Cell type labels are based on marker gene expression. c, Dot plot showing the expression z-score of lineage-specific marker genes across all clusters from (b). The dot size indicates the fraction of cells expressing a gene. d, Dot plot showing expression of lineage-specific marker genes across all clusters inferred by Seurat^5,6. See (c) for details. e, UMAP representation with links connecting cluster medoids. The thickness and color of a link indicates the transition probability between the connected clusters. (b-d) Data from n=2 biologically independent experiments.