Identification of spatial homogeneous regions in tissues with concordex.

Abstract

Spatial homogeneous regions (SHRs) in tissues are domains that are homogeneous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. The method is implemented in a tool called concordex, which relies on analysis of k-nearest-neighbor (kNN) graphs. The concordex tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.