Fig. 5

Benchmarking spatial clustering methods using synthetic data from SRTsim based on the DLPFC reference data with redesigned layers. A The reference DLPFC data contains seven layers, including six DLPFC layers and white matter (WM). Sample 151673 in the DLPFC data is used to serve as the reference. B The spatial distribution of three redesigned layers. NL1 corresponds to the original layers 1–3. NL2 corresponds to the original layers 4–5. NL3 corresponds to the original layer 6—white matter. C The spatial expression patterns of three representative genes (MOBP, PCP4, SNAP25) are displayed in the reference data. D Spatial expression patterns of three representative genes are displayed in the synthetic data with redesigned layers (nearest neighbors k=20). E Violin plots show the distributions of six metrics (six panels) in the reference data (real; x-axis) and in the synthetic data generated by SRTsim (x-axis). The six metrics include four gene-wise metrics (expression mean; variance; coefficient of variation, cv; and zero proportion) and two location-wise metrics (zero proportion and library size). F The performance of six spatial clustering methods (x-axis) is evaluated based on the adjusted Rand index (y-axis) using synthetic data with redesigned layers generated from SRTsim