Fig. 2

Simulating. A UMAP visualizations of simulate1 data. Colors represents cell types (upper) and batches (bottom), and each column responds to each method. B Boxplot of batch-effect-removing accuracy (LISI-CoM) (left) and clustering accuracy (ARI, Louvain clustering) (right) in three datasets: simulate1, simulate2, and simulate3 for eight or nine methods. C The spatial coherence score (SCS) of annotated cell types of SPIRAL and PASTE in three datasets. D spatial arrangements of cell types on original and aligned coordinates by SPIRAL and PASTE in simulate4 (upper) and simulate5 datasets (bottom). E The quantitative measurements of LISI-CoM and ARI in simulate4 and simulate5 datasets for eight or nine methods. F SCS of cell types in simulate4 and simulate5 data for SPIRAL and PASTE