Fig. 3

Evaluation of GraphPCA on mouse medial prefrontal cortex (mPFC) data generated by STARmap. a An anatomic reference atlas displays the structure of the prelimbic area in the mouse prefrontal cortex. b Manual annotation provided by the original study. c Spatial domains detected by GraphPCA. d Barplots illustrating spatial domain detection ARI by different methods on the mPFC data. e Visualization of spatial domains identified by PCA, NMF, DR-SC, and SpatialPCA. The clustering results of SpaGCN, BayesSpace, and STAGATE are shown in Additional file 1: Fig. S12a. f Trajectories of the mPFC tissue based on low-dimensional embeddings obtained by GraphPCA, PCA, SpaGCN, and SpatialPCA. Trajectories are inferred by Slingshot under default parameters. g Annotated cell type labels for the mPFC data are available from the original study. h Barplots illustrating cell type clustering ARI by different methods on the mPFC data. i Spatial composition of cell types identified by different methods. Excitatory neurons: eL2/3, L5-1, eL5-2, eL5-3, eL6-1, and eL6-2; inhibitory neurons: Reln, VIP, SST, NPY, and Lhx6; Oligo: oligodendrocytes; Smc: smooth muscle cells; Astro: astrocytes; Endo: endothelia cells; Mixed: group of cells expressing marker genes associated with multiple cell types; and Unidentified: cells with no clear marker gene expression. j Cell type identification results by GraphPCA and other methods. Top: barplots displaying the number of cell types identified by each method. Bottom: heatmap showing correlations between estimated cell type proportions from each method and the ground truth