Example 2: Analysis of mouse brain slices with complementary views.

• Run INSPIRE on the mouse brain slices with different views
  • Import packages
  • Load data
  • Data preprocessing
  • Build spatial graph
  • Run INSPIRE model
  • Access spot representations, proportions of spatial factors in spots, and gene loading matrix
  • Spatial distributions of spatial factors in tissues
  • Spot representations and spatial domain identification
  • Save results
• Analysis of spatial factors shared among slices and their gene signatures
  • Load results
  • Spatial distributions of spatial factors that are shared across slices
  • Detect top genes related to these spatial factors in hippocampus using gene loadings
  • Utilize external scRNA-seq data to confirm the correspondence of these factors to neuron types in CA1, CA2/CA3, and DG
• Analysis of spatial factors specific to one slice and their associated gene signatures
  • Load results
  • Spatial distributions of spatial factors that are specific to a single slice
  • Identify top genes associated with these spatial factors in the cerebellum using gene loadings