Example 1: Analysis of human dorsolateral prefrontal cortex (DLPFC) dataset.

• Run INSPIRE on the human DLPFC dataset
  • Import packages
  • Load data
  • Data preprocessing
  • Build spaital 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
• Calculate benchmarking scores
  • Load results
  • Calculate ASW, ARI, and NMI
  • Calculate factor diversity and factor coherence
• Perform spatial trajectory inference
  • Load results
  • Spatial trajectory inference
• Enrichment or depletion of spatial factors in cortical layers
  • Load results
  • Enrichment or depletion analysis
• Analysis of spatial factors and their associated gene signatures
  • Visualization of layer-specific spatial factors
  • Identify cell type markers using scRNA-seq data and evaluate their gene rankings for corresponding spatial factors.
  • Identify top genes related to spatial factors and check their expression patterns in scRNA-seq data
• Run INSPIRE on the human DLPFC dataset (12 sections)
  • Import packages
  • Load data
  • Run INSPIRE model
  • Spatial distributions of spatial factors in tissues
  • Spot representations and spatial domain identification
  • Spot representation scores
  • Factor scores