stGrads Tutorial Documentation

Contents:

• Installation
  • Requirements
  • Install the development version
  • (Optional) Install common dependencies for the tutorials
  • Install from a local clone (advanced)
• 10x Visium Tutorial (PDAC demo)
  • Prepare a lightweight Visium object
  • Run the stGrads Visium Demo (Step1–Step4)
  • Tips & Notes
  • Advanced function
  • Session info
• 10x Visium HD Tutorial (internal datasets)
  • Prepare environment & load the HD object
  • Run the stGrads Visium HD Demo (Step1–Step4)
  • Notes
  • Session info
• Visium HD Morphometry and Mixed-Unit Refinement
  • 1. Install and load stGrads 2.0
  • 2. Load the publication-ready demo
  • 3. Keep image coordinates and analytical coordinates separate
  • 4. Standardize undirected RCTD pairs
  • 5. Evaluate local spatial support
  • 6. Replace single markers with deterministic marker programs
  • 7. Combine cell and nuclear morphology
  • 8. Integrate evidence for composite-segment prioritization
  • 9. Extend the original stGrads gradient framework to morphology
  • 10. Calculate undirected observed-to-expected pair enrichment
  • 11. Reproducibility files
• (Advanced)Mathematical definition
  • 1. Statistical unit and notation
  • 2. Conditional heterotypic null model
  • 3. Pair-specific ROI eligibility
  • 4. Condition-level aggregation
  • 5. Primary enrichment effect size
  • 6. Observed zeros and heatmap display
  • 7. Sensitivity estimate
  • 8. Reproducible implementation
• Spatial pseudo-cells and segment-level back-mapping
  • 1. Define spatial pseudo-cells
  • 2. Run the package function
  • 3. Preserve the spatial mapping
  • 4. Plot pseudo-cell locations and projected labels
  • 5. CAF subtyping and NicheNet input
• API Reference
  • Spatial pseudo-cells and transcriptomic aggregation
  • Spatial coordinates and gradients
  • Morphology and segmentation
  • RCTD mixed units and refinement
  • Pair enrichment
  • Publication-oriented plotting
  • Compatibility and data helpers
  • Legacy API