bio-spatial-transcriptomics-spatial-communication

Ligand-Receptor Analysis with Squidpy

Goal: Identify significant ligand-receptor interactions between spatially proximal cell types.

Approach: Build a spatial neighbor graph, then run permutation-based ligand-receptor analysis using Squidpy's built-in database.

"Find cell-cell communication in my spatial data" -> Test ligand-receptor co-expression between neighboring cell types with permutation-based significance.

## Build spatial neighbors if not already done

sq.gr.spatial_neighbors(adata, coord_type='generic', n_neighs=6)

## Run ligand-receptor analysis

sq.gr.ligrec(
    adata,
    cluster_key='cell_type',  # Column with cell type annotations
    n_perms=100,  # Permutations for significance testing
    threshold=0.01,  # P-value threshold
    copy=False,
)