Cluster communication with spatial permutation — cluster_communication_spatial_permutation • COMMOTR

Permutation test that preserves spatial structure by rotating coordinates.

Usage

cluster_communication_spatial_permutation(
  seurat_obj,
  database_name,
  clustering,
  lr_pair = NULL,
  pathway_name = NULL,
  spatial_coords = NULL,
  n_permutations = 100L,
  random_seed = NULL,
  verbose = TRUE
)

Arguments

seurat_obj: Seurat object with COMMOTR results.
database_name: Database name.
clustering: Clustering column or vector.
lr_pair: LR pair name.
pathway_name: Pathway name.
spatial_coords: Spatial coordinates.
n_permutations: Number of permutations.
random_seed: Random seed.
verbose: Print progress.

Value

Seurat object with results.