Run official SpatialDM spatial ligand-receptor association analysis

Usage

RunSpatialDM(
  object,
  species = c("human", "mouse"),
  lr.database = NULL,
  assay = NULL,
  layer = "data",
  counts.layer = "counts",
  image = NULL,
  coord.cols = c("col", "row"),
  coordinate.unit = NULL,
  method = c("z-score", "permutation"),
  run.local = TRUE,
  l = NULL,
  eff_dist = NULL,
  cutoff = 0.1,
  n_neighbors = NULL,
  n_neighbor_layers = 6,
  single_cell = FALSE,
  complex.mean = c("algebra", "geometric"),
  min_cell = 3,
  n_perm = 1000,
  nproc = 1,
  seed = 1,
  global.fdr = TRUE,
  global.threshold = 0.1,
  local.fdr = FALSE,
  local.threshold = 0.1,
  result.name = "default",
  envname = "spatialdm_env",
  overwrite = FALSE,
  verbose = TRUE,
  srt = NULL
)

Arguments

object: A Seurat spatial object.
species: Built-in SpatialDM species ("human" or "mouse").
lr.database: Optional custom LR table with ligand, receptor, and annotation columns.
assay, layer, counts.layer: Assay and normalized/count expression layers.
image, coord.cols: Spatial image or metadata coordinate columns.
coordinate.unit: Unit of the raw input coordinates. Automatic unit selection uses technology-specific rules.
method: Official global/local test mode.
run.local: Whether to run locally.
l, eff_dist: SpatialDM RBF scale; one must be supplied.
cutoff: RBF weight cutoff used by SpatialDM to retain local spatial weights. This is a fraction between zero and one; it is not a Scissor alpha-search parameter.
n_neighbors: Number of neighbors to use for constructing the KNN graph.
n_neighbor_layers: Number of neighbor layers to use.
single_cell: Whether to use the single-cell spatial mode supported by SpatialDM. This is not a generic "single-cell rather than spatial" switch.
complex.mean: Mean used for complex ligand-receptor expression: "algebra" or "geometric".
min_cell: Minimum number of cells required.
n_perm: Number of permutations.
nproc: Number of parallel processes.
seed: Random seed.
global.fdr, local.fdr: Whether the corresponding p-value table uses FDR values for selection. These are logical switches, not numeric thresholds.
global.threshold, local.threshold: Selection thresholds for global and local results.
result.name: Stored result name.
envname: Conda-compatible Python environment. If NULL, the environment name will be set to "scop_env".
overwrite: Whether to overwrite existing metadata.
verbose: Whether to print messages.
srt: Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A Seurat object with a schema-v1 SpatialDM result bundle.