Run spatial neighborhood statistics — RunSpatialNeighborhood • scop

Build a standardized spatial neighborhood result bundle and optionally dispatch to a supported backend for colocalization or local-effect statistics.

Usage

RunSpatialNeighborhood(
  srt,
  group.by,
  method = NULL,
  assay = NULL,
  layer = "data",
  coord.cols = c("col", "row"),
  image = NULL,
  sample.by = NULL,
  split.by = NULL,
  subject.by = NULL,
  radius = NULL,
  k = NULL,
  features = NULL,
  from = NULL,
  to = NULL,
  tool_name = "SpatialNeighborhood",
  store_results = TRUE,
  verbose = TRUE,
  coordinate_space = c("raw", "legacy_display"),
  backend = c("cpp", "r"),
  ...
)

Arguments

srt: A Seurat object.
group.by: Metadata column containing spatial cell or spot labels.
method: Neighborhood calculation. NULL preserves compatibility by choosing "observed" when split.by is absent and "spicyR" when it is supplied. "observed" returns package KNN or radius summaries. "spicyR" runs differential neighborhood statistics and requires split.by.
assay: Assay used when features are requested.
layer: Assay layer used when features are requested.
coord.cols: Metadata coordinate columns used when no Seurat image coordinates are available.
image: Name of the Seurat spatial image. Required when multiple images are present; a single image is selected automatically when NULL.
sample.by: Metadata column identifying images or samples. If NULL, all spots are treated as one sample.
split.by: Optional metadata column identifying conditions for differential neighborhood statistics.
subject.by: Optional metadata column identifying subjects for backends that support paired or repeated designs.
radius: Optional spatial radius used for package neighborhood summaries, expressed in the selected coordinate units.
k: Optional number of nearest neighbors used for package neighborhood summaries. This is a unitless count. When both radius and k are NULL, k = 6 is used.
features: Optional features to extract into the backend input table.
from, to: Optional cell or spot label filters.
tool_name: Name used to store results in srt@tools.
store_results: Whether to store results in srt@tools.
verbose: Whether to print the message. Default is TRUE.
coordinate_space: Coordinate system used to build neighbor distances. The default is raw acquisition coordinates; "legacy_display" remains an explicit compatibility option.
backend: Backend for observed label-pair aggregation. "cpp" avoids repeated data-frame aggregation; "r" retains the reference implementation. This does not alter the external "spicyR" method.
...: Additional arguments passed to the selected backend.

Value

A Seurat object with results stored in srt@tools[[tool_name]].

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- RunSpatialNeighborhood(
  spatial,
  group.by = "coda_label",
  coord.cols = c("x", "y"),
  k = 4,
  verbose = FALSE
)

SpatialNeighborhoodPlot(spatial, plot_type = "heatmap")

SpatialNeighborhoodPlot(spatial, plot_type = "network", top_n = 12)

SpatialNeighborhoodPlot(spatial, plot_type = "stat", top_n = 12)

SpatialNeighborhoodPlot(
  spatial,
  plot_type = "spatial",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)