Run Statial Kontextual spatial relationships — RunStatialKontextual • scop

Run Statial::Kontextual() on a spatial Seurat object to quantify pairwise cell or spot label relationships relative to a parent context. Results are stored as a compact SCOP bundle with raw Statial output, standardized summary, and parameters. Statial is an optional Bioconductor dependency installable with BiocManager::install("Statial").

Usage

RunStatialKontextual(
  srt,
  group.by,
  r,
  from = NULL,
  to = NULL,
  parent = NULL,
  parent_df = NULL,
  image = NULL,
  sample.by = NULL,
  images = NULL,
  coord.cols = c("col", "row"),
  inhom = FALSE,
  edge_correct = TRUE,
  window = c("convex", "square", "concave"),
  window.length = NA_real_,
  include_original = TRUE,
  cores = 1,
  tool_name = "StatialKontextual",
  store_results = TRUE,
  store_input = FALSE,
  verbose = TRUE,
  coordinate_space = c("raw", "legacy_display"),
  ...
)

Arguments

srt: A Seurat object.
group.by: Metadata column containing cell or spot labels.
r: Numeric radius or radii used by Statial::Kontextual(), expressed in the selected coordinate units.
from, to, parent: Cell or spot labels passed to Statial::Kontextual(). Ignored when parent_df is supplied.
parent_df: Optional data frame from Statial::parentCombinations().
image: Name of the Seurat spatial image. Required when multiple images are present; a single image is selected automatically when NULL.
sample.by: Optional metadata column used as Statial imageID. If NULL, all cells or spots are treated as one image.
images: Optional Statial image filter passed to Kontextual(image = ).
coord.cols: Metadata coordinate columns used when no Seurat image coordinates are available.
inhom: Whether Statial should account for inhomogeneity.
edge_correct: Whether Statial should perform edge correction.
window, window.length: Window arguments passed to Statial::Kontextual(). Numeric window lengths use the selected coordinate units.
include_original: Whether to include original L-function values.
cores: Number of cores passed to Statial::Kontextual().
tool_name: Name used to store results in srt@tools.
store_results: Whether to store results in srt@tools.
store_input: Whether to store the backend input cell table in srt@tools.
verbose: Whether to print the message. Default is TRUE.
coordinate_space: Coordinate system used for spatial relationships. The default is raw acquisition coordinates; "legacy_display" remains an explicit compatibility option.
...: Additional named arguments passed to Statial::Kontextual().

Value

A Seurat object with Statial results stored in srt@tools[[tool_name]] when store_results = TRUE.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub

labels <- unique(as.character(spatial$coda_label))
if (length(labels) >= 2) {
  spatial <- RunStatialKontextual(
    spatial,
    group.by = "coda_label",
    r = 50,
    from = labels[1],
    to = labels[2],
    parent = labels[1:2],
    coord.cols = c("x", "y"),
    verbose = FALSE
  )
  spatial@tools$StatialKontextual$summary
}
#> $n_records
#> [1] 1
#> 
#> $n_images
#> [1] 1
#> 
#> $n_tests
#> [1] 1
#> 
#> $radii
#> [1] 50
#> 
#> $n_localized
#> [1] 0
#> 
#> $n_dispersed
#> [1] 1
#> 
#> $top_relationships
#>   imageID             test original kontextual  r inhomL
#> 1 sample1 collagen__islets      -50        -50 50  FALSE
#>