Run multi-sample spatial integration — RunSpatialIntegration • scop

Integrate spatial transcriptomics samples and identify shared domains using PRECAST.

Usage

RunSpatialIntegration(
  object,
  method = "PRECAST",
  sample.by = NULL,
  assay = NULL,
  layer = "counts",
  coord.cols = c("col", "row"),
  features = NULL,
  image = NULL,
  reduction.name = NULL,
  cluster_colname = NULL,
  tool_name = "SpatialIntegration",
  store_results = TRUE,
  store_object = TRUE,
  verbose = TRUE,
  coordinate_space = c("raw", "legacy_display"),
  ...
)

Arguments

object: A merged spatial Seurat object or a list of spatial Seurat objects.
method: Spatial integration backend. The current stable backend is "PRECAST".
sample.by: Metadata column identifying samples for a merged Seurat object. For list input, list names are copied into this column.
assay: Assay to use. NULL uses the default assay.
layer: Layer containing finite, non-negative integer counts. PRECAST normalizes this selected matrix internally; normalized expression is rejected.
coord.cols: Metadata coordinate columns used when no image is available.
features: Features to score. If NULL, current variable features are used; if no variable features are present, all assay features are used.
image: Optional image name or named character vector mapping sample names to image names. By default, resolve the unique image covering each sample independently. Every input sample must remain represented. For list input, image names refer to each original list element, before Seurat renames duplicate image keys during merging.
reduction.name: Name of the integrated embedding reduction. If NULL, a method-specific name is used.
cluster_colname: Metadata column used for spatial domain labels. If NULL, a method-specific name is used.
tool_name: Name used to store detailed results in srt@tools.
store_results: Whether to store the full result in srt@tools.
store_object: Whether to retain the complete native PRECAST object in the stored method result. Set FALSE for a lighter result bundle; standard embeddings, domains, coordinates, parameters, summaries, and plotting do not require the native object.
verbose: Whether to print the message. Default is TRUE.
coordinate_space: Coordinate system used for integration distances and aligned-coordinate input. The default is raw acquisition coordinates; "legacy_display" remains an explicit compatibility option.
...: Named backend argument lists: create_params, adj_params, par_params, run_params, and select_params. The default adjacency is adj_params = list(type = "fixed_number", number = 6), using distances in the selected coordinate space and SCOP's exact spatial KNN implementation. PRECAST's fixed-distance Visium/ST array-index mode is not compatible with these coordinates and is rejected. For generic distance-based adjacency, explicitly choose platform = "Other_SRT".

Value

A Seurat object with spatial integration results stored in metadata, reductions, and srt@tools[[tool_name]].

Details

Stored results retain a private per-cell identity metadata column for GetSpatialResult(). Preserve this column when subsetting or renaming cells. The accessor returns current-cell assignments; stored native results and fit parameters remain unchanged.

Provide spatial samples with shared genes and raw coordinates. Use sample.by to identify samples and image to select their spatial images. PRECAST integrates expression and domain representations; it is not a physical image-registration method.