Run lightweight SpatialDWLS-style deconvolution

Estimate spot-level cell-type proportions by fitting spatial expression to reference cell-type signatures with non-negative least squares-style coefficients. The output follows SCOP's deconvolution metadata convention so it can be plotted directly with SpatialSpotPlot().

Usage

RunSpatialDWLS(
  srt,
  reference,
  reference_label,
  assay = NULL,
  reference_assay = NULL,
  layer = "counts",
  reference_layer = "counts",
  features = NULL,
  image = NULL,
  coord.cols = c("col", "row"),
  min_cells = 2,
  prefix = "SpatialDWLS",
  tool_name = "SpatialDWLS",
  normalize = TRUE,
  store_results = TRUE,
  verbose = TRUE
)

Arguments

srt: Spatial Seurat object used as the RCTD query.
reference: Reference Seurat object containing annotated single cells.
reference_label: Metadata column in reference with cell type labels.
assay: Assay used in srt. If NULL, the default assay is used.
reference_assay: Assay used in reference.
layer, reference_layer: Assay layers used for spatial and reference raw counts.
features: Features used for RCTD. If NULL, shared features are used.
image: Name of the Seurat spatial image used to recover coordinates when coord.cols are not available.
coord.cols: Metadata coordinate columns used when no image coordinate source is requested or available.
min_cells: Minimum reference cells required per cell type.
prefix: Prefix for metadata columns.
tool_name: Name used to store detailed results in srt@tools.
normalize: Whether to library-size normalize and log1p transform spatial and reference matrices before fitting.
store_results: Whether to store detailed RCTD results in srt@tools.
verbose: Whether to print the message. Default is TRUE.

Value

A Seurat object with "<prefix>_prop_*", "<prefix>_dominant_type", and "<prefix>_max_prop" metadata columns. Detailed results are stored in srt@tools[[tool_name]].

Examples

if (FALSE) { # \dontrun{
spatial <- RunSpatialDWLS(
  spatial,
  reference = reference,
  reference_label = "celltype",
  coord.cols = c("x", "y")
)
SpatialSpotPlot(spatial, group.by = "SpatialDWLS_dominant_type")
SpatialSpotPlot(spatial, group.by = "SpatialDWLS_dominant_type", plot_type = "pie")
} # }