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Run SPOTlight spatial deconvolution

Source: R/RunSPOTlight.R
RunSPOTlight.Rd

Estimate spot-level cell-type proportions using SPOTlight and an annotated single-cell reference.

Usage

RunSPOTlight(
  object,
  reference,
  reference_label = "celltype",
  assay = NULL,
  reference_assay = NULL,
  layer = "counts",
  reference_layer = "counts",
  features = NULL,
  mgs = NULL,
  marker_top_n = 100,
  marker_min_logfc = 0,
  gene_id = "gene",
  group_id = "cluster",
  weight_id = "weight",
  min_prop = 0.01,
  scale = TRUE,
  prefix = "SPOTlight",
  tool_name = "SPOTlight",
  store_results = TRUE,
  verbose = TRUE,
  ...,
  srt = NULL
)

Arguments

object

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 object. If NULL, the default assay is used.

reference_assay

Assay used in reference. Only cells present in this assay are used, with reference labels aligned by cell ID.

layer, reference_layer

Assay layers used for spatial and reference raw counts.

features

Features used for SPOTlight. If NULL, shared features are used.

mgs

Optional marker-gene table passed to SPOTlight. It must contain columns named by gene_id, group_id, and weight_id. If NULL, a simple group-vs-rest marker table is generated from the reference expression matrix.

marker_top_n

Number of automatically generated marker genes retained per reference cell type.

marker_min_logfc

Minimum group-vs-rest log2 fold-change used when generating markers automatically.

gene_id, group_id, weight_id

Column names in mgs for gene IDs, cell type labels, and marker weights.

min_prop

Minimum cell-type proportion passed to SPOTlight.

scale

Whether SPOTlight scales expression internally.

prefix

Prefix for metadata columns.

tool_name

Name used to store detailed results in srt@tools.

store_results

Whether to store detailed RCTD results in srt@tools.

verbose

Whether to print the message. Default is TRUE.

...

Additional parameters passed to SPOTlight::SPOTlight().

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 SPOTlight proportion columns in metadata and dominant cell type summaries. When store_results = TRUE, detailed results are stored in srt@tools[[tool_name]].

Examples

if (FALSE) { # \dontrun{
data(visium_human_pancreas_sub)
data(panc8_sub)
keep_spots <- unique(round(seq(
  1,
  ncol(visium_human_pancreas_sub),
  length.out = 120
)))
spatial <- visium_human_pancreas_sub[, keep_spots]
# Results are conditional on the three reference cell types used here.
reference <- panc8_sub[, panc8_sub@meta.data[["celltype"]] %in%
  c("ductal", "alpha", "beta")]
reference <- Seurat::FindVariableFeatures(reference, nfeatures = 300, verbose = FALSE)
features_use <- head(intersect(
  SeuratObject::VariableFeatures(reference),
  rownames(spatial)
), 300)
spatial <- RunSPOTlight(
  object = spatial,
  reference = reference,
  reference_label = "celltype",
  assay = "Spatial",
  reference_assay = "RNA",
  features = features_use,
  marker_top_n = 20,
  verbose = FALSE
)
SpatialDeconvolutionPlot(
  spatial,
  tool_name = "SPOTlight",
  plot_type = "dominant",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)
} # }