Build a SPOTlight Model — build_model_spotlight • spacedeconv

Trains the SPOTlight model using single-cell and spatial data. Marker genes can be supplied or computed from the single-cell object.

Usage

build_model_spotlight(
  single_cell_obj,
  cell_type_col = "cell_ontology_class",
  spatial_obj,
  assay_sc = "counts",
  assay_sp = "counts",
  markers = NULL
)

Arguments

single_cell_obj: SingleCellExperiment.
cell_type_col: Column with cell type labels.
spatial_obj: SpatialExperiment.
assay_sc: Single-cell assay to use.
assay_sp: Spatial assay to use.
markers: Optional marker-gene data frame. If NULL, markers are computed from single_cell_obj using the authors' suggested approach.