Deconvolute with CARD — deconvolute_card • spacedeconv

Runs CARD deconvolution and returns a cell-type proportion matrix, with column names prefixed by result_name.

Usage

deconvolute_card(
  single_cell_obj,
  spatial_obj,
  cell_type_col = "cell_ontology_class",
  assay_sc = "counts",
  assay_sp = "counts",
  batch_id_col = "orig.ident",
  result_name = "card"
)

Arguments

single_cell_obj: SingleCellExperiment.
spatial_obj: SpatialExperiment.
cell_type_col: Column in single_cell_obj containing cell type labels.
assay_sc: Single-cell assay to use.
assay_sp: Spatial assay to use.
batch_id_col: Batch ID column in single_cell_obj.
result_name: Prefix used to label result columns (default: "card").