Sample Single Cells by Cell Type Composition

Sample single cells from the scRNA-seq dataset to match the estimated cell type composition in the ST data.

Usage

sample_cells(
  sc_data,
  cell_types,
  target_counts,
  method = c("duplicates", "synthetic"),
  seed = NULL
)

sample_cells_by_type(
  sc_data,
  cell_types,
  target_counts,
  method = c("duplicates", "synthetic"),
  seed = NULL
)

Arguments

sc_data

Single-cell expression matrix (genes x cells).

cell_types

Named character vector of cell types for each cell.

target_counts

Named integer vector of target cell counts per type.

method

Sampling method:

"duplicates"

Allow duplicating cells when needed (default). Ensures all original cells are included first.

"synthetic"

Generate synthetic cells by sampling gene expression values from the same cell type.

seed

Random seed for reproducibility.

Value

A list containing:

expression

Sampled expression matrix

cell_ids

Vector of original cell IDs

cell_types

Vector of cell types for sampled cells

is_synthetic

Logical vector indicating synthetic cells

Examples

if (FALSE) { # \dontrun{
# Define target counts per cell type
targets <- c(B_cell = 100, T_cell = 200, Macrophage = 50)

# Sample cells
sampled <- sample_cells(sc_expr, cell_labels, targets)
} # }