Estimate cell type fractions from spatial transcriptomics data
using reference-based deconvolution.
Usage
estimate_fractions(
sc_data,
cell_types,
st_data,
method = "seurat",
max_cells = 10000
)
estimate_cell_type_fractions(
sc_data,
cell_types,
st_data,
method = "seurat",
max_cells = 10000
)
Arguments
- sc_data
Single-cell expression matrix (genes x cells).
- cell_types
Named vector of cell types for each cell.
- st_data
Spatial expression matrix (genes x spots).
- method
Deconvolution method. Currently "seurat" is supported.
- max_cells
Maximum cells to use for computational efficiency.
Default is 10000.
Value
A data.frame with cell type fractions per spot.
Details
This function requires the Seurat package (v4 or v5). It uses SCTransform
for normalization and FindTransferAnchors/TransferData for deconvolution.
Examples
if (FALSE) { # \dontrun{
fractions <- estimate_fractions(sc_expr, cell_labels, st_expr)
} # }