Load a Visium spatial dataset as a SingleCellExperiment.

readVisium(dirname)

Arguments

dirname	Path to spaceranger output directory (e.g. "sampleID/outs/"). This directory must contain the counts matrix and feature/barcode TSVs in `filtered_feature_bc_matrix/`, and the spot positions at `spatial/tissue_positions_list.csv`. (These are default locations for spaceranger outputs.)

Value

SingleCellExperiment containing the counts matrix in counts and spatial data in colData. Array coordinates for each spot are stored in columns row and col, while image coordinates are stored in columns imagerow and imagecol.

Details

We store two variables associated with downstream BayesSpace functions in a list called BayesSpace.data in the SingleCellExperiment's metadata.

platform is set to "Visium", and is used to determine spot layout and neighborhood structure.
is.enhanced is set to FALSE to denote the object contains spot-level data.

Examples

if (FALSE) {
sce <- readVisium("path/to/outs/")
}