Convert a cellspec object to SpatialExperiment

Converts selected signals to the main assay, stores every raw measurement in an altExp, and records the cellspec metadata needed for a lossless round trip.

Usage

cs_as_spe(x, policy = NULL, assay_name = "intensity")

Arguments

x

A cellspec object.

policy

A signal policy. It is required when a marker has more than one compartment or statistic; otherwise it can be omitted.

assay_name

Name of the main signal assay.

Value

A SpatialExperiment with cells as columns, markers as rows, spatialCoords containing x and y, and a measurements altExp.

See also

Other interoperability: cs_as_anndata(), cs_from_spe()

Examples

# \donttest{
if (requireNamespace("SpatialExperiment", quietly = TRUE)) {
  x <- cs_example()
  policy <- cs_signal_policy(cs_markers(x))
  spe <- cs_as_spe(x, policy)
  spe
}
#> class: SpatialExperiment 
#> dim: 4 80 
#> metadata(1): cellspec
#> assays(1): intensity
#> rownames(4): DAPI CD3e Pan-Cytokeratin FOXP3
#> rowData names(0):
#> colnames(80): img1::1 img1::2 ... img2::39 img2::40
#> colData names(6): cell_id image_id ... x_px y_px
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(1): measurements
#> spatialCoords names(2) : x y
#> imgData names(0):
# }