Convert a cellspec object to AnnData

Creates an AnnData object with cells in obs, selected marker signals in X, and x/y in obsm$spatial. The optional anndataR package and its Python runtime are required.

Usage

cs_as_anndata(x, policy = NULL)

Arguments

x

A cellspec object.

policy

Signal policy used to form X. It is required when a marker has more than one compartment or statistic; otherwise it can be omitted.

Value

An AnnData object supplied by anndataR.

See also

Other interoperability: cs_as_spe(), cs_from_spe()

Examples

if (requireNamespace("anndataR", quietly = TRUE)) {
  x <- cs_example()
  cs_as_anndata(x, cs_signal_policy(cs_markers(x)))
}
#> InMemoryAnnData object with n_obs × n_vars = 80 × 4
#>     obs: 'cell_id', 'image_id', 'sample_id', 'x', 'y', 'area', 'x_px', 'y_px'
#>     var: 'marker'
#>     uns: 'cellspec'
#>     obsm: 'spatial'