Interoperability with SpatialExperiment and AnnData

The SpatialExperiment conversion keeps the selected signal as the main assay, all raw measurements as an alternative experiment, and stores the images, channels, provenance and policy in metadata.

if (requireNamespace("SpatialExperiment", quietly = TRUE)) {
  spe <- cs_as_spe(x, policy)
  dim(spe)
  y <- cs_from_spe(spe)
  identical(cs_measurements(x), cs_measurements(y))
} else {
  message("Install SpatialExperiment to run this section.")
}
#> [1] TRUE

AnnData conversion is optional and requires an anndataR installation with a working Python AnnData runtime.

if (requireNamespace("anndataR", quietly = TRUE)) {
  result <- tryCatch(cs_as_anndata(x, policy), error = function(e) e)
  if (inherits(result, "error")) message(conditionMessage(result)) else result
} else {
  message("Install anndataR to run this section.")
}
#> 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'