Extracts the anndata table from a SpatialData store and writes it as an
h5ad file. Spatial coordinates and images are embedded in the h5ad using
standard scanpy/squidpy conventions (obsm/spatial, uns/spatial).
Usage
SpatialDataToH5AD(
source,
dest,
table = "table",
overwrite = FALSE,
verbose = TRUE
)
Arguments
- source
Path to input SpatialData .zarr directory
- dest
Path for output .h5ad file
- table
Name of the table within the SpatialData store (default: "table")
- overwrite
If TRUE, overwrite existing output
- verbose
Show progress messages
Value
Invisibly returns dest