Save a Seurat object to an H5MU file

Export multimodal Seurat objects to MuData (.h5mu) format. This function wraps MuDataSeurat::WriteH5MU with additional support for spatial data preservation and Seurat V5 layer handling.

Usage

SaveH5MU(
  object,
  filename,
  assays = NULL,
  modality.names = NULL,
  include.spatial = TRUE,
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

as.h5mu(object, filename, ...)

Arguments

object: A Seurat object
filename: Output filename
assays: Character vector of assay names to export. If NULL (default), exports all assays
modality.names: Named vector mapping assay names to desired modality names in the h5mu file. If NULL, uses reverse of standard mapping (RNA→rna, ADT→prot, ATAC→atac, etc.)
include.spatial: Logical; if TRUE, includes spatial data (coordinates, images, scalefactors) in the h5mu file
overwrite: Overwrite existing file
verbose: Show progress messages
...: Additional arguments passed to SaveH5MU

Value

Invisibly returns the filename

Details

The h5mu format is designed for multimodal data and stores each Seurat assay as a separate modality under /mod/{modality_name}. This function:

Extracts each specified assay from the Seurat object
Converts assays to modality structure
Writes counts, data, and scale.data layers for each modality
Preserves cell metadata in both global /obs and per-modality obs
Includes spatial data if requested
Maintains dimensional reductions and graphs

Assay Mapping

By default, Seurat assay names are mapped to standard MuData modality names:

RNA → rna
ADT → prot
ATAC → atac
Spatial → spatial
Other names are converted to lowercase

Examples

if (FALSE) { # \dontrun{
# Save a multimodal Seurat object (CITE-seq)
SaveH5MU(seurat_obj, "multimodal_data.h5mu")

# Save specific assays only
SaveH5MU(seurat_obj, "rna_and_protein.h5mu", assays = c("RNA", "ADT"))

# Custom modality name mapping
SaveH5MU(
  seurat_obj,
  "data.h5mu",
  modality.names = c(RNA = "rna", Protein = "prot")
)

# Include spatial data
SaveH5MU(visium_obj, "spatial_multimodal.h5mu", include.spatial = TRUE)
} # }