stereo.io.stereo_to_anndata#
- stereo.io.stereo_to_anndata(data, flavor='scanpy', sample_id='sample', reindex=False, output=None, base_adata=None, split_batches=True, compression='gzip')[source]#
Transform the StereoExpData object into Anndata format.
- Parameters:
data (
StereoExpData
) – the input StereoExpData object.flavor (
Literal
['scanpy'
,'seurat'
]) – if you want to convert the output file into h5ad of Seurat, please set'seurat'
.sample_id (
str
) – the sample name which will be set asorig.ident
in obs.reindex (
bool
) – ifTrue
, the cell index will be reindexed as{sample_id}:{position_x}_{position_y}
format.output (
Optional
[str
]) – the path to output h5ad file.base_adata (
Optional
[AnnData
]) – the input Anndata object.split_batches (
bool
) – Whether to save each batch to a single file if it is a merged data, default to True.compression (
Optional
[Literal
['gzip'
,'lzf'
]]) – The compression method to be used when saving data as a h5ad file, None means uncompressed, default to gzip.
- Return type:
An object of Anndata.