SOAPy_st.pp.st_Seurat2Anndata

SOAPy_st.pp.st_Seurat2Anndata(seurat_file: PathLike, exp_mat_slot: List = ['RNA', 'counts'], res_type: str = 'lowres') → AnnData

Transform the Seurat .rds spatial omics data into Anndata.

Parameters

seurat_filePathLike

Path of seurat_obj.rds file.

exp_mat_slotlist

list with assay and slot name of expression matrix in seurat object to export to adata.X.

res_typestr

resolution type of image in Seurat object (default: ‘lowres’ in Seurat).

Returns

anndata.Anndata object