from typing import Optional, Union
from anndata import AnnData
from matplotlib import pyplot as plt
from pathlib import Path
import os
[docs]def convert_scanpy(
adata: AnnData,
use_quality: str = "hires",
) -> Optional[AnnData]:
adata.var_names_make_unique()
library_id = list(adata.uns["spatial"].keys())[0]
if use_quality == "fulres":
image_coor = adata.obsm["spatial"]
else:
scale = adata.uns["spatial"][library_id]["scalefactors"][
"tissue_" + use_quality + "_scalef"
]
image_coor = adata.obsm["spatial"] * scale
adata.obs["imagecol"] = image_coor[:, 0]
adata.obs["imagerow"] = image_coor[:, 1]
adata.uns["spatial"][library_id]["use_quality"] = use_quality
return adata