minor changes/fixes

scyan/_io.py

@@ -53,10 +53,9 @@ def read_fcs(
     )
 
     adata = AnnData(
-        X=data.loc[:, is_marker].values,
+        X=data.loc[:, is_marker].values.astype(np.float32),
         var=pd.DataFrame(index=data.columns[is_marker]),
         obs=data.loc[:, ~is_marker],
-        dtype=np.float32,
     )
 
     if "$SPILLOVER" in meta:

scyan/preprocess.py

@@ -64,9 +64,8 @@ def auto_logicle_transform(
 def _logicle_inverse_one(adata: AnnData, obsm: Optional[str], marker: str) -> np.ndarray:
     column = adata[:, marker].X if obsm is None else adata[:, marker].obsm[obsm]
     column = column.flatten()
-    return flowutils.transforms.logicle_inverse(
-        column, None, *adata.uns["scyan_logicle"][marker]
-    )
+    t, m, w = adata.uns["scyan_logicle"][marker]
+    return flowutils.transforms.logicle_inverse(column, None, t=t, m=m, w=w)
 
 
 def asinh_transform(adata: AnnData, translation: float = 0, cofactor: float = 5) -> None:

tests/test_preprocess.py

@@ -13,7 +13,7 @@ def assert_is_zero(a: np.ndarray, atol=1e-5) -> bool:
 def raw_adata() -> AnnData:
     adata, _ = scyan.data.load("aml", version="short")
     adata = adata.raw.to_adata()
-    adata.raw = adata
+    adata.raw = adata.copy()
     return adata
 
 
@@ -34,7 +34,7 @@ def test_asinh(raw_adata_cytof: AnnData):
 
 @pytest.fixture
 def test_autologicle(raw_adata: AnnData) -> AnnData:
-    scyan.preprocess.auto_logicle_transform(raw_adata)
+    scyan.preprocess.auto_logicle_transform(raw_adata, quantile_clip=None)
     return raw_adata