account for obsp/varp during transpose

anndata/_core/anndata.py

@@ -1256,6 +1256,8 @@ def transpose(self) -> "AnnData":
         Transpose whole object.
 
         Data matrix is transposed, observations and variables are interchanged.
+
+        Ignores `.raw`.
         """
         if not self.isbacked:
             X = self.X
@@ -1272,11 +1274,14 @@ def t_csr(m: sparse.spmatrix) -> sparse.csr_matrix:
 
         return AnnData(
             t_csr(X),
-            self._var,
-            self._obs,
-            self._uns,
-            self._varm.flipped(),
-            self._obsm.flipped(),
+            obs=self.var,
+            var=self.obs,
+            # we're taking a private attributes here to be able to modify uns of the original object
+            uns=self._uns,
+            obsm=self.varm.flipped(),
+            varm=self.obsm.flipped(),
+            obsp=self.varp.copy(),
+            varp=self.obsp.copy(),
             filename=self.filename,
             layers={k: t_csr(v) for k, v in self.layers.items()},
             dtype=self.X.dtype.name,

anndata/tests/test_base.py

@@ -360,26 +360,13 @@ def test_get_subset_annotation():
 
 
 def test_transpose():
-    adata = AnnData(
-        np.array([[1, 2, 3], [4, 5, 6]]),
-        dict(obs_names=["A", "B"]),
-        dict(var_names=["a", "b", "c"]),
-    )
-
+    adata = gen_adata((5, 3))
+    adata.varp = {f"varp_{k}": v for k, v in adata.varp.items()}
     adata1 = adata.T
-
-    # make sure to not modify the original!
-    assert adata.obs_names.tolist() == ["A", "B"]
-    assert adata.var_names.tolist() == ["a", "b", "c"]
-
-    assert adata1.obs_names.tolist() == ["a", "b", "c"]
-    assert adata1.var_names.tolist() == ["A", "B"]
-    assert adata1.X.shape == adata.X.T.shape
-
-    adata2 = adata.transpose()
-    assert np.array_equal(adata1.X, adata2.X)
-    assert np.array_equal(adata1.obs, adata2.obs)
-    assert np.array_equal(adata1.var, adata2.var)
+    adata1.uns["test123"] = 1
+    assert "test123" in adata.uns
+    assert_equal(adata1.X.shape, (3, 5))
+    assert_equal(adata1.obsp.keys(), adata.varp.keys())
 
 
 def test_append_col():