Don't pass dtype to AnnData

theislab · Nov 2, 2023 · c679d6f · c679d6f
1 parent 5490620
commit c679d6f
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Showing 4 changed files with 7 additions and 7 deletions.
diff --git a/src/cellrank/estimators/terminal_states/_gpcca.py b/src/cellrank/estimators/terminal_states/_gpcca.py
@@ -893,7 +893,7 @@ def plot_macrostate_composition(
             cats_colors = _create_categorical_colors(len(self.adata.obs[key].cat.categories))
         cat_color_mapper = dict(zip(self.adata.obs[key].cat.categories, cats_colors))
         x_indices = np.arange(len(macrostates.cat.categories))
-        bottom = np.zeros_like(x_indices, dtype=np.float32)
+        bottom = np.zeros_like(x_indices, dtype=float)
 
         width = min(1, max(0, width))
         fig, ax = plt.subplots(figsize=figsize, dpi=dpi, tight_layout=True)
@@ -1155,7 +1155,7 @@ def _write_macrostates(
             self._set("_coarse_stat_dist", value=stat_dist, shadow_only=True)
             self._set(
                 obj=self.adata.uns, key=Key.uns.coarse(self.backward),
-                value=AnnData(tmat, obs=dists, dtype=float)
+                value=AnnData(tmat, obs=dists),
             )
         else:
             for attr in ["_schur_vectors", "_schur_matrix", "_coarse_tmat", "_coarse_init_dist", "_coarse_stat_dist"]:

diff --git a/src/cellrank/kernels/_precomputed_kernel.py b/src/cellrank/kernels/_precomputed_kernel.py
@@ -142,7 +142,7 @@ def _from_matrix(
         # fmt: off
         if adata is None:
             logg.warning(f"Creating empty `AnnData` object of shape `{matrix.shape[0], 1}`")
-            adata = AnnData(sp.csr_matrix((matrix.shape[0], 1), dtype=np.float64))
+            adata = AnnData(sp.csr_matrix((matrix.shape[0], 1)))
         super().__init__(adata)
         self._backward: Optional[bool] = backward
         self.transition_matrix = matrix.copy() if copy else matrix

diff --git a/src/cellrank/kernels/_real_time_kernel.py b/src/cellrank/kernels/_real_time_kernel.py
@@ -448,7 +448,7 @@ def _restich_couplings(
         for ix in range(len(blocks)):
             index.extend(obs_names[ix])
 
-        tmp = AnnData(sp.bmat(blocks, format="csr"), dtype="float64")
+        tmp = AnnData(sp.bmat(blocks, format="csr"))
         tmp.obs_names = index
         tmp.var_names = index
         tmp = tmp[self.adata.obs_names, :][:, self.adata.obs_names]
@@ -520,7 +520,7 @@ def _sparsify_couplings(
             tmat = sp.csr_matrix(tmat, dtype=tmat.dtype)
             tmat.data[tmat.data < thresh] = 0.0
             tmat.eliminate_zeros()
-            couplings[key] = AnnData(tmat, obs=adata.obs, var=adata.var, dtype=tmat.dtype)
+            couplings[key] = AnnData(tmat, obs=adata.obs, var=adata.var)
 
         return couplings if copy else None
 
@@ -579,7 +579,7 @@ def assert_same(expected: Sequence[Any], actual: Sequence[Any], msg: Optional[st
     def _coupling_to_adata(self, src: Any, tgt: Any, coupling: Coupling_t) -> AnnData:
         """Convert the coupling to :class:`~anndata.AnnData`."""
         if not isinstance(coupling, AnnData):
-            coupling = AnnData(X=coupling, dtype=coupling.dtype)
+            coupling = AnnData(X=coupling)
             coupling.obs_names = np.asarray(self.adata.obs_names)[self.time == src]
             coupling.var_names = np.asarray(self.adata.obs_names)[self.time == tgt]
 

diff --git a/src/cellrank/pl/_aggregate_fate_probs.py b/src/cellrank/pl/_aggregate_fate_probs.py
@@ -328,7 +328,7 @@ def plot_violin_no_cluster_key():
         kwargs["rotation"] = xrot
 
         data = np.ravel(probs.X.T)[..., None]
-        tmp = AnnData(sp.csr_matrix(data.shape, dtype=data.dtype), dtype=data.dtype)
+        tmp = AnnData(sp.csr_matrix(data.shape, dtype=data.dtype))
         tmp.obs["fate probability"] = data
         tmp.obs[term_states] = (
             pd.Series(np.concatenate([[f"{direction.lower()} {n}"] * adata.n_obs for n in probs.names]))