Merge pull request #646 from Sichao25/debug_l

Update the reference of pandas in `get_sz_exprs()` and `set_param_kinetic()`
aristoteleo · Jan 20, 2024 · 1eaafae · 1eaafae
2 parents 6f87056 + 2c0a9eb
commit 1eaafae
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diff --git a/dynamo/preprocessing/normalization.py b/dynamo/preprocessing/normalization.py
@@ -186,7 +186,7 @@ def get_sz_exprs(
             szfactors = adata.obs[layer + "_Size_Factor"].values[:, None]
 
         if total_szfactor is not None and total_szfactor in adata.obs.keys():
-            szfactors = adata.obs[total_szfactor][:, None]
+            szfactors = adata.obs[total_szfactor].values[:, None]
         elif total_szfactor is not None:
             main_warning("`total_szfactor` is not `None` and it is not in adata object.")
     except KeyError:

diff --git a/dynamo/tools/utils.py b/dynamo/tools/utils.py
@@ -1734,7 +1734,11 @@ def set_param_kinetic(
         ) = (None, None, None, None, None, None, None, None, None, None, None)
 
     if isarray(alpha) and alpha.ndim > 1:
-        params_df.loc[valid_ind, kin_param_pre + "alpha"] = alpha.mean(1)
+        params_df.loc[valid_ind, kin_param_pre + "alpha"] = (
+            np.asarray(alpha.mean(1))
+            if sp.issparse(alpha)
+            else alpha.mean(1)
+        )
         cur_cells_ind, valid_ind_ = (
             np.where(cur_cells_bools)[0][:, np.newaxis],
             np.where(valid_ind)[0],