fix cell label assignment issue in batch removal

#86
theislab · Oct 1, 2023 · bdb646c · bdb646c
1 parent 0608477
commit bdb646c
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/scgen/_scgen.py b/scgen/_scgen.py
@@ -274,6 +274,7 @@ def batch_removal(self, adata: Optional[AnnData] = None) -> AnnData:
             corrected = AnnData(
                 self.module.generative(torch.Tensor(all_shared_ann.X))["px"]
                 .cpu()
+                .detach()
                 .numpy(),
                 obs=all_shared_ann.obs,
             )
@@ -283,7 +284,7 @@ def batch_removal(self, adata: Optional[AnnData] = None) -> AnnData:
                 adata_raw = AnnData(X=adata.raw.X, var=adata.raw.var)
                 adata_raw.obs_names = adata.obs_names
                 corrected.raw = adata_raw
-            corrected.obsm["latent"] = all_shared_ann.X
+            corrected.obsm["latent"] = all_shared_ann[corrected.obs_names,:].X
             corrected.obsm["corrected_latent"] = self.get_latent_representation(
                 corrected
             )
@@ -303,6 +304,7 @@ def batch_removal(self, adata: Optional[AnnData] = None) -> AnnData:
             corrected = AnnData(
                 self.module.generative(torch.Tensor(all_corrected_data.X))["px"]
                 .cpu()
+                .detach()
                 .numpy(),
                 obs=all_corrected_data.obs,
             )
@@ -312,7 +314,7 @@ def batch_removal(self, adata: Optional[AnnData] = None) -> AnnData:
                 adata_raw = AnnData(X=adata.raw.X, var=adata.raw.var)
                 adata_raw.obs_names = adata.obs_names
                 corrected.raw = adata_raw
-            corrected.obsm["latent"] = all_corrected_data.X
+            corrected.obsm["latent"] = all_corrected_data[corrected.obs_names,:].X
             corrected.obsm["corrected_latent"] = self.get_latent_representation(
                 corrected
             )