SURE-tools 2.0.8__tar.gz → 2.0.10__tar.gz

{sure_tools-2.0.8 → sure_tools-2.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.8
+Version: 2.0.10
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.8 → sure_tools-2.0.10}/SURE/SURE.py

@@ -816,7 +816,7 @@ class SURE(nn.Module):
     def _cell_move(self, xs, factor_idx, perturb):
         zns,_ = self.encoder_zn(xs)
         if type(factor_idx) == str:
-            factor_idx = np.where(self.cell_factor_names==factor_idx)
+            factor_idx = int(np.where(self.cell_factor_names==factor_idx)[0])
         
         if perturb.ndim==2:
             ms = self.cell_factor_effect[factor_idx]([zns, perturb])
@@ -855,11 +855,35 @@ class SURE(nn.Module):
         ps = convert_to_tensor(perturb, device=self.get_device())
         
         if type(factor_idx) == str:
-            factor_idx = np.where(self.cell_factor_names==factor_idx)
+            factor_idx = int(np.where(self.cell_factor_names==factor_idx)[0])
             
         ms = self.cell_factor_effect[factor_idx]([zs,ps])
         return tensor_to_numpy(ms)
     
+    def _get_expression_responses(self, delta_zs):
+        return self.decoder_concentrate(delta_zs)
+    
+    def get_expression_responses(self, 
+                             delta_zs, 
+                             batch_size: int = 1024):
+        """
+        Return cells' changes in the latent space induced by specific perturbation of a factor
+
+        """
+        delta_zs = convert_to_tensor(delta_zs, device=self.get_device())
+        dataset = CustomDataset(delta_zs)
+        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
+
+        R = []
+        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
+            for delta_Z_batch, _ in dataloader:
+                r = self._cell_move(delta_Z_batch)
+                R.append(tensor_to_numpy(r))
+                pbar.update(1)
+
+        R = np.concatenate(R)
+        return R
+    
     def preprocess(self, xs, threshold=0):
         if self.loss_func == 'bernoulli':
             ad = sc.AnnData(xs)

{sure_tools-2.0.8 → sure_tools-2.0.10}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.8
+Version: 2.0.10
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.8 → sure_tools-2.0.10}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.0.8',
+    version='2.0.10',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",