SURE-tools 2.0.5__py3-none-any.whl → 2.0.7__py3-none-any.whl

SURE/SURE.py

@@ -11,7 +11,7 @@ from torch.distributions import constraints
 from torch.distributions.transforms import SoftmaxTransform
 
 from .utils.custom_mlp import MLP, Exp
-from .utils.utils import CustomDataset, CustomDataset3, CustomDataset4, tensor_to_numpy, convert_to_tensor
+from .utils.utils import CustomDataset, CustomDataset2, CustomDataset4, tensor_to_numpy, convert_to_tensor
 
 
 import os
@@ -814,11 +814,13 @@ class SURE(nn.Module):
         return A
     
     def _cell_move(self, xs, factor_idx, perturb):
-        zns = self.encoder_zn(xs)
+        zns,_ = self.encoder_zn(xs)
         if type(factor_idx) == str:
             factor_idx = np.where(self.cell_factor_names==factor_idx)
         
         if perturb.ndim==2:
+            print(factor_idx)
+            print(type(perturb))
             ms = self.cell_factor_effect[factor_idx]([zns, perturb])
         else:
             ms = self.cell_factor_effect[factor_idx]([zns, perturb.reshape(-1,1)])
@@ -836,19 +838,30 @@ class SURE(nn.Module):
         """
         xs = self.preprocess(xs)
         xs = convert_to_tensor(xs, device=self.get_device())
-        dataset = CustomDataset(xs)
+        ps = convert_to_tensor(perturb, device=self.get_device())
+        dataset = CustomDataset2(xs,ps)
         dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
 
         Z = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for X_batch, _ in dataloader:
-                zns = self._cell_move(X_batch, factor_idx, perturb)
+            for X_batch, P_batch, _ in dataloader:
+                zns = self._cell_move(X_batch, factor_idx, P_batch)
                 Z.append(tensor_to_numpy(zns))
                 pbar.update(1)
 
         Z = np.concatenate(Z)
         return Z
     
+    def get_metacell_move(self, factor_idx, perturb):
+        zs = self._get_codebook()
+        ps = convert_to_tensor(perturb, device=self.get_device())
+        
+        if type(factor_idx) == str:
+            factor_idx = np.where(self.cell_factor_names==factor_idx)
+            
+        ms = self.cell_factor_effect[factor_idx]([zs,ps])
+        return tensor_to_numpy(ms)
+    
     def preprocess(self, xs, threshold=0):
         if self.loss_func == 'bernoulli':
             ad = sc.AnnData(xs)

SURE/flow/plot_quiver.py

@@ -32,7 +32,7 @@ def plot_quiver(z_points, delta_z, method='umap', figsize=(6,4), dpi=200):
         sc.pp.neighbors(ad)
         sc.tl.umap(ad)
         z_2d = ad[:z_points.shape[0]].obsm['X_umap']
-        delta_z_2d = ad[z_points.shape[0]:] - z_2d
+        delta_z_2d = ad[z_points.shape[0]:].obsm['X_umap'] - z_2d
         dim_names = ['UMAP1', 'UMAP2']
     
     # 绘制quiver图

{sure_tools-2.0.5.dist-info → sure_tools-2.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.5
+Version: 2.0.7
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.5.dist-info → sure_tools-2.0.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/SURE.py,sha256=0brySH3zXtYAW8eff5BzL1vYq_nmR82wpEPeH-FcLE8,50527
+SURE/SURE.py,sha256=08gZ70PUNeTr5XY5BpaH3H4tQ9Hq3QjKXKDy14c97us,51051
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
 SURE/__init__.py,sha256=mxdLoWa2fPEM4-WkJetMfcecpzqJ8YsM4lOoKHSLTrU,207
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -9,15 +9,15 @@ SURE/atac/utils.py,sha256=m4NYwpy9O5T1pXTzgCOCcmlwrC6GTi-cQ5sm2wZu2O8,4354
 SURE/codebook/__init__.py,sha256=2T5gjp8JIaBayrXAnOJYSebQHsWprOs87difpR1OPNw,243
 SURE/codebook/codebook.py,sha256=ZlN6gRX9Gj2D2u3P5KeOsbZri0MoMAiJo9lNeL-MK-I,17117
 SURE/flow/__init__.py,sha256=uiF9eyo6sz5qw7fRFiKipaXHboAakeIqVWo8yjkq0B0,36
-SURE/flow/plot_quiver.py,sha256=XRH1POyn2H7qJ_gSqo39YmjOR_Dn8a_9M_s-dnHJLlo,1850
+SURE/flow/plot_quiver.py,sha256=spcPC0BDpvC-FBk9XIu6rcJI64bS-U-IVmmKLYHHXgs,1865
 SURE/flow/quiver.py,sha256=_euFqSaRrDoZ_oOabOx20LOoUTJ__XPhLW-vzLNQfAo,1859
 SURE/utils/__init__.py,sha256=Htqv4KqVKcRiaaTBsR-6yZ4LSlbhbzutjNKXGD9-uds,660
 SURE/utils/custom_mlp.py,sha256=07TYX1HgxfEjb_3i5MpiZfNhOhx3dKntuwGkrpteWiM,7036
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.0.5.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.0.5.dist-info/METADATA,sha256=DSDQeffAyyRgBfKxdWTsk7DBd71C3zGdnMlKY4bz1_g,2650
-sure_tools-2.0.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.0.5.dist-info/entry_points.txt,sha256=u12payZYgCBy5FCwRHP6AlSQhKCiWSEDwj68r1DVdn8,40
-sure_tools-2.0.5.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.0.5.dist-info/RECORD,,
+sure_tools-2.0.7.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.0.7.dist-info/METADATA,sha256=qqfn9Ml8x5SDWfEB-WIaMCJCmHElRi65j99-v6uBwms,2650
+sure_tools-2.0.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.0.7.dist-info/entry_points.txt,sha256=u12payZYgCBy5FCwRHP6AlSQhKCiWSEDwj68r1DVdn8,40
+sure_tools-2.0.7.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.0.7.dist-info/RECORD,,