SURE-tools 2.0.3__py3-none-any.whl → 2.0.5__py3-none-any.whl

SURE/SURE.py

@@ -237,7 +237,7 @@ class SURE(nn.Module):
             self.cell_factor_effect = nn.ModuleList()
             for i in np.arange(self.cell_factor_size):
                 self.cell_factor_effect.append(MLP(
-                    [self.z_dim+1] + hidden_sizes + [self.z_dim],
+                    [self.latent_dim+1] + hidden_sizes + [self.latent_dim],
                     activation=activate_fct,
                     output_activation=None,
                     post_layer_fct=post_layer_fct,

SURE/flow/__init__.py

@@ -1 +1 @@
-from .quiver import plot_quiver
+from .plot_quiver import plot_quiver

SURE/flow/plot_quiver.py

@@ -0,0 +1,52 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from sklearn.decomposition import PCA
+import scanpy as sc
+
+def plot_quiver(z_points, delta_z, method='umap', figsize=(6,4), dpi=200):
+    """
+    从高维潜在空间选择2个维度进行quiver可视化
+    """
+    if method == 'variance':
+        # 方法1: 选择方差最大的2个维度
+        variances = np.var(z_points, axis=0)
+        dims = np.argsort(variances)[-2:]  # 选择方差最大的两个维度
+        dim_names = [f'z[{d}]' for d in dims]
+        
+    elif method == 'pca':
+        # 方法2: 使用PCA的前两个主成分
+        pca = PCA(n_components=2)
+        z_2d = pca.fit_transform(z_points)
+        delta_z_2d = pca.transform(z_points + delta_z) - z_2d
+        dim_names = ['PC1', 'PC2']
+        
+    elif method == 'manual':
+        # 方法3: 手动选择感兴趣的维度
+        dims = [0, 1]  # 选择前两个维度
+        z_2d = z_points[:, dims]
+        delta_z_2d = delta_z[:, dims]
+        dim_names = [f'z[{d}]' for d in dims]
+        
+    elif method == 'umap':
+        ad = sc.AnnData(np.vstack([z_points, z_points+delta_z]))
+        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
+        dim_names = ['UMAP1', 'UMAP2']
+    
+    # 绘制quiver图
+    plt.figure(figsize=figsize, dpi=dpi)
+    plt.quiver(z_2d[:, 0], z_2d[:, 1], 
+               delta_z_2d[:, 0], delta_z_2d[:, 1],
+               angles='xy', scale_units='xy', scale=1,
+               color='blue', alpha=0.6, width=0.005)
+    
+    plt.scatter(z_2d[:, 0], z_2d[:, 1], c='gray', alpha=0.5, s=10)
+    plt.xlabel(dim_names[0])
+    plt.ylabel(dim_names[1])
+    plt.title(f"Latent Space Movement ({method} projection)")
+    plt.grid(alpha=0.3)
+    plt.show()
+    
+    return z_2d, delta_z_2d

{sure_tools-2.0.3.dist-info → sure_tools-2.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.3
+Version: 2.0.5
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.3.dist-info → sure_tools-2.0.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/SURE.py,sha256=-k8CDneh7Ube3ECdpbHCfj4r4HViVyWoW0OMqvtWdgQ,50517
+SURE/SURE.py,sha256=0brySH3zXtYAW8eff5BzL1vYq_nmR82wpEPeH-FcLE8,50527
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
 SURE/__init__.py,sha256=mxdLoWa2fPEM4-WkJetMfcecpzqJ8YsM4lOoKHSLTrU,207
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -8,15 +8,16 @@ SURE/atac/__init__.py,sha256=3smP8IKHfwNCd1G_sZH3pKHXuLkLpFuLtjUTUSy7_As,34
 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=sizOyGqsjF2nfeBdwaiqXYkk8VP489F1z3Le5UF36qI,31
+SURE/flow/__init__.py,sha256=uiF9eyo6sz5qw7fRFiKipaXHboAakeIqVWo8yjkq0B0,36
+SURE/flow/plot_quiver.py,sha256=XRH1POyn2H7qJ_gSqo39YmjOR_Dn8a_9M_s-dnHJLlo,1850
 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-2.0.3.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.0.3.dist-info/METADATA,sha256=hALj9H3TDK0LM5acM-pBsLgffddHuzI36AiVQssh1mc,2650
-sure_tools-2.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.0.3.dist-info/entry_points.txt,sha256=u12payZYgCBy5FCwRHP6AlSQhKCiWSEDwj68r1DVdn8,40
-sure_tools-2.0.3.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.0.3.dist-info/RECORD,,
+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,,