SURE-tools 2.0.1__tar.gz → 2.0.2__tar.gz

{sure_tools-2.0.1 → sure_tools-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.1
+Version: 2.0.2
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.1 → sure_tools-2.0.2}/SURE/__init__.py

@@ -6,5 +6,6 @@ from . import codebook
 from . import SURE
 from . import SURE2
 from . import atac
+from . import flow 
 
-__all__ = ['SURE','SURE2', 'atac', 'utils', 'codebook']
+__all__ = ['SURE','SURE2', 'flow', 'atac', 'utils', 'codebook']

sure_tools-2.0.2/SURE/flow/__init__.py

@@ -0,0 +1 @@
+from .quiver import plot_quiver

sure_tools-2.0.2/SURE/flow/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_high_dim(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-2.0.1 → sure_tools-2.0.2}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.1
+Version: 2.0.2
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.1 → sure_tools-2.0.2}/SURE_tools.egg-info/SOURCES.txt

@@ -10,6 +10,8 @@ SURE/atac/__init__.py
 SURE/atac/utils.py
 SURE/codebook/__init__.py
 SURE/codebook/codebook.py
+SURE/flow/__init__.py
+SURE/flow/quiver.py
 SURE/utils/__init__.py
 SURE/utils/custom_mlp.py
 SURE/utils/queue.py

{sure_tools-2.0.1 → sure_tools-2.0.2}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.0.1',
+    version='2.0.2',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",