SURE-tools 2.1.10__tar.gz → 2.1.12__tar.gz

{sure_tools-2.1.10 → sure_tools-2.1.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.10
+Version: 2.1.12
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

sure_tools-2.1.12/SURE/flow/plot_quiver.py

@@ -0,0 +1,197 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from sklearn.decomposition import PCA
+import scanpy as sc
+from matplotlib.colors import ListedColormap
+
+
+def plot_quiver(z_points, delta_z, method='pca', figsize=(6,4), dpi=200, 
+                subsample=None, color_by=None, colormap='viridis', 
+                arrow_scale=1.0, arrow_width=0.005, alpha=0.8):
+    """
+    优化后的quiver可视化函数
+    
+    Args:
+        z_points: 原始潜在空间点 [n_samples, n_dims]
+        delta_z: 移动向量 [n_samples, n_dims]
+        method: 降维方法 ('pca', 'variance', 'manual', 'umap')
+        figsize: 图像大小
+        dpi: 分辨率
+        subsample: 随机采样的数据点数量 (None表示不采样)
+        color_by: 颜色标签数组 [n_samples]
+        colormap: 颜色映射名称或ListedColormap对象
+        arrow_scale: 箭头缩放因子
+        arrow_width: 箭头宽度
+        alpha: 透明度
+    """
+    # 保存原始数据用于散点图
+    original_z_points = z_points.copy()
+    original_delta_z = delta_z.copy()
+    original_color_by = color_by.copy() if color_by is not None else None
+    
+    # 数据采样（仅用于quiver）
+    quiver_indices = None
+    if subsample is not None and len(z_points) > subsample:
+        quiver_indices = np.random.choice(len(z_points), subsample, replace=False)
+        z_points_quiver = z_points[quiver_indices]
+        delta_z_quiver = delta_z[quiver_indices]
+        if color_by is not None:
+            color_by_quiver = color_by[quiver_indices]
+        else:
+            color_by_quiver = None
+    else:
+        z_points_quiver = z_points
+        delta_z_quiver = delta_z
+        color_by_quiver = color_by
+    
+    # 降维投影（使用所有数据）
+    if method == 'variance':
+        variances = np.var(original_z_points, axis=0)
+        dims = np.argsort(variances)[-2:]
+        z_2d_all = original_z_points[:, dims]
+        z_2d_quiver = z_points_quiver[:, dims]
+        delta_z_2d = delta_z_quiver[:, dims]
+        dim_names = [f'z[{d}]' for d in dims]
+        
+    elif method == 'pca':
+        pca = PCA(n_components=2)
+        z_2d_all = pca.fit_transform(original_z_points)
+        z_2d_quiver = pca.transform(z_points_quiver)
+        delta_z_2d = pca.transform(z_points_quiver + delta_z_quiver) - z_2d_quiver
+        dim_names = ['PC1', 'PC2']
+        
+    elif method == 'manual':
+        dims = [0, 1]
+        z_2d_all = original_z_points[:, dims]
+        z_2d_quiver = z_points_quiver[:, dims]
+        delta_z_2d = delta_z_quiver[:, dims]
+        dim_names = [f'z[{d}]' for d in dims]
+        
+    elif method == 'umap':
+        # 使用所有数据进行UMAP降维
+        ad = sc.AnnData(np.vstack([original_z_points, original_z_points+original_delta_z]))
+        sc.pp.neighbors(ad)
+        sc.tl.umap(ad)
+        z_2d_all = ad[:len(original_z_points)].obsm['X_umap']
+        z_2d_quiver = z_2d_all[quiver_indices] if quiver_indices is not None else z_2d_all
+        delta_z_2d = ad[len(original_z_points):].obsm['X_umap'][quiver_indices] - z_2d_quiver if quiver_indices is not None else ad[len(original_z_points):].obsm['X_umap'] - z_2d_all
+        dim_names = ['UMAP1', 'UMAP2']
+    
+    # 颜色处理（散点图使用所有数据，quiver使用采样数据）
+    if original_color_by is not None:
+        if isinstance(colormap, str):
+            cmap = plt.get_cmap(colormap)
+        else:
+            cmap = colormap
+        
+        if original_color_by.dtype.kind in ['i', 'f']:  # 数值型标签
+            # 所有数据的颜色
+            colors_all = cmap(original_color_by / max(original_color_by.max(), 1e-8))
+            # quiver数据的颜色
+            if color_by_quiver is not None:
+                colors_quiver = cmap(color_by_quiver / max(color_by_quiver.max(), 1e-8))
+            else:
+                colors_quiver = 'blue'
+            cbar_label = 'Numeric Label'
+        else:  # 类别型标签
+            unique_labels = np.unique(original_color_by)
+            color_map = {label: cmap(i/len(unique_labels)) 
+                        for i, label in enumerate(unique_labels)}
+            colors_all = [color_map[label] for label in original_color_by]
+            if color_by_quiver is not None:
+                colors_quiver = [color_map[label] for label in color_by_quiver]
+            else:
+                colors_quiver = 'blue'
+            cbar_label = 'Class Label'
+    else:
+        colors_all = 'gray'
+        colors_quiver = 'blue'
+    
+    # 绘制
+    plt.figure(figsize=figsize, dpi=dpi)
+    
+    # 1. 首先绘制所有数据点的散点图
+    plt.scatter(z_2d_all[:, 0], z_2d_all[:, 1], 
+               c=colors_all, alpha=0.3, s=5, label='All data points')
+    
+    # 2. 绘制quiver（仅采样数据）
+    if color_by_quiver is not None and isinstance(color_by_quiver[0], str):
+        for label in np.unique(color_by_quiver):
+            mask = color_by_quiver == label
+            plt.quiver(z_2d_quiver[mask, 0], z_2d_quiver[mask, 1],
+                      delta_z_2d[mask, 0], delta_z_2d[mask, 1],
+                      angles='xy', scale_units='xy', scale=1.0/arrow_scale,
+                      color=colors_quiver[mask], width=arrow_width, alpha=alpha,
+                      label=f'{label} (movement)')
+        plt.legend()
+    else:
+        q = plt.quiver(z_2d_quiver[:, 0], z_2d_quiver[:, 1],
+                      delta_z_2d[:, 0], delta_z_2d[:, 1],
+                      angles='xy', scale_units='xy', scale=1.0/arrow_scale,
+                      color=colors_quiver, width=arrow_width, alpha=alpha,
+                      label='Movement vectors')
+        
+        # 添加颜色条（数值型标签）
+        if original_color_by is not None and original_color_by.dtype.kind in ['i', 'f']:
+            plt.colorbar(plt.cm.ScalarMappable(
+                norm=plt.Normalize(original_color_by.min(), original_color_by.max()),
+                cmap=cmap), label=cbar_label)
+    
+    # 美化图形
+    plt.xlabel(dim_names[0])
+    plt.ylabel(dim_names[1])
+    plt.title(f"Latent Space Movement ({method} projection)\n{len(z_points_quiver)}/{len(original_z_points)} points with vectors")
+    plt.grid(alpha=0.2)
+    plt.legend()
+    plt.tight_layout()
+    plt.show()
+    
+    return z_2d_all, z_2d_quiver, delta_z_2d
+
+def plot_quiver_old(z_points, delta_z, method='pca', 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]:].obsm['X_umap'] - 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-2.1.10 → sure_tools-2.1.12}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.10
+Version: 2.1.12
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.10 → sure_tools-2.1.12}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.10',
+    version='2.1.12',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",

sure_tools-2.1.10/SURE/flow/plot_quiver.py

@@ -1,52 +0,0 @@
-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]:].obsm['X_umap'] - 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