sciv 0.0.84__py3-none-any.whl → 0.0.86__py3-none-any.whl

sciv/tool/_random_walk_.py

@@ -477,6 +477,7 @@ class RandomWalk:
             1. The weights used in the iteration of random walk.
             2. Assign different weight matrices to seed cells.
         """
+        ul.log(__name__).info("Obtain transition probability matrix.")
         data_weight = to_dense(cell_cell_matrix, is_array=True)
         cell_sum_weight = data_weight.sum(axis=1)[:, np.newaxis]
         cell_sum_weight[cell_sum_weight == 0] = 1
@@ -620,39 +621,33 @@ class RandomWalk:
 
         trait_values_all = to_dense(init_data.X, is_array=True)
 
-        def _process_single_trait(i: int) -> dict:
+        def _process_single_trait(i: int) -> None:
             trait_value = trait_values_all[:, i]
             trait_value_max = trait_value.max()
             trait_value_min = trait_value.min()
 
             if trait_value_min == trait_value_max:
-                return dict(
-                    seed_cell_count=0,
-                    seed_cell_threshold=0.0,
-                    seed_cell_index=None,
-                    seed_cell_weight=None,
-                    seed_cell_en_index=None,
-                    seed_cell_en_weight=None,
-                    seed_cell_matrix=None,
-                    seed_cell_matrix_en=None
-                )
-
-            # 直接获取降序索引
+                return
+
+            # Directly obtain descending index
             trait_value_sort_index = np.argpartition(trait_value, -trait_value.size)[::-1]
 
-            # 计算 >0 的细胞数
+            # Calculate the number of cells with>0
             _gt0_cell_size = (trait_value > 0).sum()
 
             _seed_cell_size = self._get_seed_cell_size_(_gt0_cell_size)
 
-            # 设置种子细胞索引与权重
+            seed_cell_count[i] = _seed_cell_size
+            seed_cell_threshold[i] = trait_value[trait_value_sort_index[_seed_cell_size]]
+
+            # Set seed cell index and weight
             _seed_cell_index = trait_value_sort_index[:_seed_cell_size]
-            _seed_cell_weight = np.zeros(n_cells)
-            _seed_cell_weight[_seed_cell_index] = self._get_seed_cell_weight_(
+            seed_cell_index[_seed_cell_index, i] = 1
+            seed_cell_weight[_seed_cell_index, i] = self._get_seed_cell_weight_(
                 seed_cell_index=_seed_cell_index, value=trait_value
             )
 
-            # 富集区间索引
+            # Enrichment interval index
             _enrichment_start = _seed_cell_size
             _enrichment_end = min(2 * _seed_cell_size, self.cell_size - 1)
 
@@ -661,56 +656,25 @@ class RandomWalk:
                 _enrichment_end = _seed_cell_size
 
             _seed_cell_en_index = trait_value_sort_index[_enrichment_start:_enrichment_end]
-            _seed_cell_en_weight = np.zeros(n_cells)
-            _tmp_weight = self._get_seed_cell_weight_(
+            seed_cell_weight_en[_seed_cell_en_index, i] = self._get_seed_cell_weight_(
                 seed_cell_index=_seed_cell_index if len(_seed_cell_en_index) == len(_seed_cell_index) else _seed_cell_en_index,
                 value=trait_value,
                 seed_cell_index_enrichment=_seed_cell_en_index
             )
-            _seed_cell_en_weight[_seed_cell_en_index] = _tmp_weight
-
-            # 无权重版本（仅在需要时计算）
-            _seed_cell_matrix = None
-            _seed_cell_matrix_en = None
 
             if not self.is_simple and self.is_ablation:
                 seed_cell_value = np.zeros(n_cells)
                 seed_cell_value[_seed_cell_index] = 1
-                _seed_cell_matrix = seed_cell_value / seed_cell_value.sum() if seed_cell_value.sum() else 0
+                seed_cell_matrix[:, i] = seed_cell_value / (1 if seed_cell_value.sum() == 0 else seed_cell_value.sum())
 
                 seed_cell_en_value = np.zeros(n_cells)
                 seed_cell_en_value[_seed_cell_en_index] = 1
-                _seed_cell_matrix_en = seed_cell_en_value / seed_cell_en_value.sum() if seed_cell_en_value.sum() else 0
-
-            return dict(
-                seed_cell_count=_seed_cell_size,
-                seed_cell_threshold=trait_value[trait_value_sort_index[_seed_cell_size]],
-                seed_cell_index=_seed_cell_index,
-                seed_cell_weight=_seed_cell_weight,
-                seed_cell_en_index=_seed_cell_en_index,
-                seed_cell_en_weight=_seed_cell_en_weight,
-                seed_cell_matrix=_seed_cell_matrix,
-                seed_cell_matrix_en=_seed_cell_matrix_en
-            )
-
-        # 并行处理所有 trait
-        results = Parallel(n_jobs=-1, backend="threading")(delayed(_process_single_trait)(i) for i in self.trait_range)
+                seed_cell_matrix_en[:, i] = seed_cell_en_value / (1 if seed_cell_en_value.sum() == 0 else seed_cell_en_value.sum())
 
-        # 将并行结果写回对应数组
-        for i, res in enumerate(results):
-
-            if res["seed_cell_index"] is None:
-                continue
-
-            seed_cell_count[i] = res["seed_cell_count"]
-            seed_cell_threshold[i] = res["seed_cell_threshold"]
-            seed_cell_index[res["seed_cell_index"], i] = 1
-            seed_cell_weight[:, i] = res["seed_cell_weight"]
-            seed_cell_weight_en[res["seed_cell_en_index"], i] = res["seed_cell_en_weight"]
-
-            if not self.is_simple and self.is_ablation:
-                seed_cell_matrix[:, i] = res["seed_cell_matrix"]
-                seed_cell_matrix_en[:, i] = res["seed_cell_matrix_en"]
+        # Parallel processing of all traits and real-time display of progress
+        Parallel(n_jobs=-1, backend="threading")(
+            delayed(_process_single_trait)(i) for i in tqdm(self.trait_range, desc="Obtain progress of seed cells with weights")
+        )
 
         return seed_cell_count, seed_cell_threshold, seed_cell_matrix, seed_cell_weight, seed_cell_index, seed_cell_matrix_en, seed_cell_weight_en
 

{sciv-0.0.84.dist-info → sciv-0.0.86.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciv
-Version: 0.0.84
+Version: 0.0.86
 Summary: Unveiling the pivotal cell types involved in variant function regulation at a single-cell resolution
 Project-URL: github, https://github.com/YuZhengM/sciv
 Author-email: Zheng-Min Yu <yuzmbio@163.com>

{sciv-0.0.84.dist-info → sciv-0.0.86.dist-info}/RECORD

@@ -29,11 +29,11 @@ sciv/preprocessing/_snapatac_.py,sha256=Dq8CHF7Psl3CQszaEokQYO56Oe2uzyWOy_cGlaOy
 sciv/tool/__init__.py,sha256=WXzHkWt6RgBC3qqD-98nR5wQmt6oC850ox_VpMrapSU,2468
 sciv/tool/_algorithm_.py,sha256=okGpH2OrBTO59LkyznT4gRi5S45oAcnO10Kxo5Xzy4I,47991
 sciv/tool/_matrix_.py,sha256=O1EAhA9wxh06P_eOxEBesK7kO7IExKlhH6uJzGh1HBM,24322
-sciv/tool/_random_walk_.py,sha256=XE7LlTFn5vHVth47cLtIJC6D4vwOsNM5sgrFwx-KL3g,48671
+sciv/tool/_random_walk_.py,sha256=FFX_yip5WPjGAYGQTJAsTDBQlU82qewMopj_wwK2V08,47228
 sciv/util/__init__.py,sha256=nOxZ8if27X7AUJ6hZwTwxOJwIBJb0obWlHjqCzjg_Gc,1964
 sciv/util/_constant_.py,sha256=w0wKQd8guLd1ZTW24_5aECrWsIWDiNQmEpLsWlHar1A,3000
 sciv/util/_core_.py,sha256=ZD2uSnEBHVu0i9TmXWzri_3bXZzYKnIZk818gW3zadE,14751
-sciv-0.0.84.dist-info/METADATA,sha256=XIG0HyGsbObIpMSR8_t0W9IZIAUy-shlHS07ziGAAGI,3465
-sciv-0.0.84.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-sciv-0.0.84.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
-sciv-0.0.84.dist-info/RECORD,,
+sciv-0.0.86.dist-info/METADATA,sha256=UWWKX6mHOyG66pESQiONa1g89ITE8RKe5vZvN8oSTAQ,3465
+sciv-0.0.86.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+sciv-0.0.86.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
+sciv-0.0.86.dist-info/RECORD,,