sciv 0.0.81__py3-none-any.whl → 0.0.83__py3-none-any.whl

sciv/tool/_algorithm_.py

@@ -1153,7 +1153,7 @@ def calculate_init_score_weight(
 
     del global_scale_data
 
-    da_peaks_adata.obsm["cluster_weight"] = to_sparse(_cluster_weight_)
+    da_peaks_adata.obsm["cluster_weight"] = to_dense(_cluster_weight_, is_array=True)
     del _cluster_weight_
 
     ul.log(__name__).info("Broadcasting the weight factor to the cellular level")
@@ -1163,9 +1163,7 @@ def calculate_init_score_weight(
 
     for cluster in da_peaks_adata.obs_names:
         mask = cluster_series == cluster
-        _cell_type_weight_[mask, :] = to_dense(
-            da_peaks_adata[cluster, :].obsm["cluster_weight"], is_array=True
-        ).flatten().astype(np.float32)
+        _cell_type_weight_[mask, :] = da_peaks_adata[cluster, :].obsm["cluster_weight"].flatten().astype(np.float32)
 
     ul.log(__name__).info("Calculate initial trait relevance scores")
     _init_trs_weight_ = np.multiply(_init_trs_ncw_, _cell_type_weight_)

sciv/tool/_matrix_.py

@@ -449,10 +449,10 @@ def matrix_operation_memory_efficient(
             result_chunk = chunk1.multiply(chunk2)
         elif operation == '/':
             # Sparse matrix division: convert to dense, perform element-wise division, then convert back to sparse
-            dense_chunk1 = chunk1.todense()
+            dense_chunk1 = chunk1 if isinstance(chunk1, dense_data) else chunk1.todense()
 
             if isinstance(data2, matrix_data):
-                dense_chunk2 = chunk2.todense()
+                dense_chunk2 = chunk2 if isinstance(chunk2, dense_data) else chunk2.todense()
                 dense_chunk2[dense_chunk2 == 0] = default
             else:
                 dense_chunk2 = data2

sciv/tool/_random_walk_.py

@@ -23,14 +23,16 @@ from ..util import (
     collection,
     check_adata_get,
     enrichment_optional,
-    check_gpu_availability
+    check_gpu_availability,
+    dense_data,
+    sparse_data
 )
 
 __name__: str = "tool_random_walk"
 
 
 def _random_walk_cpu_(
-    seed_cell_vector: collection,
+    seed_cell_vector: Union[list, np.ndarray, np.matrix],
     weight: matrix_data = None,
     gamma: float = 0.05,
     epsilon: float = 1e-5,
@@ -46,17 +48,19 @@ def _random_walk_cpu_(
     :return: The value after random walk.
     """
 
-    w = to_dense(weight)
-
     # Random walk
-    p0 = seed_cell_vector.copy()[:, np.newaxis]
+    p0 = np.asarray(seed_cell_vector, dtype=float).ravel()[:, np.newaxis]
     pt: matrix_data = p0.copy()
     k = 0
     delta = 1
 
     # iteration
     while delta > epsilon:
-        p1 = (1 - gamma) * np.dot(w, pt) + gamma * p0
+
+        if hasattr(weight, "dot"):
+            p1 = (1 - gamma) * weight.dot(pt) + gamma * p0
+        else:
+            p1 = (1 - gamma) * np.dot(weight, pt) + gamma * p0
 
         # 1 and 2, It would be faster alone
         if p == 1:
@@ -297,7 +301,6 @@ class RandomWalk:
 
         init_status.obs["clusters"] = init_status.obs["clusters"].astype(str)
 
-        self.cc_adata = cc_adata
         self.epsilon = epsilon
         self.gamma = gamma
         self.enrichment_gamma = enrichment_gamma
@@ -390,10 +393,12 @@ class RandomWalk:
             self.random_seed_cell = np.zeros(init_status.shape)
 
         # Transition Probability Matrix
-        self.weight = self._get_weight_(self.cc_adata.X)
+        self.weight = self._get_weight_(cc_adata.X)
 
         if not is_simple and self.is_ablation:
-            self.weight_m_knn = self._get_weight_(self.cc_adata.layers["cell_mutual_knn"])
+            self.weight_m_knn = self._get_weight_(cc_adata.layers["cell_mutual_knn"])
+
+        del cc_adata
 
         self.cluster_types, self.init_seed_cell_size = self._get_cluster_info_()
 
@@ -419,6 +424,9 @@ class RandomWalk:
                 self.seed_cell_weight_en_ncw
             ) = self._get_seed_cell_(init_data=init_status_no_weight, info="ablation")
 
+        del self.cell_affinity
+        del init_status
+
     def _random_walk_(
         self,
         seed_cell_data: matrix_data,
@@ -461,7 +469,7 @@ class RandomWalk:
         return self._random_walk_(seed_cell_data, weight, self.gamma)
 
     @staticmethod
-    def _get_weight_(cell_cell_matrix: matrix_data) -> matrix_data:
+    def _get_weight_(cell_cell_matrix: matrix_data) -> sparse_data:
         """
         Obtain weights in random walk
         :param cell_cell_matrix: Cell to cell connectivity matrix
@@ -472,7 +480,7 @@ class RandomWalk:
         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
-        return data_weight / cell_sum_weight
+        return to_sparse(data_weight / cell_sum_weight)
 
     def _get_cell_weight_(self, seed_cell_size: int) -> matrix_data:
         _cell_cell_knn_: matrix_data = self.cell_affinity.copy()

{sciv-0.0.81.dist-info → sciv-0.0.83.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciv
-Version: 0.0.81
+Version: 0.0.83
 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-0.0.81.dist-info → sciv-0.0.83.dist-info}/RECORD

@@ -27,13 +27,13 @@ sciv/preprocessing/_scanpy_.py,sha256=mmkk4cMCzJCziF49RnOuXBiF4frS6aSiwZdUmfDAg4
 sciv/preprocessing/_scvi_.py,sha256=ZIDkQ_4deYmzSMiAbu5C3j_jMMl7hBTFLCBXHCNj3B4,10332
 sciv/preprocessing/_snapatac_.py,sha256=Dq8CHF7Psl3CQszaEokQYO56Oe2uzyWOy_cGlaOywfc,27798
 sciv/tool/__init__.py,sha256=WXzHkWt6RgBC3qqD-98nR5wQmt6oC850ox_VpMrapSU,2468
-sciv/tool/_algorithm_.py,sha256=ab6-fRdAkNzawGBNqER481X5PWUjYPO701ehe1sayEc,48063
-sciv/tool/_matrix_.py,sha256=NDQf7yTuN4_GaKL7jK5i1BGYCIOGFQHcmpWgQkuquK8,24230
-sciv/tool/_random_walk_.py,sha256=98HLa9X2xx3Tj7VKKwQ2oS-CWL7HbOURAXiYKky2OYs,47338
+sciv/tool/_algorithm_.py,sha256=6xLGB1-FRfRiHSCVb_tHvzY_N-RoMZ79p0O2fEio688,48030
+sciv/tool/_matrix_.py,sha256=O1EAhA9wxh06P_eOxEBesK7kO7IExKlhH6uJzGh1HBM,24322
+sciv/tool/_random_walk_.py,sha256=E6QxZWXc1FY6rr0EiBNzX7TA5h9NFjt9YjpI_M4wN34,47567
 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-0.0.81.dist-info/METADATA,sha256=CorsYrplOzaSS5QtIMxMKxXysUkNbRQODcrtLIKp5BE,3465
-sciv-0.0.81.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-sciv-0.0.81.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
-sciv-0.0.81.dist-info/RECORD,,
+sciv-0.0.83.dist-info/METADATA,sha256=M5efcCSMDCUU4-8C8CVEQ2fpJw__3ltHPDU2LyYxj9Q,3465
+sciv-0.0.83.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+sciv-0.0.83.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
+sciv-0.0.83.dist-info/RECORD,,