mcDETECT 2.0.11__tar.gz → 2.0.12__tar.gz

{mcdetect-2.0.11 → mcdetect-2.0.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcDETECT
-Version: 2.0.11
+Version: 2.0.12
 Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan

mcdetect-2.0.12/mcDETECT/__init__.py

@@ -0,0 +1,6 @@
+__version__ = "2.0.12"
+
+from . import model
+from . import utils
+
+__all__ = ["model", "utils"]

{mcdetect-2.0.11 → mcdetect-2.0.12}/mcDETECT/model.py

@@ -109,26 +109,22 @@ class mcDETECT:
             
             for k in range(n_clusters):
                 
-                # record cell ids
-                if record_cell_id:
-                    temp = target[labels == k]
-                    temp_cell_id_mode = temp["cell_id"].mode()[0]
-                    cell_id.append(temp_cell_id_mode)
-                
-                # find minimum enclosing spheres
+                # ---------- find minimum enclosing spheres ---------- #
                 mask = (labels == k)
                 coords = X[mask]
                 if coords.shape[0] == 0:
                     continue
-                temp_in_nucleus = np.sum(target["overlaps_nucleus"].values[mask])
-                temp_size = coords.shape[0]
                 
                 temp = pd.DataFrame(coords, columns=["global_x", "global_y", "global_z"])
                 temp = temp.drop_duplicates()
                 coords_unique = temp.to_numpy()
+                
+                # skip clusters with too few unique points
                 if coords_unique.shape[0] < self.low_bound:
                     print(f"Skipping small cluster for gene {j}, cluster {k} (n = {coords_unique.shape[0]})")
                     continue
+                
+                # compute minimum enclosing sphere without singularity issues
                 try:
                     center, r2 = miniball.get_bounding_ball(coords_unique, epsilon=1e-8)
                 except np.linalg.LinAlgError:
@@ -136,13 +132,22 @@ class mcDETECT:
                     center = coords_unique.mean(axis=0)
                     dists = np.linalg.norm(coords_unique - center, axis=1)
                     r2 = (dists.max() ** 2)
-                
+
+                # record closest z-layer
                 if self.type != "Xenium":
                     closest_z = closest(z_grid, center[2])
                 else:
                     closest_z = center[2]
                 
-                # calculate size, composition, and in-nucleus score
+                # record cell id after filtering
+                if record_cell_id:
+                    temp_target = target[labels == k]
+                    temp_cell_id_mode = temp_target["cell_id"].mode()[0]
+                    cell_id.append(temp_cell_id_mode)
+
+                # ---------- compute sphere features (size, composition, and in-nucleus ratio) ---------- #
+                temp_in_nucleus = np.sum(target["overlaps_nucleus"].values[mask])
+                temp_size = coords.shape[0]
                 other_idx = tree.query_ball_point([center[0], center[1], center[2]], np.sqrt(r2))
                 other_trans = others.iloc[other_idx]
                 other_in_nucleus = np.sum(other_trans["overlaps_nucleus"])
@@ -152,7 +157,7 @@ class mcDETECT:
                 total_comp = 1 + other_comp
                 local_score = (temp_in_nucleus + other_in_nucleus) / total_size
                 
-                # record coordinate, radius, size, composition, and in-nucleus score
+                # record sphere features
                 sphere_x.append(center[0])
                 sphere_y.append(center[1])
                 sphere_z.append(center[2])
@@ -409,7 +414,7 @@ class mcDETECT:
         adata.var_names = genes
         adata.var_keys = genes
         return adata
-    
+
 
 # [MAIN] anndata, spot-level neuron metadata
 def spot_neuron(adata_neuron, spot, grid_len = 50, neuron_loc_key = ["global_x", "global_y"], spot_loc_key = ["global_x", "global_y"]):
@@ -434,7 +439,7 @@ def spot_neuron(adata_neuron, spot, grid_len = 50, neuron_loc_key = ["global_x",
     spot.obs["neuron_count"] = neuron_count
     return spot
 
-    
+
 # [MAIN] anndata, spot-level granule metadata
 def spot_granule(granule, spot, grid_len = 50, gnl_loc_key = ["sphere_x", "sphere_y"], spot_loc_key = ["global_x", "global_y"]):
     

{mcdetect-2.0.11 → mcdetect-2.0.12}/mcDETECT.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcDETECT
-Version: 2.0.11
+Version: 2.0.12
 Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan

{mcdetect-2.0.11 → mcdetect-2.0.12}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name = "mcDETECT",
-    version = "2.0.11",
+    version = "2.0.12",
     packages = find_packages(),
     install_requires = ["anndata", "miniball", "numpy", "pandas", "rtree", "scanpy", "scikit-learn", "scipy", "shapely"],
     author = "Chenyang Yuan",

mcdetect-2.0.11/mcDETECT/__init__.py

@@ -1,6 +0,0 @@
-__version__ = "2.0.11"
-
-from . import model
-from . import utils
-
-__all__ = ["model", "utils"]