mcDETECT 1.0.1__tar.gz → 1.0.5__tar.gz

{mcdetect-1.0.1 → mcdetect-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: mcDETECT
-Version: 1.0.1
+Version: 1.0.5
 Summary: mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan
@@ -17,9 +17,9 @@ Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: rtree
 Requires-Dist: scanpy
+Requires-Dist: scikit-learn
 Requires-Dist: scipy
 Requires-Dist: shapely
-Requires-Dist: sklearn
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{mcdetect-1.0.1 → mcdetect-1.0.5}/mcDETECT/model.py

@@ -304,7 +304,7 @@ class mcDETECT:
         return sphere
     
     
-    # [MAIN] dataframe, metadata of identified synapses
+    # [MAIN] dataframe, synapse metadata
     def detect(self):
         
         _, data_low, data_high = self.dbscan()
@@ -319,7 +319,7 @@ class mcDETECT:
             return self.nc_filter(sphere_low, sphere_high)
     
     
-    # [MAIN] anndata, spatial transcriptome profile of identified synapses
+    # [MAIN] anndata, synapse spatial transcriptome profile
     def profile(self, synapse, genes = None, print_itr = False):
         
         if genes is None:
@@ -348,4 +348,86 @@ class mcDETECT:
         adata.var['genes'] = genes
         adata.var_names = genes
         adata.var_keys = genes
-        return adata
+        return adata
+    
+    
+    # [MAIN] anndata, spot-level gene expression
+    def spot_expression(self, grid_len, genes = None):
+        
+        if genes is None:
+            genes = list(np.unique(self.transcripts['target']))
+            transcripts = self.transcripts
+        else:
+            transcripts = self.transcripts[self.transcripts['target'].isin(genes)]
+        
+        # construct bins
+        x_bins, y_bins = self.construct_grid(grid_len = None)
+        
+        # initialize data
+        X = np.zeros((len(genes), len(x_bins) * len(y_bins)))
+        global_x, global_y = [], []
+        
+        # coordinates
+        for i in list(x_bins):
+            center_x = i + 0.5 * grid_len
+            for j in list(y_bins):
+                center_y = j + 0.5 * grid_len
+                global_x.append(center_x)
+                global_y.append(center_y)
+        
+        # count matrix
+        for k_idx, k in enumerate(genes):
+            target_gene = transcripts[transcripts['feature_name'] == k]
+            count_gene, _, _ = np.histogram2d(target_gene['global_x'], target_gene['global_y'], bins = [x_bins, y_bins])
+            X[k_idx, :] = count_gene.flatten()
+            if k_idx % 50 == 0:
+                print("{} out of {} genes profiled!".format(k_idx + 1, len(genes)))
+        
+        # spot id
+        spot_id = []
+        for i in range(len(global_x)):
+            id = 'spot_' + str(i)
+            spot_id.append(id)
+        
+        # assemble data
+        adata = anndata.AnnData(X = np.transpose(X))
+        adata.obs['spot_id'] = spot_id
+        adata.obs['global_x'] = global_x
+        adata.obs['global_y'] = global_y
+        adata.var['genes'] = genes
+        adata.var_names = genes
+        adata.var_keys = genes
+        return adata
+    
+    
+    # [MAIN] anndata, spot-level synapse metadata
+    def spot_synapse(self, synapse, spot):
+        
+        x_grid, y_grid = list(np.unique(spot.obs['global_x'])), list(np.unique(spot.obs['global_y']))
+        diameter = x_grid[1] - x_grid[0]
+        
+        indicator, synapse_count, synapse_radius, synapse_size, synapse_score = [], [], [], [], []
+        for i in x_grid:
+            x_min_temp = i
+            x_max_temp = i + diameter
+            for j in y_grid:
+                y_min_temp = j
+                y_max_temp = j + diameter
+                syn_temp = synapse[(synapse['sphere_x'] > x_min_temp) & (synapse['sphere_x'] < x_max_temp) & (synapse['sphere_y'] > y_min_temp) & (synapse['sphere_y'] < y_max_temp)]
+                indicator.append(int(syn_temp.shape[0] > 0))
+                synapse_count.append(syn_temp.shape[0])
+                if syn_temp.shape[0] == 0:
+                    synapse_radius.append(0)
+                    synapse_size.append(0)
+                    synapse_score.append(0)
+                else:
+                    synapse_radius.append(np.nanmean(syn_temp['sphere_r']))
+                    synapse_size.append(np.nanmean(syn_temp['size']))
+                    synapse_score.append(np.nanmean(syn_temp['in_nucleus']))
+        
+        spot.obs['indicator'] = indicator
+        spot.obs['syn_count'] = synapse_count
+        spot.obs['syn_radius'] = synapse_radius
+        spot.obs['syn_size'] = synapse_size
+        spot.obs['syn_score'] = synapse_score
+        return spot

{mcdetect-1.0.1 → mcdetect-1.0.5}/mcDETECT.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: mcDETECT
-Version: 1.0.1
+Version: 1.0.5
 Summary: mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan
@@ -17,9 +17,9 @@ Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: rtree
 Requires-Dist: scanpy
+Requires-Dist: scikit-learn
 Requires-Dist: scipy
 Requires-Dist: shapely
-Requires-Dist: sklearn
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{mcdetect-1.0.1 → mcdetect-1.0.5}/mcDETECT.egg-info/requires.txt

@@ -4,6 +4,6 @@ numpy
 pandas
 rtree
 scanpy
+scikit-learn
 scipy
 shapely
-sklearn

{mcdetect-1.0.1 → mcdetect-1.0.5}/setup.py

@@ -2,9 +2,9 @@ from setuptools import setup, find_packages
 
 setup(
     name = "mcDETECT",
-    version = "1.0.1",
+    version = "1.0.5",
     packages = find_packages(),
-    install_requires = ["anndata", "miniball", "numpy", "pandas", "rtree", "scanpy", "scipy", "shapely", "sklearn"],
+    install_requires = ["anndata", "miniball", "numpy", "pandas", "rtree", "scanpy", "scikit-learn", "scipy", "shapely"],
     author = "Chenyang Yuan",
     author_email = "chenyang.yuan@emory.edu",
     description = "mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics",