mcDETECT 2.0.7__tar.gz → 2.0.8__tar.gz

{mcdetect-2.0.7 → mcdetect-2.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcDETECT
-Version: 2.0.7
+Version: 2.0.8
 Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan

mcdetect-2.0.8/mcDETECT/__init__.py

@@ -0,0 +1,6 @@
+__version__ = "2.0.8"
+
+from . import model
+from . import utils
+
+__all__ = ["model", "utils"]

{mcdetect-2.0.7 → mcdetect-2.0.8}/mcDETECT/model.py

@@ -20,12 +20,12 @@ from .utils import *
 class mcDETECT:
     
     
-    def __init__(self, type, transcripts, syn_genes, nc_genes = None, eps = 1.5, minspl = None, grid_len = 1.0, cutoff_prob = 0.95, alpha = 5.0, low_bound = 3,
+    def __init__(self, type, transcripts, gnl_genes, nc_genes = None, eps = 1.5, minspl = None, grid_len = 1.0, cutoff_prob = 0.95, alpha = 5.0, low_bound = 3,
                  size_thr = 4.0, in_nucleus_thr = (0.5, 0.5), l = 1.0, rho = 0.2, s = 1.0, nc_top = 20, nc_thr = 0.1):
         
         self.type = type                        # string, iST platform, now support MERSCOPE, Xenium, and CosMx
         self.transcripts = transcripts          # dataframe, transcripts file
-        self.syn_genes = syn_genes              # list, string, all synaptic markers
+        self.gnl_genes = gnl_genes              # list, string, all granule markers
         self.nc_genes = nc_genes                # list, string, all negative controls
         self.eps = eps                          # numeric, searching radius epsilon
         self.minspl = minspl                    # integer, manually select min_samples, i.e., no automatic parameter selection
@@ -74,7 +74,7 @@ class mcDETECT:
         return optimal_m
     
     
-    # [INTERMEDIATE] dictionary, low- and high-in-nucleus spheres for each synaptic marker
+    # [INTERMEDIATE] dictionary, low- and high-in-nucleus spheres for each granule marker
     def dbscan(self, target_names = None, record_cell_id = False, write_csv = False, write_path = "./"):
         
         if self.type != "Xenium":
@@ -82,7 +82,7 @@ class mcDETECT:
             z_grid.sort()
         
         if target_names is None:
-            target_names = self.syn_genes
+            target_names = self.gnl_genes
         transcripts = self.transcripts[self.transcripts["target"].isin(target_names)]
         
         num_individual, data_low, data_high = [], {}, {}
@@ -175,7 +175,7 @@ class mcDETECT:
     
     # [INNER] merge points from two overlapped spheres, input for remove_overlaps()
     def find_points(self, sphere_a, sphere_b):
-        transcripts = self.transcripts[self.transcripts["target"].isin(self.syn_genes)]
+        transcripts = self.transcripts[self.transcripts["target"].isin(self.gnl_genes)]
         tree_temp = make_tree(d1 = np.array(transcripts["global_x"]), d2 = np.array(transcripts["global_y"]), d3 = np.array(transcripts["global_z"]))
         idx_a = tree_temp.query_ball_point([sphere_a["sphere_x"], sphere_a["sphere_y"], sphere_a["sphere_z"]], sphere_a["sphere_r"])
         points_a = transcripts.iloc[idx_a]
@@ -239,10 +239,10 @@ class mcDETECT:
         return set_a, set_b
     
     
-    # [INNER] merge spheres from different synaptic markers, input for detect()
+    # [INNER] merge spheres from different granule markers, input for detect()
     def merge_sphere(self, sphere_dict):
         sphere = sphere_dict[0].copy()
-        for j in range(1, len(self.syn_genes)):
+        for j in range(1, len(self.gnl_genes)):
             target_sphere = sphere_dict[j]
             sphere, target_sphere_new = self.remove_overlaps(sphere, target_sphere)
             sphere = pd.concat([sphere, target_sphere_new])
@@ -289,7 +289,7 @@ class mcDETECT:
         return sphere
     
     
-    # [MAIN] dataframe, synapse metadata
+    # [MAIN] dataframe, granule metadata
     def detect(self):
         
         _, data_low, data_high = self.dbscan()
@@ -304,7 +304,7 @@ class mcDETECT:
             return self.nc_filter(sphere_low, sphere_high)
     
     
-    # [MAIN] anndata, synapse spatial transcriptome profile
+    # [MAIN] anndata, granule spatial transcriptome profile
     def profile(self, granule, genes = None, print_itr = False):
         
         if genes is None:

{mcdetect-2.0.7 → mcdetect-2.0.8}/mcDETECT.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcDETECT
-Version: 2.0.7
+Version: 2.0.8
 Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan

{mcdetect-2.0.7 → mcdetect-2.0.8}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name = "mcDETECT",
-    version = "2.0.7",
+    version = "2.0.8",
     packages = find_packages(),
     install_requires = ["anndata", "miniball", "numpy", "pandas", "rtree", "scanpy", "scikit-learn", "scipy", "shapely"],
     author = "Chenyang Yuan",

mcdetect-2.0.7/mcDETECT/__init__.py

@@ -1,6 +0,0 @@
-__version__ = "2.0.7"
-
-from . import model
-from . import utils
-
-__all__ = ["model", "utils"]