risk-network 0.0.7b7__py3-none-any.whl → 0.0.7b8__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.7-beta.7"
+__version__ = "0.0.7-beta.8"

risk/neighborhoods/domains.py

@@ -4,6 +4,7 @@ risk/neighborhoods/domains
 """
 
 from contextlib import suppress
+from itertools import product
 from tqdm import tqdm
 from typing import Tuple
 
@@ -165,21 +166,20 @@ def _optimize_silhouette_across_linkage_and_metrics(
     total_combinations = len(linkage_methods) * len(linkage_metrics)
 
     # Evaluating optimal linkage method and metric
-    for method in tqdm(
-        linkage_methods,
+    for method, metric in tqdm(
+        product(linkage_methods, linkage_metrics),
         desc="Evaluating optimal linkage method and metric",
         total=total_combinations,
         bar_format="{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}<{remaining}]",
     ):
-        for metric in linkage_metrics:
-            with suppress(Exception):
-                Z = linkage(m, method=method, metric=metric)
-                threshold, score = _find_best_silhouette_score(Z, m, metric, linkage_criterion)
-                if score > best_overall_score:
-                    best_overall_score = score
-                    best_overall_threshold = threshold
-                    best_overall_method = method
-                    best_overall_metric = metric
+        with suppress(Exception):
+            Z = linkage(m, method=method, metric=metric)
+            threshold, score = _find_best_silhouette_score(Z, m, metric, linkage_criterion)
+            if score > best_overall_score:
+                best_overall_score = score
+                best_overall_threshold = threshold
+                best_overall_method = method
+                best_overall_metric = metric
 
     return best_overall_method, best_overall_metric, best_overall_threshold
 

risk/neighborhoods/neighborhoods.py

@@ -54,10 +54,10 @@ def get_network_neighborhoods(
         network, edge_length_percentile=edge_length_threshold
     )
 
-    if distance_metric == "greedy_modularity":
-        return calculate_greedy_modularity_neighborhoods(network)
     if distance_metric == "louvain":
         return calculate_louvain_neighborhoods(network, louvain_resolution, random_seed=random_seed)
+    if distance_metric == "greedy_modularity":
+        return calculate_greedy_modularity_neighborhoods(network)
     if distance_metric == "label_propagation":
         return calculate_label_propagation_neighborhoods(network)
     if distance_metric == "markov_clustering":

risk/stats/hypergeom.py

@@ -22,9 +22,7 @@ def compute_hypergeom_test(
     Returns:
         dict: Dictionary containing depletion and enrichment p-values.
     """
-    # Ensure both matrices are binary (presence/absence)
-    neighborhoods = (neighborhoods > 0).astype(int)
-    annotations = (annotations > 0).astype(int)
+    # Get the total number of nodes in the network
     total_node_count = neighborhoods.shape[0]
 
     if null_distribution == "network":

risk/stats/poisson.py

@@ -22,9 +22,6 @@ def compute_poisson_test(
     Returns:
         dict: Dictionary containing depletion and enrichment p-values.
     """
-    # Ensure both matrices are binary (presence/absence)
-    neighborhoods = (neighborhoods > 0).astype(int)
-    annotations = (annotations > 0).astype(int)
     # Matrix multiplication to get the number of annotated nodes in each neighborhood
     annotated_in_neighborhood = neighborhoods @ annotations
 

{risk_network-0.0.7b7.dist-info → risk_network-0.0.7b8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b7
+Version: 0.0.7b8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b7.dist-info → risk_network-0.0.7b8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=0dNrjhRgqzBRG5Rqy_GKy_8ETWm10xSCYvaOm6fdI0Q,112
+risk/__init__.py,sha256=kEtmAgswqdIS5KBKHJO1NZkxJRF6s4ww_cjSOrBuJ4A,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=6666BzdMTgOaQl98ZKiJ19c6XBot26eTJ0iIlk-ZCZQ,20515
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
@@ -9,22 +9,22 @@ risk/log/console.py,sha256=im9DRExwf6wHlcn9fewoDcKIpo3vPcorZIaNAl-0csY,355
 risk/log/params.py,sha256=Rfdg5UcGCrG80m6V79FyORERWUqIzHFO7tGiY4zAImM,6347
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
 risk/neighborhoods/community.py,sha256=stYYBXeZlGLMV-k8ckQeIqThT6v9y-S3hETobAo9590,6817
-risk/neighborhoods/domains.py,sha256=bxJUxqFTynzX0mf3E8-AA4_Rfccje1reeVVhfzb1-pE,10672
-risk/neighborhoods/neighborhoods.py,sha256=r-JeUb6dTjzMtnaMDvJy6MI3mTl-yUzILcdcjtOhFdM,18218
+risk/neighborhoods/domains.py,sha256=vTCKtRE0oFcY862squrF7_cqCjnckiC9Sl0Qh2FM81k,10665
+risk/neighborhoods/neighborhoods.py,sha256=5WVXCZ0f-MzUfDITdNlL0NgDS3DBamdc_ZVPA-p9j7U,18218
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
 risk/network/graph.py,sha256=_LEoom4EEowGALuJKSXcev9RAAHu2FqIeq3u7mkifW0,16479
 risk/network/io.py,sha256=gG50kOknO-D3HkW1HsbHMkTMvjUtn3l4W4Jwd-rXNr8,21202
 risk/network/plot.py,sha256=3OucCoKJwx9M9H4lqAvcQdM9YiCSyIxz21jyqDbpffc,62286
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
-risk/stats/hypergeom.py,sha256=DcGYjmfcgt1qshNZPJt5IHGIHtxw9tWRS1r6QJ6V3dI,2378
-risk/stats/poisson.py,sha256=CnLk65CHViR4YhAaN3ix37iyLm_YQYGo851bSnGyyxY,1950
+risk/stats/hypergeom.py,sha256=o6Qnj31gCAKxr2uQirXrbv7XvdDJGEq69MFW-ubx_hA,2272
+risk/stats/poisson.py,sha256=8x9hB4DCukq4gNIlIKO-c_jYG1-BTwTX53oLauFyfj8,1793
 risk/stats/stats.py,sha256=kvShov-94W6ffgDUTb522vB9hDJQSyTsYif_UIaFfSM,7059
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=kmSZ7bQ-AD0TFiQDgIwfxTeqHa4pjp7fIcOzAqyhUNY,9714
 risk/stats/permutation/test_functions.py,sha256=HuDIM-V1jkkfE1rlaIqrWWBSKZt3dQ1f-YEDjWpnLSE,2343
-risk_network-0.0.7b7.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.7b7.dist-info/METADATA,sha256=LDTOo8S-g09TbNgixGR4nCBkyaHW_usy0zE8kNsqTRg,43142
-risk_network-0.0.7b7.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-risk_network-0.0.7b7.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.7b7.dist-info/RECORD,,
+risk_network-0.0.7b8.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.7b8.dist-info/METADATA,sha256=aFjqRdtk2rsHn0AHuofhj9ZtkFFuuxfgLd_DnyX52qA,43142
+risk_network-0.0.7b8.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+risk_network-0.0.7b8.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.7b8.dist-info/RECORD,,