risk-network 0.0.7b3__py3-none-any.whl → 0.0.7b4__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.3"
+__version__ = "0.0.7-beta.4"

risk/neighborhoods/neighborhoods.py

@@ -200,7 +200,6 @@ def _impute_neighbors_with_similarity(
     depth = 1
     rows_to_impute = np.where(binary_enrichment_matrix.sum(axis=1) == 0)[0]
     while len(rows_to_impute) and depth <= max_depth:
-        next_rows_to_impute = []
         # Iterate over all enriched nodes
         for row_index in range(binary_enrichment_matrix.shape[0]):
             if binary_enrichment_matrix[row_index].sum() != 0:

risk/network/graph.py

@@ -3,7 +3,6 @@ risk/network/graph
 ~~~~~~~~~~~~~~~~~~
 """
 
-import random
 from collections import defaultdict
 from typing import Any, Dict, List, Tuple, Union
 
@@ -307,7 +306,7 @@ def _get_colors(
         List[Tuple]: List of RGBA colors.
     """
     # Set random seed for reproducibility
-    random.seed(random_seed)
+    np.random.seed(random_seed)
     # Determine the number of colors to generate based on the number of domains
     num_colors_to_generate = len(domain_id_to_node_ids_map)
     if color:
@@ -322,23 +321,15 @@ def _get_colors(
     # Step 2: Calculate pairwise distances between centroids
     centroid_array = np.array(centroids)
     dist_matrix = np.linalg.norm(centroid_array[:, None] - centroid_array, axis=-1)
-
-    # Step 3: Generate positions in the colormap, with a focus on centroids that are close
-    remaining_indices = set(range(num_colors_to_generate))
-    # Assign distant colors to close centroids
-    color_positions = _assign_distant_colors(
-        remaining_indices, dist_matrix, colormap, num_colors_to_generate
-    )
-
-    # Step 4: Randomly shuffle color positions to generate a new color palette
-    # while maintaining the dissimilarity between neighboring colors. This shuffling
-    # preserves the relative distances between centroids, ensuring that close centroids
-    # remain visually distinct while introducing randomness into the overall color arrangement.
-    random.shuffle(color_positions)
-    # Ensure that all positions remain between 0 and 1
+    # Step 3: Assign distant colors to close centroids
+    color_positions = _assign_distant_colors(dist_matrix, num_colors_to_generate)
+    # Step 4: Randomly shift the entire color palette while maintaining relative distances
+    global_shift = np.random.uniform(-0.1, 0.1)  # Small global shift to change the overall palette
+    color_positions = (color_positions + global_shift) % 1  # Wrap around to keep within [0, 1]
+    # Step 5: Ensure that all positions remain between 0 and 1
     color_positions = np.clip(color_positions, 0, 1)
 
-    # Step 5: Generate colors based on positions
+    # Step 6: Generate RGBA colors based on positions
     return [colormap(pos) for pos in color_positions]
 
 
@@ -365,28 +356,26 @@ def _calculate_centroids(network, domain_id_to_node_ids_map):
     return centroids
 
 
-def _assign_distant_colors(remaining_indices, dist_matrix, colormap, num_colors_to_generate):
+def _assign_distant_colors(dist_matrix, num_colors_to_generate):
     """Assign colors to centroids that are close in space, ensuring stark color differences.
 
     Args:
-        remaining_indices (set): Indices of centroids left to color.
         dist_matrix (ndarray): Matrix of pairwise centroid distances.
-        colormap (Colormap): The colormap used to assign colors.
         num_colors_to_generate (int): Number of colors to generate.
 
     Returns:
-        np.array: Array of color positions in the colormap.
+        np.array: Array of color positions in the range [0, 1].
     """
     color_positions = np.zeros(num_colors_to_generate)
-    # Convert the set to a list to index over it
-    remaining_indices = list(remaining_indices)
-    # Sort remaining indices by centroid proximity (based on sum of distances to others)
-    proximity_order = sorted(remaining_indices, key=lambda idx: np.sum(dist_matrix[idx]))
-    # Assign colors starting with the most distant points in proximity order
+    # Step 1: Sort indices by centroid proximity (based on sum of distances to others)
+    proximity_order = sorted(
+        range(num_colors_to_generate), key=lambda idx: np.sum(dist_matrix[idx])
+    )
+    # Step 2: Assign colors starting with the most distant points in proximity order
     for i, idx in enumerate(proximity_order):
         color_positions[idx] = i / num_colors_to_generate
 
-    # Adjust colors so that centroids close to one another are maximally distant on the color spectrum
+    # Step 3: Adjust colors so that centroids close to one another are maximally distant on the color spectrum
     half_spectrum = int(num_colors_to_generate / 2)
     for i in range(half_spectrum):
         # Split the spectrum so that close centroids are assigned distant colors

risk/risk.py

@@ -315,7 +315,7 @@ class RISK(NetworkIO, AnnotationsIO):
             max_cluster_size=max_cluster_size,
         )
 
-        print_header(f"Optimizing distance threshold for domains")
+        print_header("Optimizing distance threshold for domains")
         # Define domains in the network using the specified clustering settings
         domains = self._define_domains(
             neighborhoods=processed_neighborhoods,

{risk_network-0.0.7b3.dist-info → risk_network-0.0.7b4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b3
+Version: 0.0.7b4
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b3.dist-info → risk_network-0.0.7b4.dist-info}/RECORD

@@ -1,6 +1,6 @@
-risk/__init__.py,sha256=Yoz9l74qVwPoFeWtUKqy_dgQZlDTZtaNIvtmzNx5G78,112
+risk/__init__.py,sha256=yg0YESPRjq_Td8aQO5G_h7ennsyEeHumimLbCYxX-ts,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=jhfOv60iZdOssCF35tAjJ_br9w8aIqPFT2owVTehgtA,20648
+risk/risk.py,sha256=WQKPvUO4J2oYVDytn2C8w0lSFmLBzlhsKjfjWrjDt2Y,20647
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
 risk/annotations/annotations.py,sha256=K7cUA6vYTKYAvj0xHqrAwNEYtmPq4H7LDYENAOVQdQ0,11014
 risk/annotations/io.py,sha256=lo7NKqOVkeeBp58JBxWJHtA0xjL5Yoxqe9Ox0daKlZk,9457
@@ -10,10 +10,10 @@ risk/log/params.py,sha256=Rfdg5UcGCrG80m6V79FyORERWUqIzHFO7tGiY4zAImM,6347
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
 risk/neighborhoods/community.py,sha256=7ebo1Q5KokSQISnxZIh2SQxsKXdXm8aVkp-h_DiQ3K0,6818
 risk/neighborhoods/domains.py,sha256=bxJUxqFTynzX0mf3E8-AA4_Rfccje1reeVVhfzb1-pE,10672
-risk/neighborhoods/neighborhoods.py,sha256=cEk4gDvIkBky5POZhtHnO78iV-NXu4BeV-e5XdhYOkM,17508
+risk/neighborhoods/neighborhoods.py,sha256=N02r2nnCfDtzVicuUt2WA77EUPHtruqjX8qJmXUP7ik,17475
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
-risk/network/graph.py,sha256=_ZCyT2b9RtKAYzwul-Kp9__uQwTcagECf-mPMiAmP8U,16977
+risk/network/graph.py,sha256=_LEoom4EEowGALuJKSXcev9RAAHu2FqIeq3u7mkifW0,16479
 risk/network/io.py,sha256=gG50kOknO-D3HkW1HsbHMkTMvjUtn3l4W4Jwd-rXNr8,21202
 risk/network/plot.py,sha256=F6KPjmBYWrThKZScHs9SuzoKQiytBvzrmGhGberHjwo,62063
 risk/stats/__init__.py,sha256=e-BE_Dr_jgiK6hKM-T-tlG4yvHnId8e5qjnM0pdwNVc,230
@@ -23,8 +23,8 @@ 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=qLWdwxEY6nmkYPxpM8HLDcd2mbqYv9Qr7CKtJvhLqIM,9220
 risk/stats/permutation/test_functions.py,sha256=HuDIM-V1jkkfE1rlaIqrWWBSKZt3dQ1f-YEDjWpnLSE,2343
-risk_network-0.0.7b3.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.7b3.dist-info/METADATA,sha256=6D_1SuZdpPYaUQLLzctNrVLC_gdzsTrx7V1leqBvcio,43142
-risk_network-0.0.7b3.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-risk_network-0.0.7b3.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.7b3.dist-info/RECORD,,
+risk_network-0.0.7b4.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.7b4.dist-info/METADATA,sha256=vWM06f64mDBpDM6rcbI3rP0SCAz0gbcBZPj8OCVbHjo,43142
+risk_network-0.0.7b4.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+risk_network-0.0.7b4.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.7b4.dist-info/RECORD,,