risk-network 0.0.7b2__tar.gz → 0.0.7b4__tar.gz

{risk_network-0.0.7b2 → risk_network-0.0.7b4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b2
+Version: 0.0.7b4
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.7b2 → risk_network-0.0.7b4}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.7-beta.2"
+__version__ = "0.0.7-beta.4"

{risk_network-0.0.7b2 → risk_network-0.0.7b4}/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-0.0.7b2 → risk_network-0.0.7b4}/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
 
@@ -306,7 +305,8 @@ def _get_colors(
     Returns:
         List[Tuple]: List of RGBA colors.
     """
-    random.seed(random_seed)
+    # Set random seed for reproducibility
+    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:
@@ -321,17 +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: Add some random jitter to color positions to avoid overly systematic results
-    jitter = np.random.uniform(-0.05, 0.05, size=num_colors_to_generate)
-    color_positions = np.clip(color_positions + jitter, 0, 1)
-
-    # Step 5: Generate colors based on positions
+    # 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 6: Generate RGBA colors based on positions
     return [colormap(pos) for pos in color_positions]
 
 
@@ -358,28 +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_network-0.0.7b2 → risk_network-0.0.7b4}/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-0.0.7b2 → risk_network-0.0.7b4}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.7b2
+Version: 0.0.7b4
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>