risk-network 0.0.9b7__py3-none-any.whl → 0.0.9b8__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.7"
+__version__ = "0.0.9-beta.8"

risk/network/plot/utils/colors.py

@@ -9,6 +9,7 @@ import matplotlib
 import matplotlib.colors as mcolors
 import networkx as nx
 import numpy as np
+from sklearn.cluster import AgglomerativeClustering
 
 from risk.network.graph import NetworkGraph
 from risk.network.plot.utils.layout import calculate_centroids
@@ -249,34 +250,53 @@ def _get_colors(
     """
     # 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)
+    num_domains = len(domain_id_to_node_ids_map)
     if color:
         # Generate all colors as the same specified color
-        rgba = to_rgba(color, num_repeats=num_colors_to_generate)
+        rgba = to_rgba(color, num_repeats=num_domains)
         return rgba
 
     # Load colormap
     colormap = matplotlib.colormaps.get_cmap(cmap)
     # Step 1: Calculate centroids for each domain
     centroids = calculate_centroids(network, domain_id_to_node_ids_map)
-    # Step 2: Calculate pairwise distances between centroids
     centroid_array = np.array(centroids)
+
+    # Step 2: Cluster domains based on proximity using Agglomerative Clustering
     dist_matrix = np.linalg.norm(centroid_array[:, None] - centroid_array, axis=-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)
+    max_distance = np.max(dist_matrix) if np.max(dist_matrix) != 0 else 1
+    proximity_threshold = 0.3 * max_distance
 
-    # Step 6: Generate RGBA colors based on positions
-    return [colormap(pos) for pos in color_positions]
+    clustering_model = AgglomerativeClustering(
+        n_clusters=None, distance_threshold=proximity_threshold
+    )
+    cluster_labels = clustering_model.fit_predict(centroid_array)
+    num_clusters = len(set(cluster_labels))
+
+    # Step 3: Assign base color positions for each cluster, spaced across colormap
+    cluster_positions = np.linspace(0, 1, num_clusters, endpoint=False)
+    np.random.shuffle(cluster_positions)  # Shuffle based on seed to vary color layout
+    cluster_id_to_position = {
+        cluster_id: pos for cluster_id, pos in zip(np.unique(cluster_labels), cluster_positions)
+    }
+
+    # Step 4: Assign colors to each domain based on cluster base color with a global shift
+    global_shift = np.random.uniform(-0.1, 0.1)  # Small global shift for variety
+    colors = []
+    for i in range(num_domains):
+        cluster_idx = cluster_labels[i]
+        base_position = cluster_id_to_position[cluster_idx]
+        # Add global shift and ensure it stays within [0, 1]
+        color_position = (base_position + global_shift) % 1
+        colors.append(colormap(color_position))  # Get color from colormap
+
+    return colors
 
 
 def _assign_distant_colors(dist_matrix: np.ndarray, num_colors_to_generate: int) -> np.ndarray:
-    """Assign colors to centroids that are close in space, ensuring stark color differences.
+    """Assign color positions ensuring centroids close in space are maximally separated in color.
 
     Args:
         dist_matrix (ndarray): Matrix of pairwise centroid distances.
@@ -285,22 +305,14 @@ def _assign_distant_colors(dist_matrix: np.ndarray, num_colors_to_generate: int)
     Returns:
         np.array: Array of color positions in the range [0, 1].
     """
-    color_positions = np.zeros(num_colors_to_generate)
-    # Step 1: Sort indices by centroid proximity (based on sum of distances to others)
+    # Step 1: Calculate proximity order based on the sum of distances
     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
-
-    # 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
-        color_positions[proximity_order[i]] = (i * 2) / num_colors_to_generate
-        color_positions[proximity_order[-(i + 1)]] = ((i * 2) + 1) / num_colors_to_generate
-
+    # Step 2: Generate evenly spaced color positions
+    color_positions = np.linspace(0, 1, num_colors_to_generate, endpoint=False)
+    # Step 3: Shuffle color positions based on proximity
+    color_positions = color_positions[proximity_order]
     return color_positions
 
 

{risk_network-0.0.9b7.dist-info → risk_network-0.0.9b8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b7
+Version: 0.0.9b8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b7.dist-info → risk_network-0.0.9b8.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=qkmHFIeApkRQEVhb6MctmvmD84ri0SRmooehDAeIV2k,112
+risk/__init__.py,sha256=CF_5U_LFsoHtqjLJO9F0HRUYI0sDt4UlIWwkpkOG-no,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=kntBxYwAEpoAjXN_l6BM3yxFKyuAKmd8OMGl2P00pZ4,22416
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
@@ -23,7 +23,7 @@ risk/network/plot/contour.py,sha256=VONX9l6owrZvWtR0mWQ6z2GSd1YXIv5wV_sf5ROQLT4,
 risk/network/plot/labels.py,sha256=eorP80CmAbHmt7de2qHna1tHGKL8YiHknwFW2R3tvjI,45734
 risk/network/plot/network.py,sha256=_K8Am2y6zSGrm3fAgMbXxzgspbugJi3uK4_tG8qqGoI,14015
 risk/network/plot/plotter.py,sha256=eS1vHqvOA2O001Rq7WiDcgqcehJ3fg4OPfvkezH4erw,5771
-risk/network/plot/utils/colors.py,sha256=k_461yoLgE7OxFYnpjU-Am1XFUbnOogiPqlVFYlwViQ,20803
+risk/network/plot/utils/colors.py,sha256=lNDwlTbpXCKAbaqSHsRlxxY_MRAbogma81xyqHawl3U,21005
 risk/network/plot/utils/layout.py,sha256=6o7idoWQnyzujSWOFXQykUvyPy8NuRtJV04TnlbXXBo,3647
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
 risk/stats/hypergeom.py,sha256=oc39f02ViB1vQ-uaDrxG_tzAT6dxQBRjc88EK2EGn78,2282
@@ -32,8 +32,8 @@ risk/stats/stats.py,sha256=z8NrhiVj4BzJ250bVLfytpmfC7RzYu7mBuIZD_l0aCA,7222
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=meBNSrbRa9P8WJ54n485l0H7VQJlMSfHqdN4aCKYCtQ,10105
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.9b7.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b7.dist-info/METADATA,sha256=Ss2U9ENOyI2wMdGcSPG0KVcE41sigd_hZZL0XosvpWM,47497
-risk_network-0.0.9b7.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-risk_network-0.0.9b7.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b7.dist-info/RECORD,,
+risk_network-0.0.9b8.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b8.dist-info/METADATA,sha256=JaTFHNn11mwliUNgsG6jvz2sU53goxjS3cwQXLEbcEw,47497
+risk_network-0.0.9b8.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+risk_network-0.0.9b8.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b8.dist-info/RECORD,,