risk-network 0.0.9b7__py3-none-any.whl → 0.0.9b9__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.9"

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
@@ -233,75 +234,35 @@ def _get_colors(
     color: Union[str, List, Tuple, np.ndarray, None] = None,
     random_seed: int = 888,
 ) -> List[Tuple]:
-    """Generate a list of RGBA colors based on domain centroids, ensuring that domains
-    close in space get maximally separated colors, while keeping some randomness.
+    """Generate a list of RGBA colors for domains, ensuring maximally separated colors for nearby domains.
 
     Args:
         network (nx.Graph): The graph representing the network.
         domain_id_to_node_ids_map (Dict[int, Any]): Mapping from domain IDs to lists of node IDs.
         cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
-        color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for the domains.
+        color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use.
             If None, the colormap will be used. Defaults to None.
         random_seed (int, optional): Seed for random number generation. Defaults to 888.
 
     Returns:
-        List[Tuple]: List of RGBA colors.
+        List[Tuple]: List of RGBA colors for each domain.
     """
-    # 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)
+        # If a single color is specified, apply it to all domains
+        rgba = to_rgba(color, num_repeats=num_domains)
         return rgba
 
-    # Load colormap
+    # Load colormap and generate a large, maximally separated set of colors
     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)
-    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)
-
-    # Step 6: Generate RGBA colors based on positions
-    return [colormap(pos) for pos in color_positions]
-
-
-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.
-
-    Args:
-        dist_matrix (ndarray): Matrix of pairwise centroid distances.
-        num_colors_to_generate (int): Number of colors to generate.
+    color_positions = np.linspace(0, 1, num_domains, endpoint=False)
+    # Shuffle color positions to avoid spatial clustering of similar colors
+    np.random.shuffle(color_positions)
+    # Assign colors based on positions in the colormap
+    colors = [colormap(pos) for pos in color_positions]
 
-    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)
-    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
-
-    return color_positions
+    return colors
 
 
 def _blend_colors_perceptually(

{risk_network-0.0.9b7.dist-info → risk_network-0.0.9b9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b7
+Version: 0.0.9b9
 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-0.0.9b9.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=qkmHFIeApkRQEVhb6MctmvmD84ri0SRmooehDAeIV2k,112
+risk/__init__.py,sha256=wOa6WyqiT30Dx0Mk77M-4ilHgFK5rf0eRjG7ceeU8Gw,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=9zuU2O-Nkpljb1yVGUR_IjqD1y-wH6Bf6Vm1MMVB0Lo,18718
 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-0.0.9b9.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b9.dist-info/METADATA,sha256=iBZOFuXgFhOXgRkBH90TC3Fkk7r1iAX6Yq0bPuGjxck,47497
+risk_network-0.0.9b9.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+risk_network-0.0.9b9.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b9.dist-info/RECORD,,