risk-network 0.0.8b22__py3-none-any.whl → 0.0.8b23__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.8-beta.22"
+__version__ = "0.0.8-beta.23"

risk/network/plot/utils/layout.py

@@ -30,6 +30,44 @@ def calculate_bounding_box(
     return center, radius
 
 
+def refine_center_iteratively(
+    node_coordinates: np.ndarray,
+    radius_margin: float = 1.05,
+    max_iterations: int = 10,
+    tolerance: float = 1e-2,
+) -> Tuple[np.ndarray, float]:
+    """Refine the center of the graph iteratively to minimize skew in node distribution.
+
+    Args:
+        node_coordinates (np.ndarray): Array of node coordinates (x, y).
+        radius_margin (float, optional): Margin factor to apply to the bounding box radius. Defaults to 1.05.
+        max_iterations (int, optional): Maximum number of iterations for refining the center. Defaults to 10.
+        tolerance (float, optional): Stopping tolerance for center adjustment. Defaults to 1e-2.
+
+    Returns:
+        tuple: Refined center and the final radius.
+    """
+    # Initial center and radius based on the bounding box
+    center, radius = calculate_bounding_box(node_coordinates, radius_margin)
+    for _ in range(max_iterations):
+        # Shift the coordinates based on the current center
+        shifted_coordinates = node_coordinates - center
+        # Calculate skew (difference in distance from the center)
+        skew = np.mean(shifted_coordinates, axis=0)
+        # If skew is below tolerance, stop
+        if np.linalg.norm(skew) < tolerance:
+            break
+
+        # Adjust the center by moving it in the direction opposite to the skew
+        center += skew
+
+    # After refinement, recalculate the bounding radius
+    shifted_coordinates = node_coordinates - center
+    new_radius = np.max(np.linalg.norm(shifted_coordinates, axis=1)) * radius_margin
+
+    return center, new_radius
+
+
 def calculate_centroids(network, domain_id_to_node_ids_map):
     """Calculate the centroid for each domain based on node x and y coordinates in the network.
 

{risk_network-0.0.8b22.dist-info → risk_network-0.0.8b23.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b22
+Version: 0.0.8b23
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b22.dist-info → risk_network-0.0.8b23.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=fz5ZBsLUlWdBQ5uJS0qBge1qwPNox0OYhi4OXkjQxwI,113
+risk/__init__.py,sha256=t7Ysy06wQrCx89cCOIVl2tjIIhHYi4_PNQWAUTijJAU,113
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=rjV0hllegCX978QaUo175FworKxNXlhQEQaQAPjHqos,23397
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
@@ -22,7 +22,7 @@ risk/network/plot/labels.py,sha256=ozkqwhBOTHKJLaAz4dJopXuykAvssSZUer2W5V0x2jM,4
 risk/network/plot/network.py,sha256=6RURL1OdBFyQ34qNcwM_uH3LSQGYZZ8tZT51dggH1a0,13685
 risk/network/plot/plotter.py,sha256=iTPMiTnTTatM_-q1Ox_bjt5Pvv-Lo8gceiYB6TVzDcw,5770
 risk/network/plot/utils/color.py,sha256=WSs1ge2oZ8yXwyVk2QqBF-avRd0aYT-sYZr9cxxAn7M,19626
-risk/network/plot/utils/layout.py,sha256=5DpRLvabgnPWwVJ-J3W6oFBBvbjCrudvvW4HDOzzoTo,1960
+risk/network/plot/utils/layout.py,sha256=RnJq0yODpoheZnDl7KKFPQeXrnrsS3FLIdxupoYVZq4,3553
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
 risk/stats/hypergeom.py,sha256=oc39f02ViB1vQ-uaDrxG_tzAT6dxQBRjc88EK2EGn78,2282
 risk/stats/poisson.py,sha256=polLgwS08MTCNzupYdmMUoEUYrJOjAbcYtYwjlfeE5Y,1803
@@ -30,8 +30,8 @@ risk/stats/stats.py,sha256=6iGi0-oN05mTmupg6X_VEBxEQvi2rujNhfPk4aLjwNI,7186
 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-0.0.8b22.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.8b22.dist-info/METADATA,sha256=9trSkrh2Od_B2qltA2n_uVcvX1kUlMy-QmLO4WThrds,47498
-risk_network-0.0.8b22.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-risk_network-0.0.8b22.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.8b22.dist-info/RECORD,,
+risk_network-0.0.8b23.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.8b23.dist-info/METADATA,sha256=NcDzE6PKoco47jMvWySV2Xnu8abFT5I03KI-KNGqARk,47498
+risk_network-0.0.8b23.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+risk_network-0.0.8b23.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.8b23.dist-info/RECORD,,