risk-network 0.0.8b25__py3-none-any.whl → 0.0.8b27__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.25"
+__version__ = "0.0.8-beta.27"

risk/log/__init__.py

@@ -3,7 +3,7 @@ risk/log
 ~~~~~~~~
 """
 
-from .config import logger, log_header, set_global_verbosity
+from .console import logger, log_header, set_global_verbosity
 from .params import Params
 
 params = Params()

risk/log/{config.py → console.py}

@@ -1,6 +1,6 @@
 """
-risk/log/config
-~~~~~~~~~~~~~~~
+risk/log/console
+~~~~~~~~~~~~~~~~
 """
 
 import logging

risk/log/params.py

@@ -12,7 +12,7 @@ from typing import Any, Dict
 
 import numpy as np
 
-from .config import logger, log_header
+from .console import logger, log_header
 
 # Suppress all warnings - this is to resolve warnings from multiprocessing
 warnings.filterwarnings("ignore")

risk/network/geometry.py

@@ -3,6 +3,8 @@ risk/network/geometry
 ~~~~~~~~~~~~~~~~~~~~~
 """
 
+import copy
+
 import networkx as nx
 import numpy as np
 
@@ -55,10 +57,10 @@ def assign_edge_lengths(
     if compute_sphere:
         # Map to sphere and adjust depth
         _map_to_sphere(G)
-        G_depth = _create_depth(G.copy(), surface_depth=surface_depth)
+        G_depth = _create_depth(copy.deepcopy(G), surface_depth=surface_depth)
     else:
         # Calculate edge lengths directly on the plane
-        G_depth = G.copy()
+        G_depth = copy.deepcopy(G)
 
     for u, v, _ in G_depth.edges(data=True):
         u_coords = np.array([G_depth.nodes[u]["x"], G_depth.nodes[u]["y"]])

risk/network/io.py

@@ -5,6 +5,7 @@ risk/network/io
 This file contains the code for the RISK class and command-line access.
 """
 
+import copy
 import json
 import os
 import pickle
@@ -155,7 +156,7 @@ class NetworkIO:
         self._log_loading(filetype)
 
         # Important: Make a copy of the network to avoid modifying the original
-        network_copy = network.copy()
+        network_copy = copy.deepcopy(network)
         # Initialize the graph
         return self._initialize_graph(network_copy)
 

risk/network/plot/canvas.py

@@ -36,6 +36,7 @@ class Canvas:
         font: str = "Arial",
         title_color: Union[str, List, Tuple, np.ndarray] = "black",
         subtitle_color: Union[str, List, Tuple, np.ndarray] = "gray",
+        title_x: float = 0.5,
         title_y: float = 0.975,
         title_space_offset: float = 0.075,
         subtitle_offset: float = 0.025,
@@ -52,6 +53,7 @@ class Canvas:
                 Defaults to "black".
             subtitle_color (str, List, Tuple, or np.ndarray, optional): Color of the subtitle text. Can be a string or an array of colors.
                 Defaults to "gray".
+            title_x (float, optional): X-axis position of the title. Defaults to 0.5.
             title_y (float, optional): Y-axis position of the title. Defaults to 0.975.
             title_space_offset (float, optional): Fraction of figure height to leave for the space above the plot. Defaults to 0.075.
             subtitle_offset (float, optional): Offset factor to position the subtitle below the title. Defaults to 0.025.
@@ -85,7 +87,7 @@ class Canvas:
                 fontsize=title_fontsize,
                 color=title_color,
                 fontname=font,
-                x=0.5,  # Center the title horizontally
+                x=title_x,
                 ha="center",
                 va="top",
                 y=title_y,
@@ -112,6 +114,8 @@ class Canvas:
     def plot_circle_perimeter(
         self,
         scale: float = 1.0,
+        center_offset_x: float = 0.0,
+        center_offset_y: float = 0.0,
         linestyle: str = "dashed",
         linewidth: float = 1.5,
         color: Union[str, List, Tuple, np.ndarray] = "black",
@@ -122,6 +126,10 @@ class Canvas:
 
         Args:
             scale (float, optional): Scaling factor for the perimeter diameter. Defaults to 1.0.
+            center_offset_x (float, optional): Horizontal offset as a fraction of the diameter.
+                Negative values shift the center left, positive values shift it right. Defaults to 0.0.
+            center_offset_y (float, optional): Vertical offset as a fraction of the diameter.
+                Negative values shift the center down, positive values shift it up. Defaults to 0.0.
             linestyle (str, optional): Line style for the network perimeter circle (e.g., dashed, solid). Defaults to "dashed".
             linewidth (float, optional): Width of the circle's outline. Defaults to 1.5.
             color (str, List, Tuple, or np.ndarray, optional): Color of the network perimeter circle. Defaults to "black".
@@ -134,6 +142,8 @@ class Canvas:
         params.log_plotter(
             perimeter_type="circle",
             perimeter_scale=scale,
+            perimeter_center_offset_x=center_offset_x,
+            perimeter_center_offset_y=center_offset_y,
             perimeter_linestyle=linestyle,
             perimeter_linewidth=linewidth,
             perimeter_color=(
@@ -147,6 +157,10 @@ class Canvas:
         node_coordinates = self.graph.node_coordinates
         # Calculate the center and radius of the bounding box around the network
         center, radius = calculate_bounding_box(node_coordinates)
+        # Adjust the center based on user-defined offsets
+        adjusted_center = _calculate_adjusted_center(
+            center, radius, center_offset_x, center_offset_y
+        )
         # Scale the radius by the scale factor
         scaled_radius = radius * scale
 
@@ -160,7 +174,7 @@ class Canvas:
 
         # Draw a circle to represent the network perimeter
         circle = plt.Circle(
-            center,
+            adjusted_center,
             scaled_radius,
             linestyle=linestyle,
             linewidth=linewidth,
@@ -234,3 +248,43 @@ class Canvas:
             linewidth=linewidth,
             fill_alpha=fill_alpha,
         )
+
+
+def _calculate_adjusted_center(
+    center: Tuple[float, float],
+    radius: float,
+    center_offset_x: float = 0.0,
+    center_offset_y: float = 0.0,
+) -> Tuple[float, float]:
+    """Calculate the adjusted center for the network perimeter circle based on user-defined offsets.
+
+    Args:
+        center (Tuple[float, float]): Original center coordinates of the network graph.
+        radius (float): Radius of the bounding box around the network.
+        center_offset_x (float, optional): Horizontal offset as a fraction of the diameter.
+            Negative values shift the center left, positive values shift it right. Allowed
+            values are in the range [-1, 1]. Defaults to 0.0.
+        center_offset_y (float, optional): Vertical offset as a fraction of the diameter.
+            Negative values shift the center down, positive values shift it up. Allowed
+            values are in the range [-1, 1]. Defaults to 0.0.
+
+    Returns:
+        Tuple[float, float]: Adjusted center coordinates after applying the offsets.
+
+    Raises:
+        ValueError: If the center offsets are outside the valid range [-1, 1].
+    """
+    # Flip the y-axis to match the plot orientation
+    flipped_center_offset_y = -center_offset_y
+    # Validate the center offsets
+    if not -1 <= center_offset_x <= 1:
+        raise ValueError("Horizontal center offset must be in the range [-1, 1].")
+    if not -1 <= center_offset_y <= 1:
+        raise ValueError("Vertical center offset must be in the range [-1, 1].")
+
+    # Calculate adjusted center by applying offset fractions of the diameter
+    adjusted_center_x = center[0] + (center_offset_x * radius * 2)
+    adjusted_center_y = center[1] + (flipped_center_offset_y * radius * 2)
+
+    # Return the adjusted center coordinates
+    return adjusted_center_x, adjusted_center_y

risk/network/plot/labels.py

@@ -3,6 +3,7 @@ risk/network/plot/labels
 ~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
+import copy
 from typing import Any, Dict, List, Tuple, Union
 
 import matplotlib.pyplot as plt
@@ -723,12 +724,19 @@ def _combine_words(words: List[str], max_chars_per_line: int, max_label_lines: i
     # Main logic: start with max_label_lines number of words
     combined_lines = try_combinations(words[:max_label_lines])
     remaining_words = words[max_label_lines:]  # Remaining words after the initial batch
+    # Track words that have already been added
+    existing_words = set(" ".join(combined_lines).split())
 
     # Continue pulling more words until we fill the lines
     while remaining_words and len(combined_lines) < max_label_lines:
         available_slots = max_label_lines - len(combined_lines)
-        words_to_add = remaining_words[:available_slots]
+        words_to_add = [
+            word for word in remaining_words[:available_slots] if word not in existing_words
+        ]
         remaining_words = remaining_words[available_slots:]
+        # Update the existing words set
+        existing_words.update(words_to_add)
+        # Add to combined_lines only unique words
         combined_lines += try_combinations(words_to_add)
 
     # Join the final combined lines with TERM_DELIMITER, a special separator for line breaks
@@ -862,7 +870,7 @@ def _swap_and_evaluate(
     """
     # Get the list of labels from the dictionary keys
     labels = list(label_positions.keys())
-    swapped_positions = label_positions.copy()
+    swapped_positions = copy.deepcopy(label_positions)
     # Swap the positions of the two specified labels
     swapped_positions[labels[i]], swapped_positions[labels[j]] = (
         swapped_positions[labels[j]],

risk/risk.py

@@ -3,6 +3,7 @@ risk/risk
 ~~~~~~~~~
 """
 
+import copy
 from typing import Any, Dict, List, Tuple, Union
 
 import networkx as nx
@@ -94,7 +95,7 @@ class RISK(NetworkIO, AnnotationsIO):
         )
 
         # Make a copy of the network to avoid modifying the original
-        network = network.copy()
+        network = copy.deepcopy(network)
 
         # Load neighborhoods based on the network and distance metric
         neighborhoods = self._load_neighborhoods(
@@ -154,7 +155,7 @@ class RISK(NetworkIO, AnnotationsIO):
         )
 
         # Make a copy of the network to avoid modifying the original
-        network = network.copy()
+        network = copy.deepcopy(network)
 
         # Load neighborhoods based on the network and distance metric
         neighborhoods = self._load_neighborhoods(
@@ -223,7 +224,7 @@ class RISK(NetworkIO, AnnotationsIO):
         )
 
         # Make a copy of the network to avoid modifying the original
-        network = network.copy()
+        network = copy.deepcopy(network)
 
         # Load neighborhoods based on the network and distance metric
         neighborhoods = self._load_neighborhoods(
@@ -305,7 +306,7 @@ class RISK(NetworkIO, AnnotationsIO):
         )
 
         # Make a copy of the network to avoid modifying the original
-        network = network.copy()
+        network = copy.deepcopy(network)
 
         logger.debug(f"p-value cutoff: {pval_cutoff}")
         logger.debug(f"FDR BH cutoff: {fdr_cutoff}")

{risk_network-0.0.8b25.dist-info → risk_network-0.0.8b27.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b25
+Version: 0.0.8b27
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b25.dist-info → risk_network-0.0.8b27.dist-info}/RECORD

@@ -1,24 +1,24 @@
-risk/__init__.py,sha256=Qyc4qWblCngk-E90hZv6DYKLI0-FV0bvyLCGHF1TvgA,113
+risk/__init__.py,sha256=ac92cxvpV3NMnUqcZb1WHPrNCiY2Du_Nl1UOytIwoyg,113
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=7JERU-ZkDuESY3LJDyqEJGVs-YdYQwCt2SO3nHGYk0E,23809
+risk/risk.py,sha256=8GTUpj3TC7XLwEUD22-fDTKXtW7PndzW9TixWaZ23bI,23853
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
 risk/annotations/annotations.py,sha256=dHO6kQOQjMA57nYA-yTAU1uB-ieiZ5sknAKvX6vF0Os,13024
 risk/annotations/io.py,sha256=powWzeimVdE0WCwlBCXyu5otMyZZHQujC0DS3m5DC0c,9505
-risk/log/__init__.py,sha256=aDUz5LMFQsz0UlsQI2EdXtiBKRLfml1UMeZKC7QQIGU,134
-risk/log/config.py,sha256=m8pzj-hN4vI_2JdJUfyOoSvzT8_lhoIfBt27sKbnOes,4535
-risk/log/params.py,sha256=rvyg86RnkHwotST7x42RgsiYfq2HB-9BZxp6KkT_04o,6415
+risk/log/__init__.py,sha256=xKeU9uK1AnVk7Yt9GTp-E-dn7Ealow2igEXZZnQRa2c,135
+risk/log/console.py,sha256=C52s3FgQ2e9kQWcXL8m7rs_pnKXt5Yy8PBHmQkOTiNo,4537
+risk/log/params.py,sha256=qSTktJ3OazldTzgtDGZkh0s30vu5kiXPkiNGLdSFDvg,6416
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
 risk/neighborhoods/community.py,sha256=MAgIblbuisEPwVU6mFZd4Yd9NUKlaHK99suw51r1Is0,7065
 risk/neighborhoods/domains.py,sha256=3iV0-nRLF2sL9_7epHY5b9AtTU-QQ84hOWO76VwFcrs,11685
 risk/neighborhoods/neighborhoods.py,sha256=cT9CCi1uQLn9Kv9Lxt8AN_4s63SKIlOZspvUZnx27nE,21832
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
-risk/network/geometry.py,sha256=Y3Brp0XYWoBL2VHJX7I-gW5x-q7lGiEMqr2kqtutgkQ,6811
+risk/network/geometry.py,sha256=gFtYUj9j9aul4paKq_qSGJn39Nazxu_MXv8m-tYYtrk,6840
 risk/network/graph.py,sha256=-tslu8nSbuBaqNGf6TQ8ON7C27v-BLH_37J2aC6Ke14,9602
-risk/network/io.py,sha256=u0PPcKjp6Xze--7eDOlvalYkjQ9S2sjiC-ac2476PUI,22942
+risk/network/io.py,sha256=-NJ9Tg1s-DxhlDbwQGO4o87rbMqO4-BzShgnIgFoRRE,22962
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
-risk/network/plot/canvas.py,sha256=ZO6bHw1chIsUqtE7IkPKdgX4tFLA-T5OwN5SojqGSNU,10672
+risk/network/plot/canvas.py,sha256=TlCpNtvoceizAumNr9I02JcBrBO6FiAFAa2ZC0bx3SU,13356
 risk/network/plot/contour.py,sha256=CwX4i3uE5HL0W4kfx34U7YyoTTqMxyb7xaXKRVoNLzY,15265
-risk/network/plot/labels.py,sha256=1c7R3aXd_9jBqkvt70bvxqJOkZm4NGQzR_OxbHJcLfU,45171
+risk/network/plot/labels.py,sha256=fNccRds6seShMFPN6WX_7M1_qnscBkcWEH3QOJAKalk,45502
 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
@@ -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-0.0.8b25.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.8b25.dist-info/METADATA,sha256=4EgVGDOFG3aT9ruKe6oSuml4Fk2khMv4qcyXHJnSWKo,47498
-risk_network-0.0.8b25.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-risk_network-0.0.8b25.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.8b25.dist-info/RECORD,,
+risk_network-0.0.8b27.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.8b27.dist-info/METADATA,sha256=7PXFvXkTlaMC7TB5B7P1ePXPwDPZqpXMeeKb_pVZL8o,47498
+risk_network-0.0.8b27.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+risk_network-0.0.8b27.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.8b27.dist-info/RECORD,,

{risk_network-0.0.8b25.dist-info → risk_network-0.0.8b27.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: setuptools (75.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any