risk-network 0.0.8b20__py3-none-any.whl → 0.0.8b21__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.20"
+__version__ = "0.0.8-beta.21"

risk/network/io.py

@@ -491,7 +491,7 @@ class NetworkIO:
             if "x" not in attrs or "y" not in attrs:
                 if (
                     "pos" in attrs
-                    and isinstance(attrs["pos"], (List, Tuple, np.ndarray))
+                    and isinstance(attrs["pos"], (list, tuple, np.ndarray))
                     and len(attrs["pos"]) >= 2
                 ):
                     attrs["x"], attrs["y"] = attrs["pos"][

risk/network/plot/canvas.py

@@ -137,7 +137,7 @@ class Canvas:
             perimeter_linestyle=linestyle,
             perimeter_linewidth=linewidth,
             perimeter_color=(
-                "custom" if isinstance(color, (List, Tuple, np.ndarray)) else color
+                "custom" if isinstance(color, (list, tuple, np.ndarray)) else color
             ),  # np.ndarray usually indicates custom colors
             perimeter_outline_alpha=outline_alpha,
             perimeter_fill_alpha=fill_alpha,
@@ -210,7 +210,7 @@ class Canvas:
             perimeter_grid_size=grid_size,
             perimeter_linestyle=linestyle,
             perimeter_linewidth=linewidth,
-            perimeter_color=("custom" if isinstance(color, (List, Tuple, np.ndarray)) else color),
+            perimeter_color=("custom" if isinstance(color, (list, tuple, np.ndarray)) else color),
             perimeter_outline_alpha=outline_alpha,
             perimeter_fill_alpha=fill_alpha,
         )

risk/network/plot/contour.py

@@ -122,7 +122,7 @@ class Contour:
             ValueError: If no valid nodes are found in the network graph.
         """
         # Check if nodes is a list of lists or a flat list
-        if any(isinstance(item, (List, Tuple, np.ndarray)) for item in nodes):
+        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
             # If it's a list of lists, iterate over sublists
             node_groups = nodes
             # Convert color to RGBA arrays to match the number of groups

risk/network/plot/labels.py

@@ -282,7 +282,7 @@ class Labels:
             arrow_tip_shrink (float, optional): Distance between the arrow tip and the centroid. Defaults to 0.0.
         """
         # Check if nodes is a list of lists or a flat list
-        if any(isinstance(item, (List, Tuple, np.ndarray)) for item in nodes):
+        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
             # If it's a list of lists, iterate over sublists
             node_groups = nodes
             # Convert fontcolor and arrow_color to RGBA arrays to match the number of groups

risk/network/plot/network.py

@@ -141,7 +141,7 @@ class Network:
             ValueError: If no valid nodes are found in the network graph.
         """
         # Flatten nested lists of nodes, if necessary
-        if any(isinstance(item, (List, Tuple, np.ndarray)) for item in nodes):
+        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
             nodes = [node for sublist in nodes for node in sublist]
 
         # Filter to get node IDs and their coordinates

risk/network/plot/utils/color.py

@@ -377,7 +377,7 @@ def to_rgba(
         if isinstance(c, str):
             # Convert color names or hex values (e.g., 'red', '#FF5733') to RGBA
             rgba = np.array(mcolors.to_rgba(c))
-        elif isinstance(c, (List, Tuple, np.ndarray)) and len(c) in [3, 4]:
+        elif isinstance(c, (list, tuple, np.ndarray)) and len(c) in [3, 4]:
             # Convert RGB (3) or RGBA (4) values to RGBA format
             rgba = np.array(mcolors.to_rgba(c))
         else:
@@ -396,8 +396,8 @@ def to_rgba(
     # Handle a single color (string or RGB/RGBA list/tuple)
     if (
         isinstance(color, str)
-        or isinstance(color, (List, Tuple, np.ndarray))
-        and not any(isinstance(c, (str, List, Tuple, np.ndarray)) for c in color)
+        or isinstance(color, (list, tuple, np.ndarray))
+        and not any(isinstance(c, (str, list, tuple, np.ndarray)) for c in color)
     ):
         rgba_color = convert_to_rgba(color)
         if num_repeats:
@@ -407,7 +407,7 @@ def to_rgba(
         return np.array([rgba_color])  # Return a single color wrapped in a numpy array
 
     # Handle a list/array of colors
-    elif isinstance(color, (List, Tuple, np.ndarray)):
+    elif isinstance(color, (list, tuple, np.ndarray)):
         rgba_colors = np.array(
             [convert_to_rgba(c) for c in color]
         )  # Convert each color in the list to RGBA

risk/risk.py

@@ -3,7 +3,7 @@ risk/risk
 ~~~~~~~~~
 """
 
-from typing import Any, Dict, Tuple, Union
+from typing import Any, Dict, List, Tuple, Union
 
 import networkx as nx
 import numpy as np
@@ -58,9 +58,9 @@ class RISK(NetworkIO, AnnotationsIO):
         self,
         network: nx.Graph,
         annotations: Dict[str, Any],
-        distance_metric: str = "louvain",
+        distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
-        edge_length_threshold: float = 0.5,
+        edge_length_threshold: Union[float, List, Tuple, np.ndarray] = 0.5,
         null_distribution: str = "network",
         random_seed: int = 888,
     ) -> Dict[str, Any]:
@@ -69,9 +69,13 @@ class RISK(NetworkIO, AnnotationsIO):
         Args:
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
-            distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "louvain".
+            distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
-            edge_length_threshold (float, optional): Edge length threshold for neighborhood analysis. Defaults to 0.5.
+            edge_length_threshold (float, List, Tuple, or np.ndarray, optional): Edge length threshold(s) for creating subgraphs.
+                Can be a single float for one threshold or a list/tuple of floats corresponding to multiple thresholds.
+                Defaults to 0.5.
             null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
             random_seed (int, optional): Seed for random number generation. Defaults to 888.
 
@@ -111,9 +115,9 @@ class RISK(NetworkIO, AnnotationsIO):
         self,
         network: nx.Graph,
         annotations: Dict[str, Any],
-        distance_metric: str = "louvain",
+        distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
-        edge_length_threshold: float = 0.5,
+        edge_length_threshold: Union[float, List, Tuple, np.ndarray] = 0.5,
         null_distribution: str = "network",
         random_seed: int = 888,
     ) -> Dict[str, Any]:
@@ -122,9 +126,13 @@ class RISK(NetworkIO, AnnotationsIO):
         Args:
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
-            distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "louvain".
+            distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
-            edge_length_threshold (float, optional): Edge length threshold for neighborhood analysis. Defaults to 0.5.
+            edge_length_threshold (float, List, Tuple, or np.ndarray, optional): Edge length threshold(s) for creating subgraphs.
+                Can be a single float for one threshold or a list/tuple of floats corresponding to multiple thresholds.
+                Defaults to 0.5.
             null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
             random_seed (int, optional): Seed for random number generation. Defaults to 888.
 
@@ -164,9 +172,9 @@ class RISK(NetworkIO, AnnotationsIO):
         self,
         network: nx.Graph,
         annotations: Dict[str, Any],
-        distance_metric: str = "louvain",
+        distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
-        edge_length_threshold: float = 0.5,
+        edge_length_threshold: Union[float, List, Tuple, np.ndarray] = 0.5,
         score_metric: str = "sum",
         null_distribution: str = "network",
         num_permutations: int = 1000,
@@ -178,9 +186,13 @@ class RISK(NetworkIO, AnnotationsIO):
         Args:
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
-            distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "louvain".
+            distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
-            edge_length_threshold (float, optional): Edge length threshold for neighborhood analysis. Defaults to 0.5.
+            edge_length_threshold (float, List, Tuple, or np.ndarray, optional): Edge length threshold(s) for creating subgraphs.
+                Can be a single float for one threshold or a list/tuple of floats corresponding to multiple thresholds.
+                Defaults to 0.5.
             score_metric (str, optional): Scoring metric for neighborhood significance. Defaults to "sum".
             null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
             num_permutations (int, optional): Number of permutations for significance testing. Defaults to 1000.
@@ -353,7 +365,7 @@ class RISK(NetworkIO, AnnotationsIO):
     def load_plotter(
         self,
         graph: NetworkGraph,
-        figsize: Tuple = (10, 10),
+        figsize: Union[List, Tuple, np.ndarray] = (10, 10),
         background_color: str = "white",
         background_alpha: Union[float, None] = 1.0,
         pad: float = 0.3,
@@ -362,7 +374,7 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             graph (NetworkGraph): The graph to plot.
-            figsize (Tuple, optional): Size of the figure. Defaults to (10, 10).
+            figsize (List, Tuple, or np.ndarray, optional): Size of the plot. Defaults to (10, 10)., optional): Size of the figure. Defaults to (10, 10).
             background_color (str, optional): Background color of the plot. Defaults to "white".
             background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides
                 any existing alpha values found in background_color. Defaults to 1.0.
@@ -385,9 +397,9 @@ class RISK(NetworkIO, AnnotationsIO):
     def _load_neighborhoods(
         self,
         network: nx.Graph,
-        distance_metric: str = "louvain",
+        distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
-        edge_length_threshold: float = 0.5,
+        edge_length_threshold: Union[float, List, Tuple, np.ndarray] = 0.5,
         random_seed: int = 888,
     ) -> np.ndarray:
         """Load significant neighborhoods for the network.

{risk_network-0.0.8b20.dist-info → risk_network-0.0.8b21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b20
+Version: 0.0.8b21
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b20.dist-info → risk_network-0.0.8b21.dist-info}/RECORD

@@ -1,6 +1,6 @@
-risk/__init__.py,sha256=MOWrmv2B-I1GTr0sgWTb-CLgeMWceWa6q2E6oeGC2CA,113
+risk/__init__.py,sha256=rwU6NXlpU-Cu31fRh5iXEwcYq9jIr2prM7bv_iAaksI,113
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=_ufeTLOAAT4QwrRysvDJOQeE0qMvpp3BSSayfFLhGJE,21720
+risk/risk.py,sha256=8J2cvtXYy99PCoOHEYNXt0vcYrcHqxi2O1VvYQNNPt4,23217
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
 risk/annotations/annotations.py,sha256=KHGeF5vBDmX711nA08DfhxI9z7Z1Oaeo91ueWhM6vs8,11370
 risk/annotations/io.py,sha256=powWzeimVdE0WCwlBCXyu5otMyZZHQujC0DS3m5DC0c,9505
@@ -14,14 +14,14 @@ risk/neighborhoods/neighborhoods.py,sha256=OPGNfeGQR533vWjger7f34ZPSgw9250LQXcTE
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=Y3Brp0XYWoBL2VHJX7I-gW5x-q7lGiEMqr2kqtutgkQ,6811
 risk/network/graph.py,sha256=-91JL84LYbdWohzybKFQ3NdWnervxP-wwbpaUOdRVLE,8576
-risk/network/io.py,sha256=w_9fUcZUVXAPRKGhLBc7xhIJs8l83szHiBQTdaNN0gk,22942
+risk/network/io.py,sha256=u0PPcKjp6Xze--7eDOlvalYkjQ9S2sjiC-ac2476PUI,22942
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
-risk/network/plot/canvas.py,sha256=hdrmGd2TCuii8wn6jDQfyJTI5YXDNGYFLiU4TyqAYbE,10778
-risk/network/plot/contour.py,sha256=xxTf6iNSlpe2S8aalt2mzivmR0wuGUOh_F3-IL6UbEU,15027
-risk/network/plot/labels.py,sha256=bFsP9NA3Fp0GhX62ArRP9tSqPCgUthKE9aFe0imoPcI,45115
-risk/network/plot/network.py,sha256=nfTmQxx1YwS3taXwq8WSCfu6nfKFOyxj7T5605qLXVM,13615
+risk/network/plot/canvas.py,sha256=P8XzcesrbxjLcrT40hf15QgLTvearER2Yid3QefQF20,10778
+risk/network/plot/contour.py,sha256=vo1BeXrMKW-EipLB-9pB5AMfzmiJJduo2H_xgWUoDYo,15027
+risk/network/plot/labels.py,sha256=wdIi5UfAGVeZ1UM6AAuOQ0I4dBqQqzVe1euGCdiv91o,45115
+risk/network/plot/network.py,sha256=U-3oYxq-QTZolc72khmesS85pNlep6L40kIT-qZVljE,13615
 risk/network/plot/plotter.py,sha256=iTPMiTnTTatM_-q1Ox_bjt5Pvv-Lo8gceiYB6TVzDcw,5770
-risk/network/plot/utils/color.py,sha256=HtUaGnqJPVNbRyUhQMlBonfHc_2Ci8BtTI3y424p8Cs,19626
+risk/network/plot/utils/color.py,sha256=WSs1ge2oZ8yXwyVk2QqBF-avRd0aYT-sYZr9cxxAn7M,19626
 risk/network/plot/utils/layout.py,sha256=5DpRLvabgnPWwVJ-J3W6oFBBvbjCrudvvW4HDOzzoTo,1960
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
 risk/stats/hypergeom.py,sha256=oc39f02ViB1vQ-uaDrxG_tzAT6dxQBRjc88EK2EGn78,2282
@@ -30,8 +30,8 @@ risk/stats/stats.py,sha256=07yMULKlCurK62x674SHKJavZtz9ge2K2ZsHix_z_pw,7088
 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-0.0.8b20.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.8b20.dist-info/METADATA,sha256=UnAgNaBf77W4-Vo5YGPJktwy5WQaEwWU2ByhSbyfEVg,47498
-risk_network-0.0.8b20.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-risk_network-0.0.8b20.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.8b20.dist-info/RECORD,,
+risk_network-0.0.8b21.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.8b21.dist-info/METADATA,sha256=WAMLlJBw45mKR3apG1PxGAQfMOm9flaJxsz_h_rwnGs,47498
+risk_network-0.0.8b21.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+risk_network-0.0.8b21.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.8b21.dist-info/RECORD,,