risk-network 0.0.6b0__tar.gz → 0.0.6b2__tar.gz

{risk_network-0.0.6b0 → risk_network-0.0.6b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.6b0
+Version: 0.0.6b2
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.6b0 → risk_network-0.0.6b2}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.6-beta.0"
+__version__ = "0.0.6-beta.2"

{risk_network-0.0.6b0 → risk_network-0.0.6b2}/risk/annotations/io.py

@@ -36,13 +36,15 @@ class AnnotationsIO:
             dict: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
         """
         filetype = "JSON"
+        # Log the loading of the JSON file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Open and read the JSON file
         with open(filepath, "r") as file:
             annotations_input = json.load(file)
 
-        # Process the JSON data and return it in the context of the network
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
     def load_excel_annotation(
@@ -69,14 +71,18 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "Excel"
+        # Log the loading of the Excel file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the specified sheet from the Excel file
         df = pd.read_excel(filepath, sheet_name=sheet_name)
         # Split the nodes column by the specified nodes_delimiter
         df[nodes_colname] = df[nodes_colname].apply(lambda x: x.split(nodes_delimiter))
         # Convert the DataFrame to a dictionary pairing labels with their corresponding nodes
         label_node_dict = df.set_index(label_colname)[nodes_colname].to_dict()
+
+        # Load the annotations into the provided network
         return load_annotations(network, label_node_dict)
 
     def load_csv_annotation(
@@ -101,13 +107,16 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "CSV"
+        # Log the loading of the CSV file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the CSV file into a dictionary
         annotations_input = _load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter=",", nodes_delimiter=nodes_delimiter
         )
-        # Process and return the annotations in the context of the network
+
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
     def load_tsv_annotation(
@@ -132,13 +141,16 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "TSV"
+        # Log the loading of the TSV file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the TSV file into a dictionary
         annotations_input = _load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter="\t", nodes_delimiter=nodes_delimiter
         )
-        # Process and return the annotations in the context of the network
+
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
 

{risk_network-0.0.6b0 → risk_network-0.0.6b2}/risk/neighborhoods/community.py

@@ -25,10 +25,14 @@ def calculate_dijkstra_neighborhoods(network: nx.Graph) -> np.ndarray:
 
     # Populate the neighborhoods matrix based on Dijkstra's distances
     for source, targets in all_dijkstra_paths.items():
+        max_length = max(targets.values()) if targets else 1  # Handle cases with no targets
         for target, length in targets.items():
-            neighborhoods[source, target] = (
-                1 if np.isnan(length) or length == 0 else np.sqrt(1 / length)
-            )
+            if np.isnan(length):
+                neighborhoods[source, target] = max_length  # Use max distance for NaN
+            elif length == 0:
+                neighborhoods[source, target] = 1  # Assign 1 for zero-length paths (self-loops)
+            else:
+                neighborhoods[source, target] = 1 / length  # Inverse of the distance
 
     return neighborhoods
 

{risk_network-0.0.6b0 → risk_network-0.0.6b2}/risk/neighborhoods/neighborhoods.py

@@ -4,7 +4,7 @@ risk/neighborhoods/neighborhoods
 """
 
 import warnings
-from typing import Any, Dict, Tuple
+from typing import Any, Dict, List, Tuple
 
 import networkx as nx
 import numpy as np
@@ -305,7 +305,7 @@ def _get_node_position(network: nx.Graph, node: Any) -> np.ndarray:
     )
 
 
-def _calculate_threshold(average_distances: list, distance_threshold: float) -> float:
+def _calculate_threshold(average_distances: List, distance_threshold: float) -> float:
     """Calculate the distance threshold based on the given average distances and a percentile threshold.
 
     Args:

{risk_network-0.0.6b0 → risk_network-0.0.6b2}/risk/network/graph.py

@@ -101,31 +101,32 @@ class NetworkGraph:
 
     def get_domain_colors(
         self,
+        cmap: str = "gist_rainbow",
+        color: Union[str, None] = None,
         min_scale: float = 0.8,
         max_scale: float = 1.0,
         scale_factor: float = 1.0,
         random_seed: int = 888,
-        **kwargs,
     ) -> np.ndarray:
-        """Generate composite colors for domains.
-
-        This method generates composite colors for nodes based on their enrichment scores and transforms
-        them to ensure proper alpha values and intensity. For nodes with alpha == 0, it assigns new colors
-        based on the closest valid neighbors within a specified distance.
+        """Generate composite colors for domains based on enrichment or specified colors.
 
         Args:
-            min_scale (float, optional): Minimum scale for color intensity. Defaults to 0.8.
-            max_scale (float, optional): Maximum scale for color intensity. Defaults to 1.0.
-            scale_factor (float, optional): Exponent for scaling, where values > 1 increase contrast by dimming small
-                values more. Defaults to 1.0.
-            random_seed (int, optional): Seed for random number generation. Defaults to 888.
-            **kwargs: Additional keyword arguments for color generation.
+            cmap (str, optional): Name of the colormap to use for generating domain colors. Defaults to "gist_rainbow".
+            color (str or None, optional): A specific color to use for all generated colors. Defaults to None.
+            min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap.
+                Controls the dimmest colors. Defaults to 0.8.
+            max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap.
+                Controls the brightest colors. Defaults to 1.0.
+            scale_factor (float, optional): Exponent for adjusting the color scaling based on enrichment scores.
+                A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
+            random_seed (int, optional): Seed for random number generation to ensure reproducibility of color assignments.
+                Defaults to 888.
 
         Returns:
-            np.ndarray: Array of transformed colors.
+            np.ndarray: Array of RGBA colors generated for each domain, based on enrichment or the specified color.
         """
         # Get colors for each domain
-        domain_colors = self._get_domain_colors(random_seed=random_seed)
+        domain_colors = self._get_domain_colors(cmap=cmap, color=color, random_seed=random_seed)
         # Generate composite colors for nodes
         node_colors = self._get_composite_node_colors(domain_colors)
         # Transform colors to ensure proper alpha values and intensity
@@ -161,12 +162,16 @@ class NetworkGraph:
         return composite_colors
 
     def _get_domain_colors(
-        self, color: Union[str, None] = None, random_seed: int = 888
+        self,
+        cmap: str = "gist_rainbow",
+        color: Union[str, None] = None,
+        random_seed: int = 888,
     ) -> Dict[str, Any]:
         """Get colors for each domain.
 
         Args:
-            color (Union[str, None], optional): Specific color to use for all domains. If specified, it will overwrite the colormap.
+            cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
+            color (str or None, optional): A specific color to use for all generated colors. Defaults to None.
             random_seed (int, optional): Seed for random number generation. Defaults to 888.
 
         Returns:
@@ -178,7 +183,7 @@ class NetworkGraph:
         ]
         domains = np.sort(numeric_domains)
         domain_colors = _get_colors(
-            num_colors_to_generate=len(domains), color=color, random_seed=random_seed
+            num_colors_to_generate=len(domains), cmap=cmap, color=color, random_seed=random_seed
         )
         return dict(zip(self.domain_to_nodes.keys(), domain_colors))
 
@@ -273,17 +278,17 @@ def _extract_node_coordinates(G: nx.Graph) -> np.ndarray:
 
 def _get_colors(
     num_colors_to_generate: int = 10,
-    cmap: str = "hsv",
-    random_seed: int = 888,
+    cmap: str = "gist_rainbow",
     color: Union[str, None] = None,
+    random_seed: int = 888,
 ) -> List[Tuple]:
     """Generate a list of RGBA colors from a specified colormap or use a direct color string.
 
     Args:
         num_colors_to_generate (int): The number of colors to generate. Defaults to 10.
-        cmap (str): The name of the colormap to use. Defaults to "hsv".
+        cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
+        color (str or None, optional): A specific color to use for all generated colors.
         random_seed (int): Seed for random number generation. Defaults to 888.
-        color (str, optional): Specific color to use for all nodes. If specified, it will overwrite the colormap.
             Defaults to None.
 
     Returns:

{risk_network-0.0.6b0 → risk_network-0.0.6b2}/risk/network/io.py

@@ -48,6 +48,7 @@ class NetworkIO:
         self.min_edges_per_node = min_edges_per_node
         self.include_edge_weight = include_edge_weight
         self.weight_label = weight_label
+        # Log the initialization of the NetworkIO class
         params.log_network(
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
@@ -98,11 +99,14 @@ class NetworkIO:
             nx.Graph: Loaded and processed network.
         """
         filetype = "GPickle"
+        # Log the loading of the GPickle file
         params.log_network(filetype=filetype, filepath=filepath)
         self._log_loading(filetype, filepath=filepath)
+
         with open(filepath, "rb") as f:
             G = pickle.load(f)
 
+        # Initialize the graph
         return self._initialize_graph(G)
 
     @classmethod
@@ -147,8 +151,11 @@ class NetworkIO:
             nx.Graph: Processed network.
         """
         filetype = "NetworkX"
+        # Log the loading of the NetworkX graph
         params.log_network(filetype=filetype)
         self._log_loading(filetype)
+
+        # Initialize the graph
         return self._initialize_graph(network)
 
     @classmethod
@@ -213,8 +220,10 @@ class NetworkIO:
             nx.Graph: Loaded and processed network.
         """
         filetype = "Cytoscape"
+        # Log the loading of the Cytoscape file
         params.log_network(filetype=filetype, filepath=str(filepath))
         self._log_loading(filetype, filepath=filepath)
+
         cys_files = []
         tmp_dir = ".tmp_cytoscape"
         # Try / finally to remove unzipped files
@@ -295,6 +304,7 @@ class NetworkIO:
                     node
                 ]  # Assuming you have a dict `node_y_positions` for y coordinates
 
+            # Initialize the graph
             return self._initialize_graph(G)
 
         finally:
@@ -354,6 +364,7 @@ class NetworkIO:
             NetworkX graph: Loaded and processed network.
         """
         filetype = "Cytoscape JSON"
+        # Log the loading of the Cytoscape JSON file
         params.log_network(filetype=filetype, filepath=str(filepath))
         self._log_loading(filetype, filepath=filepath)