risk-network 0.0.6b9__tar.gz → 0.0.7b0__tar.gz

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.6b9
+Version: 0.0.7b0
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.6-beta.9"
+__version__ = "0.0.7-beta.0"

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/risk/annotations/annotations.py

@@ -132,27 +132,32 @@ def define_top_annotations(
             nx.connected_components(enriched_network), key=len, reverse=True
         )
         size_connected_components = np.array([len(c) for c in connected_components])
+
+        # Filter the size of connected components by min_cluster_size and max_cluster_size
+        filtered_size_connected_components = size_connected_components[
+            (size_connected_components >= min_cluster_size)
+            & (size_connected_components <= max_cluster_size)
+        ]
+        # Calculate the number of connected components and large connected components
         num_connected_components = len(connected_components)
-        num_large_connected_components = np.sum(
-            np.logical_and(
-                size_connected_components >= min_cluster_size,
-                size_connected_components <= max_cluster_size,
-            )
-        )
+        num_large_connected_components = len(filtered_size_connected_components)
+
+        # Assign the number of connected components
         annotations_enrichment_matrix.loc[attribute, "num connected components"] = (
             num_connected_components
         )
-        annotations_enrichment_matrix.at[attribute, "size connected components"] = (
-            size_connected_components
-        )
+        # Filter out attributes with more than one connected component
+        annotations_enrichment_matrix.loc[
+            annotations_enrichment_matrix["num connected components"] > 1, "top attributes"
+        ] = False
+        # Assign the number of large connected components
         annotations_enrichment_matrix.loc[attribute, "num large connected components"] = (
             num_large_connected_components
         )
-
-    # Filter out attributes with more than one connected component
-    annotations_enrichment_matrix.loc[
-        annotations_enrichment_matrix["num connected components"] > 1, "top attributes"
-    ] = False
+        # Assign the size of connected components, ensuring it is always a list
+        annotations_enrichment_matrix.at[attribute, "size connected components"] = (
+            filtered_size_connected_components.tolist()
+        )
 
     return annotations_enrichment_matrix
 

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/risk/log/params.py

@@ -7,6 +7,7 @@ import csv
 import json
 import warnings
 from datetime import datetime
+from functools import wraps
 from typing import Any, Dict
 
 import numpy as np
@@ -27,6 +28,7 @@ def _safe_param_export(func):
         function: The wrapped function with error handling.
     """
 
+    @wraps(func)
     def wrapper(*args, **kwargs):
         try:
             result = func(*args, **kwargs)

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/risk/neighborhoods/domains.py

@@ -23,7 +23,8 @@ def define_domains(
     linkage_method: str,
     linkage_metric: str,
 ) -> pd.DataFrame:
-    """Define domains and assign nodes to these domains based on their enrichment scores and clustering.
+    """Define domains and assign nodes to these domains based on their enrichment scores and clustering,
+    handling errors by assigning unique domains when clustering fails.
 
     Args:
         top_annotations (pd.DataFrame): DataFrame of top annotations data for the network nodes.
@@ -35,31 +36,29 @@ def define_domains(
     Returns:
         pd.DataFrame: DataFrame with the primary domain for each node.
     """
-    # Check if there's more than one column in significant_neighborhoods_enrichment
-    if significant_neighborhoods_enrichment.shape[1] == 1:
-        print("Single annotation detected. Skipping clustering.")
-        top_annotations["domain"] = 1  # Assign a default domain or handle appropriately
-    else:
-        # Perform hierarchical clustering on the binary enrichment matrix
+    try:
+        # Transpose the matrix to cluster annotations
         m = significant_neighborhoods_enrichment[:, top_annotations["top attributes"]].T
         best_linkage, best_metric, best_threshold = _optimize_silhouette_across_linkage_and_metrics(
             m, linkage_criterion, linkage_method, linkage_metric
         )
-        try:
-            Z = linkage(m, method=best_linkage, metric=best_metric)
-        except ValueError as e:
-            raise ValueError("No significant annotations found.") from e
-
+        # Perform hierarchical clustering
+        Z = linkage(m, method=best_linkage, metric=best_metric)
         print(
             f"Linkage criterion: '{linkage_criterion}'\nLinkage method: '{best_linkage}'\nLinkage metric: '{best_metric}'"
         )
         print(f"Optimal linkage threshold: {round(best_threshold, 3)}")
-
+        # Calculate the optimal threshold for clustering
         max_d_optimal = np.max(Z[:, 2]) * best_threshold
-        domains = fcluster(Z, max_d_optimal, criterion=linkage_criterion)
         # Assign domains to the annotations matrix
+        domains = fcluster(Z, max_d_optimal, criterion=linkage_criterion)
         top_annotations["domain"] = 0
         top_annotations.loc[top_annotations["top attributes"], "domain"] = domains
+    except ValueError:
+        # If a ValueError is encountered, handle it by assigning unique domains
+        n_rows = len(top_annotations)
+        print(f"Error encountered. Skipping clustering and assigning {n_rows} unique domains.")
+        top_annotations["domain"] = range(1, n_rows + 1)  # Assign unique domains
 
     # Create DataFrames to store domain information
     node_to_enrichment = pd.DataFrame(

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/risk/network/plot.py

@@ -1123,7 +1123,9 @@ def _to_rgba(
     """
     # Handle single color case (string, RGB, or RGBA)
     if isinstance(color, str) or (
-        isinstance(color, (list, tuple, np.ndarray)) and len(color) in [3, 4]
+        isinstance(color, (list, tuple, np.ndarray))
+        and len(color) in [3, 4]
+        and not any(isinstance(c, (list, tuple, np.ndarray)) for c in color)
     ):
         rgba_color = np.array(mcolors.to_rgba(color))
         # Only set alpha if the input is an RGB color or a string (not RGBA)

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/risk/risk.py

@@ -62,7 +62,7 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (pd.DataFrame): The matrix of annotations associated with the network.
+            annotations (dict): The annotations associated with the network.
             distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "dijkstra".
             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.
@@ -131,7 +131,7 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (pd.DataFrame): The matrix of annotations associated with the network.
+            annotations (dict): The annotations associated with the network.
             distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "dijkstra".
             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.
@@ -187,7 +187,7 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (pd.DataFrame): The matrix of annotations associated with the network.
+            annotations (dict): The annotations associated with the network.
             distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "dijkstra".
             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.

{risk_network-0.0.6b9 → risk_network-0.0.7b0}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.6b9
+Version: 0.0.7b0
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>