risk-network 0.0.2__tar.gz → 0.0.3__tar.gz

{risk_network-0.0.2 → risk_network-0.0.3}/MANIFEST.in

@@ -1,6 +1,5 @@
-# Include all Python and Cython source files
+# Include all Python source files
 recursive-include risk *.py
-recursive-include risk *.pyx
 
 # Include important project files in the distribution
 include README.md

{risk_network-0.0.2 → risk_network-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.2
+Version: 0.0.3
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -694,13 +694,13 @@ Classifier: Development Status :: 4 - Beta
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: cython
 Requires-Dist: ipywidgets
 Requires-Dist: markov_clustering
 Requires-Dist: matplotlib
 Requires-Dist: networkx
 Requires-Dist: nltk==3.8.1
 Requires-Dist: numpy
+Requires-Dist: openpyxl
 Requires-Dist: pandas
 Requires-Dist: python-louvain
 Requires-Dist: scikit-learn
@@ -709,15 +709,21 @@ Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 
-# RISK
-
-<ins>Regional Inference of Significant Kinships</ins>
+<p align="center">
+  <img src="./docs/github/risk-logo-dark.png#gh-dark-mode-only" width="400" />
+  <img src="./docs/github/risk-logo-light.png#gh-light-mode-only" width="400" />
+</p>
 
-<p align="left">
-    <img src="./docs/github/risk-logo-dark.png#gh-dark-mode-only" width="40%" />
-    <img src="./docs/github/risk-logo-light.png#gh-light-mode-only" width="40%" />
+<p align="center">
+  <a href="https://pypi.python.org/pypi/risk-network"><img src="https://img.shields.io/pypi/v/risk-network.svg" alt="pypiv"></a>
+  <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/python-3.7+-blue.svg" alt="Python 3.7+"></a>
+  <a href="https://raw.githubusercontent.com/irahorecka/chrono24/main/LICENSE"><img src="https://img.shields.io/badge/License-GPLv3-blue.svg" alt="License: GPL v3"></a>
 </p>
 
+## RISK
+
+#### Regional Inference of Significant Kinships
+
 RISK is a software tool for visualizing spatial relationships in networks. It aims to enhance network analysis by integrating advanced network annotation algorithms, such as Louvain and Markov Clustering, to identify key functional modules and pathways.
 
 ## Features
@@ -730,7 +736,7 @@ RISK is a software tool for visualizing spatial relationships in networks. It ai
 
 *Saccharomyces cerevisiae* proteins oriented by physical interactions discovered through affinity enrichment and mass spectrometry (Michaelis et al., 2023).
 
-![Metabolic Network Demo](./docs/github/network.png)
+![PPI Network Demo](./docs/github/network.png)
 
 ## Installation
 

risk_network-0.0.3/README.md

@@ -0,0 +1,40 @@
+<p align="center">
+  <img src="./docs/github/risk-logo-dark.png#gh-dark-mode-only" width="400" />
+  <img src="./docs/github/risk-logo-light.png#gh-light-mode-only" width="400" />
+</p>
+
+<p align="center">
+  <a href="https://pypi.python.org/pypi/risk-network"><img src="https://img.shields.io/pypi/v/risk-network.svg" alt="pypiv"></a>
+  <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/python-3.7+-blue.svg" alt="Python 3.7+"></a>
+  <a href="https://raw.githubusercontent.com/irahorecka/chrono24/main/LICENSE"><img src="https://img.shields.io/badge/License-GPLv3-blue.svg" alt="License: GPL v3"></a>
+</p>
+
+## RISK
+
+#### Regional Inference of Significant Kinships
+
+RISK is a software tool for visualizing spatial relationships in networks. It aims to enhance network analysis by integrating advanced network annotation algorithms, such as Louvain and Markov Clustering, to identify key functional modules and pathways.
+
+## Features
+
+- Spatial analysis of biological networks
+- Functional enrichment detection
+- Optimized performance
+
+## Example
+
+*Saccharomyces cerevisiae* proteins oriented by physical interactions discovered through affinity enrichment and mass spectrometry (Michaelis et al., 2023).
+
+![PPI Network Demo](./docs/github/network.png)
+
+## Installation
+
+Coming soon...
+
+## Usage
+
+Coming soon...
+
+## License
+
+This project is licensed under the GPL-3.0 license.

{risk_network-0.0.2 → risk_network-0.0.3}/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel", "Cython", "numpy"]
+requires = ["setuptools", "wheel", "numpy"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -26,13 +26,13 @@ classifiers = [
     "Development Status :: 4 - Beta",
 ]
 dependencies = [
-    "cython",
     "ipywidgets",
     "markov_clustering",
     "matplotlib",
     "networkx",
     "nltk==3.8.1",
     "numpy",
+    "openpyxl",
     "pandas",
     "python-louvain",
     "scikit-learn",

{risk_network-0.0.2 → risk_network-0.0.3}/risk/__init__.py

@@ -10,4 +10,4 @@ RISK: RISK Infers Spatial Kinship
 
 from risk.risk import RISK
 
-__version__ = "0.0.2"
+__version__ = "0.0.3"

{risk_network-0.0.2 → risk_network-0.0.3}/risk/annotations/annotations.py

@@ -139,15 +139,15 @@ def define_top_annotations(
                 size_connected_components <= max_cluster_size,
             )
         )
-        annotations_enrichment_matrix.loc[
-            attribute, "num connected components"
-        ] = num_connected_components
-        annotations_enrichment_matrix.at[
-            attribute, "size connected components"
-        ] = size_connected_components
-        annotations_enrichment_matrix.loc[
-            attribute, "num large connected components"
-        ] = num_large_connected_components
+        annotations_enrichment_matrix.loc[attribute, "num connected components"] = (
+            num_connected_components
+        )
+        annotations_enrichment_matrix.at[attribute, "size connected components"] = (
+            size_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[

{risk_network-0.0.2 → risk_network-0.0.3}/risk/annotations/io.py

@@ -45,66 +45,70 @@ class AnnotationsIO:
         # Process the JSON data and return it in the context of the network
         return load_annotations(network, annotations_input)
 
-    def load_csv_annotation(
+    def load_excel_annotation(
         self,
         filepath: str,
         network: nx.Graph,
         label_colname: str = "label",
         nodes_colname: str = "nodes",
-        delimiter: str = ";",
+        sheet_name: str = "Sheet1",
+        nodes_delimiter: str = ";",
     ) -> Dict[str, Any]:
-        """Load annotations from a CSV file and convert them to a DataFrame.
+        """Load annotations from an Excel file and associate them with the network.
 
         Args:
-            filepath (str): Path to the CSV annotations file.
-            network (NetworkX graph): The network to which the annotations are related.
-            label_colname (str): Name of the column containing the labels.
-            nodes_colname (str): Name of the column containing the nodes.
-            delimiter (str): Delimiter used to parse the nodes column (default is ';').
+            filepath (str): Path to the Excel annotations file.
+            network (nx.Graph): The NetworkX graph to which the annotations are related.
+            label_colname (str): Name of the column containing the labels (e.g., GO terms).
+            nodes_colname (str): Name of the column containing the nodes associated with each label.
+            sheet_name (str, optional): The name of the Excel sheet to load (default is 'Sheet1').
+            nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
 
         Returns:
-            pd.DataFrame: DataFrame containing the labels and parsed nodes.
+            Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes,
+                            linked to the provided network.
         """
-        filetype = "CSV"
+        filetype = "Excel"
         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)
-        # Process and return the annotations in the context of the network
-        return load_annotations(network, annotations_input)
+        # 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()
+        return load_annotations(network, label_node_dict)
 
-    def load_excel_annotation(
+    def load_csv_annotation(
         self,
         filepath: str,
         network: nx.Graph,
         label_colname: str = "label",
         nodes_colname: str = "nodes",
-        sheet_name: str = "Sheet1",
-        delimiter: str = ";",
+        nodes_delimiter: str = ";",
     ) -> Dict[str, Any]:
-        """Load annotations from an Excel file and convert them to a dictionary.
+        """Load annotations from a CSV file and associate them with the network.
 
         Args:
-            filepath (str): Path to the Excel annotations file.
-            network (NetworkX graph): The network to which the annotations are related.
-            label_colname (str): Name of the column containing the labels.
-            nodes_colname (str): Name of the column containing the nodes.
-            sheet_name (str): The name of the Excel sheet to load (default is 'Sheet1').
-            delimiter (str): Delimiter used to parse the nodes column (default is ';').
+            filepath (str): Path to the CSV annotations file.
+            network (nx.Graph): The NetworkX graph to which the annotations are related.
+            label_colname (str): Name of the column containing the labels (e.g., GO terms).
+            nodes_colname (str): Name of the column containing the nodes associated with each label.
+            nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
 
         Returns:
-            dict: A dictionary where each label is paired with its respective list of nodes.
+            Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes,
+                            linked to the provided network.
         """
-        filetype = "Excel"
+        filetype = "CSV"
         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 delimiter
-        df[nodes_colname] = df[nodes_colname].apply(lambda x: x.split(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()
-        return load_annotations(network, label_node_dict)
+        # 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
+        return load_annotations(network, annotations_input)
 
     def load_tsv_annotation(
         self,
@@ -112,47 +116,56 @@ class AnnotationsIO:
         network: nx.Graph,
         label_colname: str = "label",
         nodes_colname: str = "nodes",
+        nodes_delimiter: str = ";",
     ) -> Dict[str, Any]:
-        """Load annotations from a TSV file and convert them to a DataFrame.
+        """Load annotations from a TSV file and associate them with the network.
 
         Args:
             filepath (str): Path to the TSV annotations file.
-            network (NetworkX graph): The network to which the annotations are related.
-            label_colname (str): Name of the column containing the labels.
-            nodes_colname (str): Name of the column containing the nodes.
+            network (nx.Graph): The NetworkX graph to which the annotations are related.
+            label_colname (str): Name of the column containing the labels (e.g., GO terms).
+            nodes_colname (str): Name of the column containing the nodes associated with each label.
+            nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
 
         Returns:
-            pd.DataFrame: DataFrame containing the labels and parsed nodes.
+            Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes,
+                            linked to the provided network.
         """
         filetype = "TSV"
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
-        # Load the TSV file with tab delimiter and convert to dictionary
+        # Load the TSV file into a dictionary
         annotations_input = _load_matrix_file(
-            filepath, label_colname, nodes_colname, delimiter="\t"
+            filepath, label_colname, nodes_colname, delimiter="\t", nodes_delimiter=nodes_delimiter
         )
         # Process and return the annotations in the context of the network
         return load_annotations(network, annotations_input)
 
 
 def _load_matrix_file(
-    filepath: str, label_colname: str, nodes_colname: str, delimiter: str = ";"
+    filepath: str,
+    label_colname: str,
+    nodes_colname: str,
+    delimiter: str = ",",
+    nodes_delimiter: str = ";",
 ) -> Dict[str, Any]:
     """Load annotations from a CSV or TSV file and convert them to a dictionary.
 
     Args:
         filepath (str): Path to the annotation file.
-        label_colname (str): Name of the column containing the labels.
-        nodes_colname (str): Name of the column containing the nodes.
-        delimiter (str): Delimiter used to parse the nodes column (default is ';').
+        label_colname (str): Name of the column containing the labels (e.g., GO terms).
+        nodes_colname (str): Name of the column containing the nodes associated with each label.
+        delimiter (str, optional): Delimiter used to separate columns in the file (default is ',').
+        nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
 
     Returns:
-        dict: A dictionary where each label is paired with its respective list of nodes.
+        Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes.
     """
-    df = pd.read_csv(filepath)
-    # Split the nodes column by the delimiter
-    df[nodes_colname] = df[nodes_colname].apply(lambda x: x.split(delimiter))
-    # Create a dictionary pairing labels with their corresponding nodes
+    # Load the CSV or TSV file into a DataFrame
+    df = pd.read_csv(filepath, delimiter=delimiter)
+    # Split the nodes column by the nodes_delimiter to handle multiple nodes per label
+    df[nodes_colname] = df[nodes_colname].apply(lambda x: x.split(nodes_delimiter))
+    # Create a dictionary pairing labels with their corresponding list of nodes
     label_node_dict = df.set_index(label_colname)[nodes_colname].to_dict()
     return label_node_dict
 

{risk_network-0.0.2 → risk_network-0.0.3}/risk/log/params.py

@@ -147,14 +147,11 @@ class Params:
         params = self.load()
         # Open the file in write mode
         with open(filepath, "w") as txt_file:
-            for key, nested_dict in params.items():
-                # Write the key
-                txt_file.write(f"{key}:\n")
-                # Write the nested dictionary values, one per line
-                for nested_key, nested_value in nested_dict.items():
-                    txt_file.write(f"  {nested_key}: {nested_value}\n")
-                # Add a blank line between different keys
-                txt_file.write("\n")
+            for key, value in params.items():
+                # Write the key and its corresponding value
+                txt_file.write(f"{key}: {value}\n")
+            # Add a blank line after each entry
+            txt_file.write("\n")
 
     def load(self) -> Dict[str, Any]:
         """Load and process various parameters, converting any np.ndarray values to lists.

risk_network-0.0.2/risk/neighborhoods/graph.py → risk_network-0.0.3/risk/neighborhoods/community.py

@@ -1,6 +1,6 @@
 """
-risk/neighborhoods/graph
-~~~~~~~~~~~~~~~~~~~~~~~~
+risk/neighborhoods/community
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 import community as community_louvain

{risk_network-0.0.2 → risk_network-0.0.3}/risk/neighborhoods/neighborhoods.py

@@ -10,7 +10,7 @@ import networkx as nx
 import numpy as np
 from sklearn.exceptions import DataConversionWarning
 
-from risk.neighborhoods.graph import (
+from risk.neighborhoods.community import (
     calculate_dijkstra_neighborhoods,
     calculate_label_propagation_neighborhoods,
     calculate_louvain_neighborhoods,

{risk_network-0.0.2 → risk_network-0.0.3}/risk/network/io.py

@@ -29,9 +29,6 @@ class NetworkIO:
         self,
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
-        distance_metric: str = "dijkstra",
-        edge_length_threshold: float = 0.5,
-        louvain_resolution: float = 0.1,
         min_edges_per_node: int = 0,
         include_edge_weight: bool = True,
         weight_label: str = "weight",
@@ -40,9 +37,6 @@ class NetworkIO:
         self.surface_depth = surface_depth
         self.include_edge_weight = include_edge_weight
         self.weight_label = weight_label
-        self.distance_metric = distance_metric
-        self.edge_length_threshold = edge_length_threshold
-        self.louvain_resolution = louvain_resolution
         self.min_edges_per_node = min_edges_per_node
 
     def load_gpickle_network(self, filepath: str) -> nx.Graph:
@@ -317,10 +311,9 @@ class NetworkIO:
         print(f"Filetype: {filetype}")
         if filepath:
             print(f"Filepath: {filepath}")
-        print(f"Project to sphere: {self.compute_sphere}")
+        print(f"Projection: {'Sphere' if self.compute_sphere else 'Plane'}")
         if self.compute_sphere:
             print(f"Surface depth: {self.surface_depth}")
-        print(f"Edge length threshold: {self.edge_length_threshold}")
-        print(f"Include edge weights: {self.include_edge_weight}")
+        print(f"Edge weight: {'Included' if self.include_edge_weight else 'Excluded'}")
         if self.include_edge_weight:
             print(f"Weight label: {self.weight_label}")

{risk_network-0.0.2 → risk_network-0.0.3}/risk/network/plot.py

@@ -45,21 +45,24 @@ class NetworkPlotter:
             outline_scale (float, optional): Outline scaling factor for the perimeter diameter. Defaults to 1.0.
         """
         self.network_graph = network_graph
-        self.ax = None  # Initialize the axis attribute
-        # Initialize the plot with the given parameters
-        self._initialize_plot(figsize, background_color, plot_outline, outline_color, outline_scale)
+        # Initialize the plot with the specified parameters
+        self.ax = self._initialize_plot(
+            network_graph, figsize, background_color, plot_outline, outline_color, outline_scale
+        )
 
     def _initialize_plot(
         self,
+        network_graph: NetworkGraph,
         figsize: tuple,
         background_color: str,
         plot_outline: bool,
         outline_color: str,
         outline_scale: float,
-    ) -> tuple:
+    ) -> plt.Axes:
         """Set up the plot with figure size, optional circle perimeter, and background color.
 
         Args:
+            network_graph (NetworkGraph): The network data and attributes to be visualized.
             figsize (tuple): Size of the figure in inches (width, height).
             background_color (str): Background color of the plot.
             plot_outline (bool): Whether to plot the network perimeter circle.
@@ -67,10 +70,10 @@ class NetworkPlotter:
             outline_scale (float): Outline scaling factor for the perimeter diameter.
 
         Returns:
-            tuple: The created matplotlib figure and axis.
+            plt.Axes: The axis object for the plot.
         """
         # Extract node coordinates from the network graph
-        node_coordinates = self.network_graph.node_coordinates
+        node_coordinates = network_graph.node_coordinates
         # Calculate the center and radius of the bounding box around the network
         center, radius = _calculate_bounding_box(node_coordinates)
         # Scale the radius by the outline_scale factor
@@ -107,9 +110,7 @@ class NetworkPlotter:
         ax.set_yticks([])
         ax.patch.set_visible(False)  # Hide the axis background
 
-        # Store the axis for further use and return the figure and axis
-        self.ax = ax
-        return fig, ax
+        return ax
 
     def plot_network(
         self,
@@ -401,7 +402,7 @@ class NetworkPlotter:
         fontcolor: Union[str, np.ndarray] = "black",
         arrow_linewidth: float = 1,
         arrow_color: Union[str, np.ndarray] = "black",
-        num_words: int = 10,
+        max_words: int = 10,
         min_words: int = 1,
     ) -> None:
         """Annotate the network graph with labels for different domains, positioned around the network for clarity.
@@ -414,7 +415,7 @@ class NetworkPlotter:
             fontcolor (str or np.ndarray, optional): Color of the label text. Can be a string or RGBA array. Defaults to "black".
             arrow_linewidth (float, optional): Line width of the arrows pointing to centroids. Defaults to 1.
             arrow_color (str or np.ndarray, optional): Color of the arrows. Can be a string or RGBA array. Defaults to "black".
-            num_words (int, optional): Maximum number of words in a label. Defaults to 10.
+            max_words (int, optional): Maximum number of words in a label. Defaults to 10.
             min_words (int, optional): Minimum number of words required to display a label. Defaults to 1.
         """
         # Log the plotting parameters
@@ -426,7 +427,7 @@ class NetworkPlotter:
             label_fontcolor="custom" if isinstance(fontcolor, np.ndarray) else fontcolor,
             label_arrow_linewidth=arrow_linewidth,
             label_arrow_color="custom" if isinstance(arrow_color, np.ndarray) else arrow_color,
-            label_num_words=num_words,
+            label_max_words=max_words,
             label_min_words=min_words,
         )
         # Convert color strings to RGBA arrays if necessary
@@ -436,7 +437,12 @@ class NetworkPlotter:
             arrow_color = self.get_annotated_contour_colors(color=arrow_color)
 
         # Calculate the center and radius of the network
-        domain_centroids = self._calculate_domain_centroids()
+        domain_centroids = {}
+        for domain, nodes in self.network_graph.domain_to_nodes.items():
+            if nodes:  # Skip if the domain has no nodes
+                domain_centroids[domain] = self._calculate_domain_centroid(nodes)
+
+        # Calculate the bounding box around the network
         center, radius = _calculate_bounding_box(
             self.network_graph.node_coordinates, radius_margin=perimeter_scale
         )
@@ -445,7 +451,7 @@ class NetworkPlotter:
         filtered_domains = {
             domain: centroid
             for domain, centroid in domain_centroids.items()
-            if len(self.network_graph.trimmed_domain_to_term[domain].split(" ")[:num_words])
+            if len(self.network_graph.trimmed_domain_to_term[domain].split(" ")[:max_words])
             >= min_words
         }
         # Calculate the best positions for labels around the perimeter
@@ -453,7 +459,7 @@ class NetworkPlotter:
         # Annotate the network with labels
         for idx, (domain, pos) in enumerate(best_label_positions.items()):
             centroid = filtered_domains[domain]
-            annotations = self.network_graph.trimmed_domain_to_term[domain].split(" ")[:num_words]
+            annotations = self.network_graph.trimmed_domain_to_term[domain].split(" ")[:max_words]
             self.ax.annotate(
                 "\n".join(annotations),
                 xy=centroid,
@@ -467,31 +473,26 @@ class NetworkPlotter:
                 arrowprops=dict(arrowstyle="->", color=arrow_color[idx], linewidth=arrow_linewidth),
             )
 
-    def _calculate_domain_centroids(self) -> Dict[Any, np.ndarray]:
-        """Calculate the most centrally located node within each domain based on the node positions.
+    def _calculate_domain_centroid(self, nodes: list) -> tuple:
+        """Calculate the most centrally located node in .
+
+        Args:
+            nodes (list): List of node labels to include in the subnetwork.
 
         Returns:
-            Dict[Any, np.ndarray]: A dictionary mapping each domain to its central node's coordinates.
+            tuple: A tuple containing the domain's central node coordinates.
         """
-        domain_central_nodes = {}
-        for domain, nodes in self.network_graph.domain_to_nodes.items():
-            if not nodes:  # Skip if the domain has no nodes
-                continue
-
-            # Extract positions of all nodes in the domain
-            node_positions = self.network_graph.node_coordinates[nodes, :]
-            # Calculate the pairwise distance matrix between all nodes in the domain
-            distances_matrix = np.linalg.norm(
-                node_positions[:, np.newaxis] - node_positions, axis=2
-            )
-            # Sum the distances for each node to all other nodes in the domain
-            sum_distances = np.sum(distances_matrix, axis=1)
-            # Identify the node with the smallest total distance to others (the centroid)
-            central_node_idx = np.argmin(sum_distances)
-            # Map the domain to the coordinates of its central node
-            domain_central_nodes[domain] = node_positions[central_node_idx]
-
-        return domain_central_nodes
+        # Extract positions of all nodes in the domain
+        node_positions = self.network_graph.node_coordinates[nodes, :]
+        # Calculate the pairwise distance matrix between all nodes in the domain
+        distances_matrix = np.linalg.norm(node_positions[:, np.newaxis] - node_positions, axis=2)
+        # Sum the distances for each node to all other nodes in the domain
+        sum_distances = np.sum(distances_matrix, axis=1)
+        # Identify the node with the smallest total distance to others (the centroid)
+        central_node_idx = np.argmin(sum_distances)
+        # Map the domain to the coordinates of its central node
+        domain_central_node = node_positions[central_node_idx]
+        return domain_central_node
 
     def get_annotated_node_colors(
         self, nonenriched_color: str = "white", random_seed: int = 888, **kwargs
@@ -604,16 +605,6 @@ class NetworkPlotter:
 
         return np.array(annotated_colors)
 
-    @staticmethod
-    def close(*args, **kwargs) -> None:
-        """Close the current plot.
-
-        Args:
-            *args: Positional arguments passed to `plt.close`.
-            **kwargs: Keyword arguments passed to `plt.close`.
-        """
-        plt.close(*args, **kwargs)
-
     @staticmethod
     def savefig(*args, **kwargs) -> None:
         """Save the current plot to a file.