risk-network 0.0.8b27__py3-none-any.whl → 0.0.9__py3-none-any.whl

{risk_network-0.0.8b27.dist-info → risk_network-0.0.9.dist-info}/METADATA

@@ -1,10 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.8b27
+Version: 0.0.9
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
-License: GNU GENERAL PUBLIC LICENSE
+License:                     GNU GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
         
          Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
@@ -695,19 +695,23 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ipywidgets
-Requires-Dist: markov-clustering
+Requires-Dist: leidenalg
+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-igraph
 Requires-Dist: python-louvain
 Requires-Dist: scikit-learn
 Requires-Dist: scipy
 Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
+Dynamic: author
+Dynamic: requires-python
 
 # RISK Network
 
@@ -724,78 +728,59 @@ Requires-Dist: tqdm
 ![Downloads](https://img.shields.io/pypi/dm/risk-network)
 ![Platforms](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey)
 
-**RISK (RISK Infers Spatial Kinships)** is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
+**RISK** (Regional Inference of Significant Kinships) is a next-generation tool for biological network annotation and visualization. RISK integrates community detection-based clustering, rigorous statistical enrichment analysis, and a modular framework to uncover biologically meaningful relationships and generate high-resolution visualizations. RISK supports diverse data formats and is optimized for large-scale network analysis, making it a valuable resource for researchers in systems biology and beyond.
 
 ## Documentation and Tutorial
 
-- **Documentation**: Comprehensive documentation is available [here](Documentation link).
-- **Tutorial**: An interactive Jupyter notebook tutorial can be found [here](https://github.com/riskportal/network-tutorial).
-We highly recommend new users to consult the documentation and tutorial early on to fully leverage RISK's capabilities.
+An interactive Jupyter notebook tutorial can be found [here](https://github.com/riskportal/network-tutorial). We highly recommend new users to consult the documentation and tutorial early on to fully utilize RISK's capabilities.
 
 ## Installation
 
-RISK is compatible with Python 3.8 and later versions and operates on all major operating systems. Install RISK via pip:
+RISK is compatible with Python 3.8 or later and runs on all major operating systems. To install the latest version of RISK, run:
 
 ```bash
-pip install risk-network
+pip install risk-network --upgrade
 ```
 
 ## Features
 
-- **Comprehensive Network Analysis**: Analyze biological networks such as protein–protein interaction (PPI) and gene regulatory networks, as well as non-biological networks.
-- **Advanced Clustering Algorithms**: Utilize algorithms like Louvain, Markov Clustering, Spinglass, and more to identify key functional modules.
-- **Flexible Visualization**: Generate clear, publication-quality figures with customizable node and edge attributes, including colors, shapes, sizes, and labels.
-- **Efficient Data Handling**: Optimized for large datasets, supporting multiple file formats such as JSON, CSV, TSV, Excel, Cytoscape, and GPickle.
-- **Statistical Analysis**: Integrated statistical tests, including hypergeometric, permutation, and Poisson tests, to assess the significance of enriched regions.
+- **Comprehensive Network Analysis**: Analyze biological networks (e.g., protein–protein interaction and genetic interaction networks) as well as non-biological networks.
+- **Advanced Clustering Algorithms**: Supports Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap for identifying structured network regions.
+- **Flexible Visualization**: Produce customizable, high-resolution network visualizations with kernel density estimate overlays, adjustable node and edge attributes, and export options in SVG, PNG, and PDF formats.
+- **Efficient Data Handling**: Supports multiple input/output formats, including JSON, CSV, TSV, Excel, Cytoscape, and GPickle.
+- **Statistical Analysis**: Assess functional enrichment using hypergeometric, permutation, binomial, chi-squared, Poisson, and z-score tests, ensuring statistical adaptability across datasets.
 - **Cross-Domain Applicability**: Suitable for network analysis across biological and non-biological domains, including social and communication networks.
 
 ## Example Usage
 
-We applied RISK to a *Saccharomyces cerevisiae* protein–protein interaction network, revealing both established and novel functional relationships. The visualization below highlights key biological processes such as ribosomal assembly and mitochondrial organization.
+We applied RISK to a *Saccharomyces cerevisiae* protein–protein interaction network from Michaelis et al. (2023), filtering for proteins with six or more interactions to emphasize core functional relationships. RISK identified compact, statistically enriched clusters corresponding to biological processes such as ribosomal assembly and mitochondrial organization.
 
-![RISK Main Figure](https://i.imgur.com/5OP3Hqe.jpeg)
+[![Figure 1](https://i.imgur.com/lJHJrJr.jpeg)](https://i.imgur.com/lJHJrJr.jpeg)
 
-RISK successfully detected both known and novel functional clusters within the yeast interactome. Clusters related to Golgi transport and actin nucleation were clearly defined and closely located, showcasing RISK's ability to map well-characterized interactions. Additionally, RISK identified links between mRNA processing pathways and vesicle trafficking proteins, consistent with recent studies demonstrating the role of vesicles in mRNA localization and stability.
+This figure highlights RISK’s capability to detect both established and novel functional modules within the yeast interactome.
 
 ## Citation
 
-If you use RISK in your research, please cite the following:
+If you use RISK in your research, please cite:
 
-**Horecka**, *et al.*, "RISK: a next-generation tool for biological network annotation and visualization", **[Journal Name]**, 2024. DOI: [10.1234/zenodo.xxxxxxx](https://doi.org/10.1234/zenodo.xxxxxxx)
+**Horecka et al.**, "RISK: a next-generation tool for biological network annotation and visualization", **Bioinformatics**, 2025. DOI: [10.1234/zenodo.xxxxxxx](https://doi.org/10.1234/zenodo.xxxxxxx)
 
 ## Software Architecture and Implementation
 
-RISK features a streamlined, modular architecture designed to meet diverse research needs. Each module focuses on a specific task—such as network input/output, statistical analysis, or visualization—ensuring ease of adaptation and extension. This design enhances flexibility and reduces development overhead for users integrating RISK into their workflows.
+RISK features a streamlined, modular architecture designed to meet diverse research needs. It includes dedicated modules for:
 
-### Supported Data Formats
-
-- **Input/Output**: JSON, CSV, TSV, Excel, Cytoscape, GPickle.
-- **Visualization Outputs**: SVG, PNG, PDF.
-
-### Clustering Algorithms
-
-- **Available Algorithms**:
-  - Greedy Modularity
-  - Label Propagation
-  - Louvain
-  - Markov Clustering
-  - Spinglass
-  - Walktrap
-- **Distance Metrics**: Supports both spherical and Euclidean distance metrics.
-
-### Statistical Tests
-
-- **Hypergeometric Test**
-- **Permutation Test** (single- or multi-process modes)
-- **Poisson Test**
+- **Data I/O**: Supports JSON, CSV, TSV, Excel, Cytoscape, and GPickle formats.
+- **Clustering**: Supports multiple clustering methods, including Louvain, Leiden, Markov Clustering, Greedy Modularity, Label Propagation, Spinglass, and Walktrap. Provides flexible distance metrics tailored to network structure.
+- **Statistical Analysis**: Provides a suite of tests for overrepresentation analysis of annotations.
+- **Visualization**: Offers customizable, high-resolution output in multiple formats, including SVG, PNG, and PDF.
 
 ## Performance and Efficiency
 
-In benchmarking tests using the yeast interactome network, RISK demonstrated substantial improvements over previous tools in both computational performance and memory efficiency. RISK processed the dataset approximately **3.25 times faster**, reducing CPU time by **69%**, and required **25% less peak memory usage**, underscoring its efficient utilization of computational resources.
+Benchmarking results demonstrate that RISK efficiently scales to networks exceeding hundreds of thousands of edges, maintaining low execution times and optimal memory usage across statistical tests.
 
 ## Contributing
 
-We welcome contributions from the community. Please use the following resources:
+We welcome contributions from the community:
 
 - [Issues Tracker](https://github.com/irahorecka/risk/issues)
 - [Source Code](https://github.com/irahorecka/risk/tree/main/risk)
@@ -806,8 +791,8 @@ If you encounter issues or have suggestions for new features, please use the [Is
 
 ## License
 
-RISK is freely available as open-source software under the [GNU General Public License v3.0](https://www.gnu.org/licenses/gpl-3.0.en.html).
+RISK is open source under the [GNU General Public License v3.0](https://www.gnu.org/licenses/gpl-3.0.en.html).
 
 ---
 
-**Note**: For detailed documentation and to access the interactive tutorial, please visit the links provided in the [Documentation and Tutorial](#documentation-and-tutorial) section.
+**Note**: For detailed documentation and to access the interactive tutorial, please visit the links above.

risk_network-0.0.9.dist-info/RECORD

@@ -0,0 +1,40 @@
+risk/__init__.py,sha256=XK5JlkLoKOn6dp3xXQmg08sN2QpAhnv3ds_26j9CxaY,119
+risk/risk.py,sha256=s827_lRknFseOP9O4zW8sP-IcCd2EzrpV_tnVY_tz5s,1104
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+risk/annotations/annotations.py,sha256=5X2R8RFxgK6kgSoj05UdCPcpkRRPOaHjGwnIrjeD5Ww,16299
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+risk/neighborhoods/api.py,sha256=ywngw2TQVV27gYlWDXcs8-qnmeepnvb-W9ov6J6VEPM,23341
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+risk_network-0.0.9.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9.dist-info/METADATA,sha256=tg_hgIBU82xx59c4IAlsq6WyvkQOk7JWurwPZK96PwE,46971
+risk_network-0.0.9.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+risk_network-0.0.9.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9.dist-info/RECORD,,

{risk_network-0.0.8b27.dist-info → risk_network-0.0.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

risk/constants.py

@@ -1,31 +0,0 @@
-"""
-risk/constants
-~~~~~~~~~~~~~~
-"""
-
-GROUP_LINKAGE_METHODS = ["single", "complete", "average", "weighted", "centroid", "median", "ward"]
-
-GROUP_DISTANCE_METRICS = [
-    "braycurtis",
-    "canberra",
-    "chebyshev",
-    "cityblock",
-    "correlation",
-    "cosine",
-    "dice",
-    "euclidean",
-    "hamming",
-    "jaccard",
-    "jensenshannon",
-    "kulczynski1",
-    "mahalanobis",
-    "matching",
-    "minkowski",
-    "rogerstanimoto",
-    "russellrao",
-    "seuclidean",
-    "sokalmichener",
-    "sokalsneath",
-    "sqeuclidean",
-    "yule",
-]

risk/network/plot/__init__.py

@@ -1,6 +0,0 @@
-"""
-risk/network/plot
-~~~~~~~~~~~~~~~~~
-"""
-
-from risk.network.plot.plotter import NetworkPlotter

risk/stats/hypergeom.py

@@ -1,54 +0,0 @@
-"""
-risk/stats/hypergeom
-~~~~~~~~~~~~~~~~~~~~
-"""
-
-from typing import Any, Dict
-
-import numpy as np
-from scipy.stats import hypergeom
-
-
-def compute_hypergeom_test(
-    neighborhoods: np.ndarray, annotations: np.ndarray, null_distribution: str = "network"
-) -> Dict[str, Any]:
-    """Compute hypergeometric test for enrichment and depletion in neighborhoods with selectable null distribution.
-
-    Args:
-        neighborhoods (np.ndarray): Binary matrix representing neighborhoods.
-        annotations (np.ndarray): Binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
-
-    Returns:
-        Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
-    """
-    # Get the total number of nodes in the network
-    total_node_count = neighborhoods.shape[0]
-
-    if null_distribution == "network":
-        # Case 1: Use all nodes as the background
-        background_population = total_node_count
-        neighborhood_sums = np.sum(neighborhoods, axis=0, keepdims=True).T
-        annotation_sums = np.sum(annotations, axis=0, keepdims=True)
-    elif null_distribution == "annotations":
-        # Case 2: Only consider nodes with at least one annotation
-        annotated_nodes = np.sum(annotations, axis=1) > 0
-        background_population = np.sum(annotated_nodes)
-        neighborhood_sums = np.sum(neighborhoods[annotated_nodes], axis=0, keepdims=True).T
-        annotation_sums = np.sum(annotations[annotated_nodes], axis=0, keepdims=True)
-    else:
-        raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
-        )
-
-    # Matrix multiplication for annotated nodes in each neighborhood
-    annotated_in_neighborhood = neighborhoods.T @ annotations
-    # Calculate depletion and enrichment p-values using the hypergeometric distribution
-    depletion_pvals = hypergeom.cdf(
-        annotated_in_neighborhood, background_population, annotation_sums, neighborhood_sums
-    )
-    enrichment_pvals = hypergeom.sf(
-        annotated_in_neighborhood - 1, background_population, annotation_sums, neighborhood_sums
-    )
-
-    return {"depletion_pvals": depletion_pvals, "enrichment_pvals": enrichment_pvals}

risk/stats/poisson.py

@@ -1,44 +0,0 @@
-"""
-risk/stats/poisson
-~~~~~~~~~~~~~~~~~~
-"""
-
-from typing import Any, Dict
-
-import numpy as np
-from scipy.stats import poisson
-
-
-def compute_poisson_test(
-    neighborhoods: np.ndarray, annotations: np.ndarray, null_distribution: str = "network"
-) -> Dict[str, Any]:
-    """Compute Poisson test for enrichment and depletion in neighborhoods with selectable null distribution.
-
-    Args:
-        neighborhoods (np.ndarray): Binary matrix representing neighborhoods.
-        annotations (np.ndarray): Binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
-
-    Returns:
-        Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
-    """
-    # Matrix multiplication to get the number of annotated nodes in each neighborhood
-    annotated_in_neighborhood = neighborhoods @ annotations
-
-    # Compute lambda_expected based on the chosen null distribution
-    if null_distribution == "network":
-        # Use the mean across neighborhoods (axis=1)
-        lambda_expected = np.mean(annotated_in_neighborhood, axis=1, keepdims=True)
-    elif null_distribution == "annotations":
-        # Use the mean across annotations (axis=0)
-        lambda_expected = np.mean(annotated_in_neighborhood, axis=0, keepdims=True)
-    else:
-        raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
-        )
-
-    # Compute p-values for enrichment and depletion using Poisson distribution
-    enrichment_pvals = 1 - poisson.cdf(annotated_in_neighborhood - 1, lambda_expected)
-    depletion_pvals = poisson.cdf(annotated_in_neighborhood, lambda_expected)
-
-    return {"enrichment_pvals": enrichment_pvals, "depletion_pvals": depletion_pvals}

risk_network-0.0.8b27.dist-info/RECORD

@@ -1,37 +0,0 @@
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