risk-network 0.0.8b9__tar.gz → 0.0.8b11__tar.gz

{risk_network-0.0.8b9 → risk_network-0.0.8b11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b9
+Version: 0.0.8b11
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -709,7 +709,7 @@ Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 
-# RISK
+# RISK Network
 
 <p align="center">
   <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
@@ -728,8 +728,8 @@ Requires-Dist: tqdm
 
 ## Documentation and Tutorial
 
-- **Documentation**: Comprehensive documentation is available at [Documentation link].
-- **Tutorial**: An interactive Jupyter notebook tutorial can be found at [Tutorial link].
+- **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.
 
 ## Installation
@@ -753,7 +753,7 @@ pip install risk-network
 
 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.
 
-![RISK Main Figure](https://i.imgur.com/TUVfvfH.jpeg)
+![RISK Main Figure](https://i.imgur.com/5OP3Hqe.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.
 

{risk_network-0.0.8b9 → risk_network-0.0.8b11}/README.md

@@ -1,4 +1,4 @@
-# RISK
+# RISK Network
 
 <p align="center">
   <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
@@ -17,8 +17,8 @@
 
 ## Documentation and Tutorial
 
-- **Documentation**: Comprehensive documentation is available at [Documentation link].
-- **Tutorial**: An interactive Jupyter notebook tutorial can be found at [Tutorial link].
+- **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.
 
 ## Installation
@@ -42,7 +42,7 @@ pip install risk-network
 
 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.
 
-![RISK Main Figure](https://i.imgur.com/TUVfvfH.jpeg)
+![RISK Main Figure](https://i.imgur.com/5OP3Hqe.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.
 

{risk_network-0.0.8b9 → risk_network-0.0.8b11}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.8-beta.9"
+__version__ = "0.0.8-beta.11"

{risk_network-0.0.8b9 → risk_network-0.0.8b11}/risk/neighborhoods/domains.py

@@ -121,7 +121,7 @@ def trim_domains_and_top_annotations(
     ].transform(lambda x: (x.rank(pct=True) * 10).apply(np.ceil).astype(int))
     # Multiply 'words' column by normalized values
     top_annotations["words"] = top_annotations.apply(
-        lambda row: " ".join([row["words"]] * row["normalized_value"]), axis=1
+        lambda row: " ".join([str(row["words"])] * row["normalized_value"]), axis=1
     )
 
     # Generate domain labels

{risk_network-0.0.8b9 → risk_network-0.0.8b11}/risk/network/io.py

@@ -13,6 +13,7 @@ import zipfile
 from xml.dom import minidom
 
 import networkx as nx
+import numpy as np
 import pandas as pd
 
 from risk.network.geometry import assign_edge_lengths
@@ -490,7 +491,7 @@ class NetworkIO:
             if "x" not in attrs or "y" not in attrs:
                 if (
                     "pos" in attrs
-                    and isinstance(attrs["pos"], (tuple, list))
+                    and isinstance(attrs["pos"], (list, tuple, np.ndarray))
                     and len(attrs["pos"]) >= 2
                 ):
                     attrs["x"], attrs["y"] = attrs["pos"][

{risk_network-0.0.8b9 → risk_network-0.0.8b11}/risk/network/plot/labels.py

@@ -462,9 +462,10 @@ class Labels:
         def calculate_distance(centroid1, centroid2):
             return np.linalg.norm(centroid1 - centroid2)
 
+        # Domains to plot on network
+        selected_domains = []
         # Find the farthest apart domains using centroids
         if remaining_domains and remaining_labels:
-            selected_domains = []
             first_domain = next(iter(remaining_domains))  # Pick the first domain to start
             selected_domains.append(first_domain)
 

{risk_network-0.0.8b9 → risk_network-0.0.8b11}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b9
+Version: 0.0.8b11
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -709,7 +709,7 @@ Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 
-# RISK
+# RISK Network
 
 <p align="center">
   <img src="https://i.imgur.com/8TleEJs.png" width="50%" />
@@ -728,8 +728,8 @@ Requires-Dist: tqdm
 
 ## Documentation and Tutorial
 
-- **Documentation**: Comprehensive documentation is available at [Documentation link].
-- **Tutorial**: An interactive Jupyter notebook tutorial can be found at [Tutorial link].
+- **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.
 
 ## Installation
@@ -753,7 +753,7 @@ pip install risk-network
 
 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.
 
-![RISK Main Figure](https://i.imgur.com/TUVfvfH.jpeg)
+![RISK Main Figure](https://i.imgur.com/5OP3Hqe.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.