risk-network 0.0.8b8__tar.gz → 0.0.8b10__tar.gz

{risk_network-0.0.8b8 → risk_network-0.0.8b10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b8
+Version: 0.0.8b10
 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-0.0.8b8 → risk_network-0.0.8b10}/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-0.0.8b8 → risk_network-0.0.8b10}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.8-beta.8"
+__version__ = "0.0.8-beta.10"

{risk_network-0.0.8b8 → risk_network-0.0.8b10}/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-0.0.8b8 → risk_network-0.0.8b10}/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-0.0.8b8 → risk_network-0.0.8b10}/risk/network/plot/canvas.py

@@ -44,8 +44,8 @@ class Canvas:
         Args:
             title (str, optional): Title of the plot. Defaults to None.
             subtitle (str, optional): Subtitle of the plot. Defaults to None.
-            title_fontsize (int, optional): Font size for the title. Defaults to 16.
-            subtitle_fontsize (int, optional): Font size for the subtitle. Defaults to 12.
+            title_fontsize (int, optional): Font size for the title. Defaults to 20.
+            subtitle_fontsize (int, optional): Font size for the subtitle. Defaults to 14.
             font (str, optional): Font family used for both title and subtitle. Defaults to "Arial".
             title_color (str, optional): Color of the title text. Defaults to "black".
             subtitle_color (str, optional): Color of the subtitle text. Defaults to "gray".
@@ -90,11 +90,14 @@ class Canvas:
 
         # Plot subtitle if provided
         if subtitle:
-            # Calculate the subtitle's y position based on title's position and subtitle_offset
-            subtitle_y_position = title_y - subtitle_offset
+            # Calculate the subtitle's y position based on the midpoint of the title and subtitle_offset
+            # Calculate the approximate height of the title in relative axis units
+            title_height = title_fontsize / fig.bbox.height
+            # Position the subtitle relative to the title's center (title_y - half the title height)
+            subtitle_y_position = title_y - (title_height / 2) - subtitle_offset
             self.ax.figure.text(
                 0.5,  # Ensure horizontal centering for subtitle
-                subtitle_y_position,
+                subtitle_y_position,  # Position subtitle based on the center of the title
                 subtitle,
                 ha="center",
                 va="top",

{risk_network-0.0.8b8 → risk_network-0.0.8b10}/risk/network/plot/plotter.py

@@ -8,6 +8,7 @@ from typing import List, Tuple, Union
 import matplotlib.pyplot as plt
 import numpy as np
 
+from risk.log import params
 from risk.network.graph import NetworkGraph
 from risk.network.plot.canvas import Canvas
 from risk.network.plot.contour import Contour
@@ -30,6 +31,7 @@ class NetworkPlotter(Canvas, Network, Contour, Labels):
         figsize: Tuple = (10, 10),
         background_color: Union[str, List, Tuple, np.ndarray] = "white",
         background_alpha: Union[float, None] = 1.0,
+        pad: float = 0.3,
     ) -> None:
         """Initialize the NetworkPlotter with a NetworkGraph object and plotting parameters.
 
@@ -39,6 +41,7 @@ class NetworkPlotter(Canvas, Network, Contour, Labels):
             background_color (str, list, tuple, np.ndarray, optional): Background color of the plot. Defaults to "white".
             background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides
                 any existing alpha values found in background_color. Defaults to 1.0.
+            pad (float, optional): Padding value to adjust the axis limits. Defaults to 0.3.
         """
         self.graph = graph
         # Initialize the plot with the specified parameters
@@ -47,6 +50,7 @@ class NetworkPlotter(Canvas, Network, Contour, Labels):
             figsize=figsize,
             background_color=background_color,
             background_alpha=background_alpha,
+            pad=pad,
         )
         super().__init__(graph=graph, ax=self.ax)
 
@@ -56,6 +60,7 @@ class NetworkPlotter(Canvas, Network, Contour, Labels):
         figsize: Tuple,
         background_color: Union[str, List, Tuple, np.ndarray],
         background_alpha: Union[float, None],
+        pad: float,
     ) -> plt.Axes:
         """Set up the plot with figure size and background color.
 
@@ -65,10 +70,19 @@ class NetworkPlotter(Canvas, Network, Contour, Labels):
             background_color (str): Background color of the plot.
             background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides any
             existing alpha values found in background_color.
+            pad (float, optional): Padding value to adjust the axis limits.
 
         Returns:
             plt.Axes: The axis object for the plot.
         """
+        # Log the plotter settings
+        params.log_plotter(
+            figsize=figsize,
+            background_color=background_color,
+            background_alpha=background_alpha,
+            pad=pad,
+        )
+
         # Extract node coordinates from the network graph
         node_coordinates = graph.node_coordinates
         # Calculate the center and radius of the bounding box around the network
@@ -78,8 +92,8 @@ class NetworkPlotter(Canvas, Network, Contour, Labels):
         fig, ax = plt.subplots(figsize=figsize)
         fig.tight_layout()  # Adjust subplot parameters to give specified padding
         # Set axis limits based on the calculated bounding box and radius
-        ax.set_xlim([center[0] - radius - 0.3, center[0] + radius + 0.3])
-        ax.set_ylim([center[1] - radius - 0.3, center[1] + radius + 0.3])
+        ax.set_xlim([center[0] - radius - pad, center[0] + radius + pad])
+        ax.set_ylim([center[1] - radius - pad, center[1] + radius + pad])
         ax.set_aspect("equal")  # Ensure the aspect ratio is equal
 
         # Set the background color of the plot

{risk_network-0.0.8b8 → risk_network-0.0.8b10}/risk/risk.py

@@ -356,6 +356,7 @@ class RISK(NetworkIO, AnnotationsIO):
         figsize: Tuple = (10, 10),
         background_color: str = "white",
         background_alpha: Union[float, None] = 1.0,
+        pad: float = 0.3,
     ) -> NetworkPlotter:
         """Get a NetworkPlotter object for plotting.
 
@@ -365,16 +366,12 @@ class RISK(NetworkIO, AnnotationsIO):
             background_color (str, optional): Background color of the plot. Defaults to "white".
             background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides
                 any existing alpha values found in background_color. Defaults to 1.0.
+            pad (float, optional): Padding value to adjust the axis limits. Defaults to 0.3.
 
         Returns:
             NetworkPlotter: A NetworkPlotter object configured with the given parameters.
         """
         log_header("Loading plotter")
-        # Log the plotter settings
-        params.log_plotter(
-            figsize=figsize,
-            background_color=background_color,
-        )
 
         # Initialize and return a NetworkPlotter object
         return NetworkPlotter(
@@ -382,6 +379,7 @@ class RISK(NetworkIO, AnnotationsIO):
             figsize=figsize,
             background_color=background_color,
             background_alpha=background_alpha,
+            pad=pad,
         )
 
     def _load_neighborhoods(

{risk_network-0.0.8b8 → risk_network-0.0.8b10}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b8
+Version: 0.0.8b10
 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.