risk-network 0.0.8b8__tar.gz → 0.0.8b9__tar.gz

{risk_network-0.0.8b8 → risk_network-0.0.8b9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b8
+Version: 0.0.8b9
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b8 → risk_network-0.0.8b9}/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.9"

{risk_network-0.0.8b8 → risk_network-0.0.8b9}/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-0.0.8b9}/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-0.0.8b9}/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-0.0.8b9}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b8
+Version: 0.0.8b9
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>