risk-network 0.0.5b1__tar.gz → 0.0.5b3__tar.gz

{risk_network-0.0.5b1 → risk_network-0.0.5b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b1
+Version: 0.0.5b3
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.5b1 → risk_network-0.0.5b3}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.5-beta.1"
+__version__ = "0.0.5-beta.3"

{risk_network-0.0.5b1 → risk_network-0.0.5b3}/risk/network/graph.py

@@ -11,7 +11,6 @@ import networkx as nx
 import numpy as np
 import pandas as pd
 import matplotlib
-import matplotlib.cm as cm
 
 
 class NetworkGraph:
@@ -270,7 +269,7 @@ def _get_colors(
         rgba = matplotlib.colors.to_rgba(kwargs["color"])
         rgbas = [rgba] * num_colors_to_generate
     else:
-        colormap = cm.get_cmap(cmap)
+        colormap = matplotlib.colormaps.get_cmap(cmap)
         # Generate evenly distributed color positions
         color_positions = np.linspace(0, 1, num_colors_to_generate)
         random.shuffle(color_positions)  # Shuffle the positions to randomize colors

{risk_network-0.0.5b1 → risk_network-0.0.5b3}/risk/network/plot.py

@@ -413,6 +413,8 @@ class NetworkPlotter:
         max_labels: Union[int, None] = None,
         max_words: int = 10,
         min_words: int = 1,
+        max_word_length: int = 20,
+        min_word_length: int = 1,
         words_to_omit: Union[List[str], None] = None,
     ) -> None:
         """Annotate the network graph with labels for different domains, positioned around the network for clarity.
@@ -428,6 +430,8 @@ class NetworkPlotter:
             max_labels (int, optional): Maximum number of labels to plot. Defaults to None (no limit).
             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.
+            max_word_length (int, optional): Maximum number of characters in a word to display. Defaults to 20.
+            min_word_length (int, optional): Minimum number of characters in a word to display. Defaults to 1.
             words_to_omit (List[str], optional): List of words to omit from the labels. Defaults to None.
         """
         # Log the plotting parameters
@@ -442,7 +446,9 @@ class NetworkPlotter:
             label_max_labels=max_labels,
             label_max_words=max_words,
             label_min_words=min_words,
-            label_words_to_omit=words_to_omit,  # Log words_to_omit parameter
+            label_max_word_length=max_word_length,
+            label_min_word_length=min_word_length,
+            label_words_to_omit=words_to_omit,
         )
 
         # Convert color strings to RGBA arrays if necessary
@@ -471,13 +477,15 @@ class NetworkPlotter:
             # Remove words_to_omit
             if words_to_omit:
                 terms = [term for term in terms if term.lower() not in words_to_omit]
+            # Filter words based on length
+            terms = [term for term in terms if min_word_length <= len(term) <= max_word_length]
             # Trim to max_words
             terms = terms[:max_words]
             # Check if the domain passes the word count condition
             if len(terms) >= min_words:
                 # Add to filtered_domain_centroids
                 filtered_domain_centroids[domain] = centroid
-                # Store the trimmed terms
+                # Store the filtered and trimmed terms
                 filtered_domain_terms[domain] = " ".join(terms)
                 # Keep track of the valid index
                 valid_indices.append(idx)
@@ -499,10 +507,6 @@ class NetworkPlotter:
             fontcolor = fontcolor[selected_indices]
             arrow_color = arrow_color[selected_indices]
 
-        # Update the terms in the graph after omitting words and filtering
-        for domain, terms in filtered_domain_terms.items():
-            self.graph.trimmed_domain_to_term[domain] = terms
-
         # Calculate the bounding box around the network
         center, radius = _calculate_bounding_box(
             self.graph.node_coordinates, radius_margin=perimeter_scale
@@ -514,7 +518,7 @@ class NetworkPlotter:
         # Annotate the network with labels
         for idx, (domain, pos) in enumerate(best_label_positions.items()):
             centroid = filtered_domain_centroids[domain]
-            annotations = self.graph.trimmed_domain_to_term[domain].split(" ")[:max_words]
+            annotations = filtered_domain_terms[domain].split(" ")[:max_words]
             self.ax.annotate(
                 "\n".join(annotations),
                 xy=centroid,

{risk_network-0.0.5b1 → risk_network-0.0.5b3}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b1
+Version: 0.0.5b3
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>