risk-network 0.0.5b4__py3-none-any.whl → 0.0.5b5__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.5-beta.4"
+__version__ = "0.0.5-beta.5"

risk/annotations/annotations.py

@@ -207,7 +207,7 @@ def _simplify_word_list(words: List[str], threshold: float = 0.80) -> List[str]:
         similar_words = [
             other_word
             for other_word in word_counts
-            if _jaccard_index(word_set, set(other_word)) >= threshold
+            if _calculate_jaccard_index(word_set, set(other_word)) >= threshold
         ]
         # Sort by frequency and choose the most frequent word
         similar_words.sort(key=lambda w: word_counts[w], reverse=True)
@@ -220,7 +220,7 @@ def _simplify_word_list(words: List[str], threshold: float = 0.80) -> List[str]:
     return final_words
 
 
-def _jaccard_index(set1: Set[Any], set2: Set[Any]) -> float:
+def _calculate_jaccard_index(set1: Set[Any], set2: Set[Any]) -> float:
     """Calculate the Jaccard Index of two sets.
 
     Args:

risk/network/graph.py

@@ -5,7 +5,7 @@ risk/network/graph
 
 import random
 from collections import defaultdict
-from typing import Any, Dict, List, Tuple
+from typing import Any, Dict, List, Tuple, Union
 
 import networkx as nx
 import numpy as np
@@ -100,7 +100,12 @@ class NetworkGraph:
         self.node_coordinates = _extract_node_coordinates(G_2d)
 
     def get_domain_colors(
-        self, min_scale: float = 0.8, max_scale: float = 1.0, random_seed: int = 888, **kwargs
+        self,
+        min_scale: float = 0.8,
+        max_scale: float = 1.0,
+        scale_factor: float = 1.0,
+        random_seed: int = 888,
+        **kwargs,
     ) -> np.ndarray:
         """Generate composite colors for domains.
 
@@ -111,6 +116,8 @@ class NetworkGraph:
         Args:
             min_scale (float, optional): Minimum scale for color intensity. Defaults to 0.8.
             max_scale (float, optional): Maximum scale for color intensity. Defaults to 1.0.
+            scale_factor (float, optional): Exponent for scaling, where values > 1 increase contrast by dimming small
+                values more. Defaults to 1.0.
             random_seed (int, optional): Seed for random number generation. Defaults to 888.
             **kwargs: Additional keyword arguments for color generation.
 
@@ -118,7 +125,7 @@ class NetworkGraph:
             np.ndarray: Array of transformed colors.
         """
         # Get colors for each domain
-        domain_colors = self._get_domain_colors(**kwargs, random_seed=random_seed)
+        domain_colors = self._get_domain_colors(random_seed=random_seed)
         # Generate composite colors for nodes
         node_colors = self._get_composite_node_colors(domain_colors)
         # Transform colors to ensure proper alpha values and intensity
@@ -127,6 +134,7 @@ class NetworkGraph:
             self.node_enrichment_sums,
             min_scale=min_scale,
             max_scale=max_scale,
+            scale_factor=scale_factor,
         )
 
         return transformed_colors
@@ -152,9 +160,15 @@ class NetworkGraph:
 
         return composite_colors
 
-    def _get_domain_colors(self, **kwargs) -> Dict[str, Any]:
+    def _get_domain_colors(
+        self, color: Union[str, None] = None, random_seed: int = 888
+    ) -> Dict[str, Any]:
         """Get colors for each domain.
 
+        Args:
+            color (Union[str, None], optional): Specific color to use for all domains. If specified, it will overwrite the colormap.
+            random_seed (int, optional): Seed for random number generation. Defaults to 888.
+
         Returns:
             dict: A dictionary mapping domain keys to their corresponding RGBA colors.
         """
@@ -163,20 +177,28 @@ class NetworkGraph:
             col for col in self.domains.columns if isinstance(col, (int, np.integer))
         ]
         domains = np.sort(numeric_domains)
-        domain_colors = _get_colors(**kwargs, num_colors_to_generate=len(domains))
+        domain_colors = _get_colors(
+            num_colors_to_generate=len(domains), color=color, random_seed=random_seed
+        )
         return dict(zip(self.domain_to_nodes.keys(), domain_colors))
 
 
 def _transform_colors(
-    colors: np.ndarray, enrichment_sums: np.ndarray, min_scale: float = 0.8, max_scale: float = 1.0
+    colors: np.ndarray,
+    enrichment_sums: np.ndarray,
+    min_scale: float = 0.8,
+    max_scale: float = 1.0,
+    scale_factor: float = 1.0,
 ) -> np.ndarray:
-    """Transform colors to ensure proper alpha values and intensity based on enrichment sums.
+    """Transform colors using power scaling to emphasize high enrichment sums more.
 
     Args:
         colors (np.ndarray): An array of RGBA colors.
         enrichment_sums (np.ndarray): An array of enrichment sums corresponding to the colors.
         min_scale (float, optional): Minimum scale for color intensity. Defaults to 0.8.
         max_scale (float, optional): Maximum scale for color intensity. Defaults to 1.0.
+        scale_factor (float, optional): Exponent for scaling, where values > 1 increase contrast by dimming small
+            values more. Defaults to 1.0.
 
     Returns:
         np.ndarray: The transformed array of RGBA colors with adjusted intensities.
@@ -184,11 +206,12 @@ def _transform_colors(
     if min_scale == max_scale:
         min_scale = max_scale - 10e-6  # Avoid division by zero
 
-    log_enrichment_sums = np.log1p(enrichment_sums)  # Use log1p to avoid log(0)
-    # Normalize the capped enrichment sums to the range [0, 1]
-    normalized_sums = log_enrichment_sums / np.max(log_enrichment_sums)
-    # Scale normalized sums to the specified color range [min_scale, max_scale]
-    scaled_sums = min_scale + (max_scale - min_scale) * normalized_sums
+    # Normalize the enrichment sums to the range [0, 1]
+    normalized_sums = enrichment_sums / np.max(enrichment_sums)
+    # Apply power scaling to dim lower values and emphasize higher values
+    scaled_sums = normalized_sums**scale_factor
+    # Linearly scale the normalized sums to the range [min_scale, max_scale]
+    scaled_sums = min_scale + (max_scale - min_scale) * scaled_sums
     # Adjust RGB values based on scaled sums
     for i in range(3):  # Only adjust RGB values
         colors[:, i] = scaled_sums * colors[:, i]
@@ -249,7 +272,10 @@ def _extract_node_coordinates(G: nx.Graph) -> np.ndarray:
 
 
 def _get_colors(
-    num_colors_to_generate: int = 10, cmap: str = "hsv", random_seed: int = 888, **kwargs
+    num_colors_to_generate: int = 10,
+    cmap: str = "hsv",
+    random_seed: int = 888,
+    color: Union[str, None] = None,
 ) -> List[Tuple]:
     """Generate a list of RGBA colors from a specified colormap or use a direct color string.
 
@@ -257,16 +283,17 @@ def _get_colors(
         num_colors_to_generate (int): The number of colors to generate. Defaults to 10.
         cmap (str): The name of the colormap to use. Defaults to "hsv".
         random_seed (int): Seed for random number generation. Defaults to 888.
-        **kwargs: Additional keyword arguments, such as 'color' for a specific color.
+        color (str, optional): Specific color to use for all nodes. If specified, it will overwrite the colormap.
+            Defaults to None.
 
     Returns:
         list of tuple: List of RGBA colors.
     """
     # Set random seed for reproducibility
     random.seed(random_seed)
-    if kwargs.get("color"):
-        # If a direct color string is provided, generate a list with that color
-        rgba = matplotlib.colors.to_rgba(kwargs["color"])
+    if color:
+        # If a direct color is provided, generate a list with that color
+        rgba = matplotlib.colors.to_rgba(color)
         rgbas = [rgba] * num_colors_to_generate
     else:
         colormap = matplotlib.colormaps.get_cmap(cmap)

risk/network/plot.py

@@ -512,7 +512,7 @@ class NetworkPlotter:
             self.graph.node_coordinates, radius_margin=perimeter_scale
         )
         # Calculate the best positions for labels around the perimeter
-        best_label_positions = _best_label_positions(
+        best_label_positions = _calculate_best_label_positions(
             filtered_domain_centroids, center, radius, offset
         )
         # Annotate the network with labels - valid_indices is used for fontcolor and arrow_color
@@ -795,7 +795,7 @@ def _calculate_bounding_box(
     return center, radius
 
 
-def _best_label_positions(
+def _calculate_best_label_positions(
     filtered_domain_centroids: Dict[str, Any], center: np.ndarray, radius: float, offset: float
 ) -> Dict[str, Any]:
     """Calculate and optimize label positions for clarity.
@@ -811,7 +811,9 @@ def _best_label_positions(
     """
     num_domains = len(filtered_domain_centroids)
     # Calculate equidistant positions around the center for initial label placement
-    equidistant_positions = _equidistant_angles_around_center(center, radius, offset, num_domains)
+    equidistant_positions = _calculate_equidistant_positions_around_center(
+        center, radius, offset, num_domains
+    )
     # Create a mapping of domains to their initial label positions
     label_positions = {
         domain: position
@@ -821,7 +823,7 @@ def _best_label_positions(
     return _optimize_label_positions(label_positions, filtered_domain_centroids)
 
 
-def _equidistant_angles_around_center(
+def _calculate_equidistant_positions_around_center(
     center: np.ndarray, radius: float, label_offset: float, num_domains: int
 ) -> List[np.ndarray]:
     """Calculate positions around a center at equidistant angles.

{risk_network-0.0.5b4.dist-info → risk_network-0.0.5b5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b4
+Version: 0.0.5b5
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.5b4.dist-info → risk_network-0.0.5b5.dist-info}/RECORD

@@ -1,8 +1,8 @@
-risk/__init__.py,sha256=bzj1Zn2Vm3Nh5mYk1ZoFg3njX6gjTO8aKOI6Zi_6JuE,112
+risk/__init__.py,sha256=zGjRj03AbzDx0VGLJyR7TPzNLA1XQ5eLF7gbAKK507o,112
 risk/constants.py,sha256=AICk3x5qRQhls_ijTb4VdbdxU6mZ1aLGbAjLEdBwfJI,550
 risk/risk.py,sha256=UYM_Pf2Db-lbf4O5T2v5zKutz_GLXK-f43PgYT6xRyY,21328
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
-risk/annotations/annotations.py,sha256=t4aLwROCFHcqk8g-viuwkFG--HqVpVN_2yVVcjhg6wI,10534
+risk/annotations/annotations.py,sha256=DRUTdGzMdqo62NWSapBUksbvPr9CrzD76qtOcxeNKmo,10554
 risk/annotations/io.py,sha256=TMicRACfY8bNtmbvVrxHoh8zkOVLOIhZwWrpxUlR28Q,7988
 risk/log/__init__.py,sha256=xuLImfxFlKpnVhzi_gDYlr2_c9cLkrw2c_3iEsXb1as,107
 risk/log/console.py,sha256=im9DRExwf6wHlcn9fewoDcKIpo3vPcorZIaNAl-0csY,355
@@ -13,9 +13,9 @@ risk/neighborhoods/domains.py,sha256=HwuChmZH0RGD9eQOvk2-ezQDJRUHHn93vhVgHb-kX6I
 risk/neighborhoods/neighborhoods.py,sha256=SqYJaT49rUj77ts0XsPXb9cURM11aGh2Teks0nBH_4s,13939
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
-risk/network/graph.py,sha256=F_SY7nZev6XZuHwkJnVdeow-oMSmR4u8AUiFCrh6yvk,11543
+risk/network/graph.py,sha256=DTjNRQwgQbt6jJYDBHm7sgrdbZUDLL4HiZpdixkSI7Y,12433
 risk/network/io.py,sha256=otiRG6uT6HLgbbJql7X2wjYxab8OFJSgRoWJlcDoyu4,20291
-risk/network/plot.py,sha256=Ti0nT49NffoQc9qjXOclEFBRuuN_4LLntpBZn3cp5Fo,40882
+risk/network/plot.py,sha256=rg4pB0sndOnoayeNZSu4sU3sQ2P8x9ksE4XRTRP2HPM,40942
 risk/stats/__init__.py,sha256=e-BE_Dr_jgiK6hKM-T-tlG4yvHnId8e5qjnM0pdwNVc,230
 risk/stats/fisher_exact.py,sha256=-bPwzu76-ob0HzrTV20mXUTot7v-MLuqFaAoab-QxPg,4966
 risk/stats/hypergeom.py,sha256=lrIFdhCWRjvM4apYw1MlOKqT_IY5OjtCwrjdtJdt6Tg,4954
@@ -23,8 +23,8 @@ risk/stats/stats.py,sha256=kvShov-94W6ffgDUTb522vB9hDJQSyTsYif_UIaFfSM,7059
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=qLWdwxEY6nmkYPxpM8HLDcd2mbqYv9Qr7CKtJvhLqIM,9220
 risk/stats/permutation/test_functions.py,sha256=HuDIM-V1jkkfE1rlaIqrWWBSKZt3dQ1f-YEDjWpnLSE,2343
-risk_network-0.0.5b4.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.5b4.dist-info/METADATA,sha256=tSh6tuMzdhFwIJ4XzzccgnONtulZDNCfLkHEAV7XtSI,43236
-risk_network-0.0.5b4.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-risk_network-0.0.5b4.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.5b4.dist-info/RECORD,,
+risk_network-0.0.5b5.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.5b5.dist-info/METADATA,sha256=qSRqHP8c46IzvZU--rO7eUeir3LErWx98mPIbh0Q_c4,43236
+risk_network-0.0.5b5.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+risk_network-0.0.5b5.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.5b5.dist-info/RECORD,,