risk-network 0.0.8b11__py3-none-any.whl → 0.0.8b12__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.8-beta.11"
+__version__ = "0.0.8-beta.12"

risk/annotations/annotations.py

@@ -186,9 +186,7 @@ def get_description(words_column: pd.Series) -> str:
 
     # Ensure that all values in 'words' are strings and include both alphabetic and numeric tokens
     words = [
-        str(
-            word.lower() if word.istitle() else word
-        )  # Convert to string and lowercase all words except proper nouns (e.g., RNA, mRNA)
+        str(word)  # Convert to string to ensure consistent processing
         for word in tokens
         if word.isalpha()
         or word.replace(".", "", 1).isdigit()  # Keep alphabetic words and numeric strings

risk/network/graph.py

@@ -216,9 +216,17 @@ def _transform_colors(
     Returns:
         np.ndarray: The transformed array of RGBA colors with adjusted intensities.
     """
+    # Ensure that min_scale is less than max_scale
     if min_scale == max_scale:
         min_scale = max_scale - 10e-6  # Avoid division by zero
 
+    # Replace black colors (#000000) with very dark grey (#1A1A1A)
+    black_color = np.array([0.0, 0.0, 0.0])  # Pure black RGB
+    dark_grey = np.array([0.1, 0.1, 0.1])  # Very dark grey RGB (#1A1A1A)
+    # Check where colors are black (very close to [0, 0, 0]) and replace with dark grey
+    is_black = np.all(colors[:, :3] == black_color, axis=1)
+    colors[is_black, :3] = dark_grey
+
     # 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

risk/network/plot/canvas.py

@@ -208,8 +208,8 @@ class Canvas:
             perimeter_fill_alpha=fill_alpha,
         )
 
-        # Convert color to RGBA using the to_rgba helper function - use outline_alpha for the perimeter
-        color = to_rgba(color=color, alpha=outline_alpha)
+        # Convert color to RGBA using outline_alpha for the line (outline)
+        outline_color = to_rgba(color=color)
         # Extract node coordinates from the network graph
         node_coordinates = self.graph.node_coordinates
         # Scale the node coordinates if needed
@@ -222,8 +222,9 @@ class Canvas:
             levels=levels,
             bandwidth=bandwidth,
             grid_size=grid_size,
-            color=color,
+            color=outline_color,
             linestyle=linestyle,
             linewidth=linewidth,
-            alpha=fill_alpha,
+            alpha=outline_alpha,
+            fill_alpha=fill_alpha,
         )

risk/network/plot/labels.py

@@ -34,6 +34,7 @@ class Labels:
         scale: float = 1.05,
         offset: float = 0.10,
         font: str = "Arial",
+        fontcase: Union[str, None] = None,
         fontsize: int = 10,
         fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
         fontalpha: Union[float, None] = 1.0,
@@ -59,6 +60,8 @@ class Labels:
             scale (float, optional): Scale factor for positioning labels around the perimeter. Defaults to 1.05.
             offset (float, optional): Offset distance for labels from the perimeter. Defaults to 0.10.
             font (str, optional): Font name for the labels. Defaults to "Arial".
+            fontcase (str, None, optional): Case transformation for the labels. Can be "capitalize", "lower", "title",
+                "upper", or None. Defaults to None.
             fontsize (int, optional): Font size for the labels. Defaults to 10.
             fontcolor (str, list, tuple, or np.ndarray, optional): Color of the label text. Can be a string or RGBA array.
                 Defaults to "black".
@@ -92,6 +95,7 @@ class Labels:
             label_perimeter_scale=scale,
             label_offset=offset,
             label_font=font,
+            label_fontcase=fontcase,
             label_fontsize=fontsize,
             label_fontcolor=(
                 "custom" if isinstance(fontcolor, np.ndarray) else fontcolor
@@ -198,6 +202,8 @@ class Labels:
             centroid = filtered_domain_centroids[domain]
             # Split by special key TERM_DELIMITER to split annotation into multiple lines
             annotations = filtered_domain_terms[domain].split(TERM_DELIMITER)
+            if fontcase is not None:
+                annotations = _apply_str_transformation(words=annotations, transformation=fontcase)
             self.ax.annotate(
                 "\n".join(annotations),
                 xy=centroid,
@@ -847,3 +853,25 @@ def _swap_and_evaluate(
     )
     # Calculate and return the total distance after the swap
     return _calculate_total_distance(swapped_positions, domain_centroids)
+
+
+def _apply_str_transformation(words: List[str], transformation: str) -> List[str]:
+    """Apply a user-specified case transformation to each word in the list without appending duplicates.
+
+    Args:
+        words (List[str]): A list of words to transform.
+        transformation (str): The case transformation to apply (e.g., 'lower', 'upper', 'title', 'capitalize').
+
+    Returns:
+        List[str]: A list of transformed words with no duplicates.
+    """
+    transformed_words = []
+    for word in words:
+        if hasattr(word, transformation):
+            transformed_word = getattr(word, transformation)()  # Apply the string method
+
+            # Only append if the transformed word is not already in the list
+            if transformed_word not in transformed_words:
+                transformed_words.append(transformed_word)
+
+    return transformed_words

{risk_network-0.0.8b11.dist-info → risk_network-0.0.8b12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b11
+Version: 0.0.8b12
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b11.dist-info → risk_network-0.0.8b12.dist-info}/RECORD

@@ -1,8 +1,8 @@
-risk/__init__.py,sha256=ZJtZA9wcK29HLGsFPkNjrQgiIa3Le1AHM1yAgOa77WA,113
+risk/__init__.py,sha256=likYFfZ5PmIhnkglQu8_zeaHGOBKURKzUUbrBCBZY8o,113
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=slJXca_a726_D7oXwe765HaKTv3ZrOvhttyrWdCGPkA,21231
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
-risk/annotations/annotations.py,sha256=ySc_N3nXnKx5RnOpFaEkM6zvTbswbrRcfFLzM0KdOck,11391
+risk/annotations/annotations.py,sha256=7ilzXxrlHqN75J3q8WeHz0n79D-jAtUQx5czvC9wfIM,11303
 risk/annotations/io.py,sha256=TTXVJQgUGAlKpnGBcx7Dow146IGyozA03nSbl3S7M5M,9475
 risk/log/__init__.py,sha256=aDUz5LMFQsz0UlsQI2EdXtiBKRLfml1UMeZKC7QQIGU,134
 risk/log/config.py,sha256=m8pzj-hN4vI_2JdJUfyOoSvzT8_lhoIfBt27sKbnOes,4535
@@ -13,12 +13,12 @@ risk/neighborhoods/domains.py,sha256=D5MUIghbwyKKCAE8PN_HXvsO9NxLTGejQmyEqetD1Bk
 risk/neighborhoods/neighborhoods.py,sha256=M-wL4xB_BUTlSZg90swygO5NdrZ6hFUFqs6jsiZaqHk,18260
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
-risk/network/graph.py,sha256=EwD4-1THC5YNdP6PY01Oe35k2QYYqtZpxWraPVH6wa4,16426
+risk/network/graph.py,sha256=yuWqXG4p3Pmad_7dHcPweLgOd8t4LoeP9uQQ-ZZEdAY,16866
 risk/network/io.py,sha256=u0PPcKjp6Xze--7eDOlvalYkjQ9S2sjiC-ac2476PUI,22942
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
-risk/network/plot/canvas.py,sha256=-Y2shCy4Udp-stB9tBXGZRTASQZiv8RVqVcQ5lBhVu0,10291
+risk/network/plot/canvas.py,sha256=LXHndwanWIBShChoPag8zgGHF2P9MFWYdEnLKc2eeb0,10295
 risk/network/plot/contour.py,sha256=YPG8Uz0VlJ4skLdGaTH_FmQN6A_ArK8XSTNo1LzkSws,14276
-risk/network/plot/labels.py,sha256=MXUo5F5H1ynzEBkrh5XKE-COLuZ-4LhSxiUvkXSZKYQ,40810
+risk/network/plot/labels.py,sha256=PV21hig6gQJZRgfUAP9-zpn4wEmQFEjS2_X63SgzWMs,42064
 risk/network/plot/network.py,sha256=83ZXjGGrgRprWvDldWfhRe6SFXTv_QoI20OWzyEmVJU,12593
 risk/network/plot/plotter.py,sha256=rQV4Db6Ud86FJm11uaBvgSuzpmGsrZxnsRnUKjg6w84,5572
 risk/network/plot/utils.py,sha256=jZgI8EysSjviQmdYAceZk2MwJXcdeFAkYp-odZNqV0k,6316
@@ -29,8 +29,8 @@ 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=D84Rcpt6iTQniK0PfQGcw9bLcHbMt9p-ARcurUnIXZQ,10095
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.8b11.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.8b11.dist-info/METADATA,sha256=nlUZJH0fpHPUq9lgGvlNJY0Ibf5QBLYoQ6WB6dlGqNc,47498
-risk_network-0.0.8b11.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-risk_network-0.0.8b11.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.8b11.dist-info/RECORD,,
+risk_network-0.0.8b12.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.8b12.dist-info/METADATA,sha256=-wKC6cGDbBGW7fG0wmdkxHRZKHvC5knHUYMqD0egagI,47498
+risk_network-0.0.8b12.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+risk_network-0.0.8b12.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.8b12.dist-info/RECORD,,