risk-network 0.0.8b13__py3-none-any.whl → 0.0.8b15__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.13"
+__version__ = "0.0.8-beta.15"

risk/network/graph.py

@@ -203,7 +203,8 @@ def _transform_colors(
     max_scale: float = 1.0,
     scale_factor: float = 1.0,
 ) -> np.ndarray:
-    """Transform colors using power scaling to emphasize high enrichment sums more.
+    """Transform colors using power scaling to emphasize high enrichment sums more. Black colors are replaced with
+    very dark grey to avoid issues with color scaling (rgb(0.1, 0.1, 0.1)).
 
     Args:
         colors (np.ndarray): An array of RGBA colors.

risk/network/plot/labels.py

@@ -34,7 +34,7 @@ class Labels:
         scale: float = 1.05,
         offset: float = 0.10,
         font: str = "Arial",
-        fontcase: Union[str, None] = None,
+        fontcase: Union[str, Dict[str, str], None] = None,
         fontsize: int = 10,
         fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
         fontalpha: Union[float, None] = 1.0,
@@ -60,8 +60,10 @@ 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.
+            fontcase (Union[str, Dict[str, str], None]): Defines how to transform the case of words.
+                - If a string (e.g., 'upper', 'lower', 'title'), applies the transformation to all words.
+                - If a dictionary, maps specific cases ('lower', 'upper', 'title') to transformations (e.g., 'lower'='upper').
+                - If None, no transformation is applied.
             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".
@@ -855,23 +857,43 @@ def _swap_and_evaluate(
     return _calculate_total_distance(swapped_positions, domain_centroids)
 
 
-def _apply_str_transformation(words: List[str], transformation: str) -> List[str]:
+def _apply_str_transformation(
+    words: List[str], transformation: Union[str, Dict[str, 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').
+        transformation (Union[str, Dict[str, str]]): A single transformation (e.g., 'lower', 'upper', 'title', 'capitalize')
+            or a dictionary mapping cases ('lower', 'upper', 'title') to transformations (e.g., 'lower'='upper').
 
     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)
+        # Convert the word to a string if it is not already
+        word = str(word)
+        transformed_word = word  # Start with the original word
+        # If transformation is a string, apply it to all words
+        if isinstance(transformation, str):
+            if hasattr(word, transformation):
+                transformed_word = getattr(
+                    word, transformation
+                )()  # Apply the single transformation
+
+        # If transformation is a dictionary, apply case-specific transformations
+        elif isinstance(transformation, dict):
+            for case_type, transform in transformation.items():
+                if case_type == "lower" and word.islower() and transform:
+                    transformed_word = getattr(word, transform)()
+                elif case_type == "upper" and word.isupper() and transform:
+                    transformed_word = getattr(word, transform)()
+                elif case_type == "title" and word.istitle() and transform:
+                    transformed_word = getattr(word, transform)()
+
+        # 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/plot/network.py

@@ -234,22 +234,18 @@ class Network:
         network_colors[:, 3] = alpha  # Apply the alpha value to the enriched nodes' A channel
         # Convert the non-enriched color to RGBA using the to_rgba helper function
         nonenriched_color = to_rgba(color=nonenriched_color, alpha=nonenriched_alpha)
-
-        # Compute the sum of RGB values for each color (ignoring alpha)
-        color_sums = network_colors[:, :3].sum(axis=1)
-        # Find the index of the darkest color (the lowest sum of RGB values)
-        darkest_color_index = np.argmin(color_sums)
-        # Extract the darkest color's RGB values
-        darkest_color = network_colors[darkest_color_index, :3]
-        # Adjust node colors: replace the darkest color with the non-enriched color
+        # Adjust node colors: replace any nodes where all three RGB values are equal and less than 0.1
+        # 0.1 is a predefined threshold for the minimum color intensity
         adjusted_network_colors = np.where(
-            np.all(
-                network_colors[:, :3] == darkest_color, axis=1, keepdims=True
-            ),  # Check if the color matches the darkest color
-            np.array(nonenriched_color),  # Apply the non-enriched color with alpha
-            network_colors,  # Keep the original colors for enriched nodes
+            (
+                np.all(network_colors[:, :3] < 0.1, axis=1)
+                & np.all(network_colors[:, :3] == network_colors[:, 0:1], axis=1)
+            )[:, None],
+            np.tile(
+                np.array(nonenriched_color), (network_colors.shape[0], 1)
+            ),  # Replace with the full RGBA non-enriched color
+            network_colors,  # Keep the original colors where no match is found
         )
-
         return adjusted_network_colors
 
     def get_annotated_node_sizes(

{risk_network-0.0.8b13.dist-info → risk_network-0.0.8b15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b13
+Version: 0.0.8b15
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b13.dist-info → risk_network-0.0.8b15.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=NFLV6xDRDZaq7QKj28pf0H3eQA2SphZ1FXgsKXfGbkk,113
+risk/__init__.py,sha256=IvvDrNrYMIFlFEmfZ6J1gTBoHqc33MwADdxoLjnyZg4,113
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=slJXca_a726_D7oXwe765HaKTv3ZrOvhttyrWdCGPkA,21231
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
@@ -13,13 +13,13 @@ 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=yuWqXG4p3Pmad_7dHcPweLgOd8t4LoeP9uQQ-ZZEdAY,16866
+risk/network/graph.py,sha256=WxWh1BZvH9E_kgDb5HrwcQ-30hM8aNHPkBm2l3vzkAw,16973
 risk/network/io.py,sha256=u0PPcKjp6Xze--7eDOlvalYkjQ9S2sjiC-ac2476PUI,22942
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
 risk/network/plot/canvas.py,sha256=LXHndwanWIBShChoPag8zgGHF2P9MFWYdEnLKc2eeb0,10295
 risk/network/plot/contour.py,sha256=YPG8Uz0VlJ4skLdGaTH_FmQN6A_ArK8XSTNo1LzkSws,14276
-risk/network/plot/labels.py,sha256=PV21hig6gQJZRgfUAP9-zpn4wEmQFEjS2_X63SgzWMs,42064
-risk/network/plot/network.py,sha256=iikZpPKFxeIJgAlp0Wd6kXVzVp341wHpvQ2vLFdQELw,13000
+risk/network/plot/labels.py,sha256=MQqM6iJJW91JI_dHzaFRbkrjK0yxJc5WBhTc_ea7Unk,43371
+risk/network/plot/network.py,sha256=t5eMh7mBJOh_Wa19aK8g_1zpL7maiXZAYw-TEFHxAVM,12819
 risk/network/plot/plotter.py,sha256=rQV4Db6Ud86FJm11uaBvgSuzpmGsrZxnsRnUKjg6w84,5572
 risk/network/plot/utils.py,sha256=jZgI8EysSjviQmdYAceZk2MwJXcdeFAkYp-odZNqV0k,6316
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
@@ -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-0.0.8b13.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.8b13.dist-info/METADATA,sha256=_Fn1n_WLyoZ8NTHq_bfr3tnx9_16CXcmvyWWrclNNFY,47498
-risk_network-0.0.8b13.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-risk_network-0.0.8b13.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.8b13.dist-info/RECORD,,
+risk_network-0.0.8b15.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.8b15.dist-info/METADATA,sha256=4hN4nT8j1a52ghqyJQ0mhjaVuhw2mt3EgKMAjpYTagY,47498
+risk_network-0.0.8b15.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+risk_network-0.0.8b15.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.8b15.dist-info/RECORD,,