risk-network 0.0.9b3__py3-none-any.whl → 0.0.9b5__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.3"
+__version__ = "0.0.9-beta.5"

risk/annotations/annotations.py

@@ -65,8 +65,9 @@ def load_annotations(network: nx.Graph, annotations_input: Dict[str, Any]) -> Di
             "No annotations found in the annotations file for the nodes in the network."
         )
 
-    # Remove columns with all zeros to improve performance
-    annotations_pivot = annotations_pivot.loc[:, annotations_pivot.sum(axis=0) != 0]
+    # Remove columns with all zeros and those with only a single '1' to improve statistical performance
+    # (i.e., it's unreliable to compute the significance of an annotation in a node cluster based on a single occurrence).
+    annotations_pivot = annotations_pivot.loc[:, (annotations_pivot.sum(axis=0) > 1)]
     # Extract ordered nodes and annotations
     ordered_nodes = tuple(annotations_pivot.index)
     ordered_annotations = tuple(annotations_pivot.columns)

risk/network/graph/network.py

@@ -114,21 +114,38 @@ class NetworkGraph:
     def _create_domain_id_to_domain_info_map(
         trimmed_domains: pd.DataFrame,
     ) -> Dict[int, Dict[str, Any]]:
-        """Create a mapping from domain IDs to their corresponding full description and significance score.
+        """Create a mapping from domain IDs to their corresponding full description and significance score,
+        with scores sorted in descending order.
 
         Args:
             trimmed_domains (pd.DataFrame): DataFrame containing domain IDs, full descriptions, and significance scores.
 
         Returns:
-            Dict[int, Dict[str, Any]]: A dictionary mapping domain IDs (int) to a dictionary with 'full_descriptions' and 'significance_scores'.
+            Dict[int, Dict[str, Any]]: A dictionary mapping domain IDs (int) to a dictionary with 'full_descriptions' and
+                'significance_scores', both sorted by significance score in descending order.
         """
-        return {
-            int(id_): {
-                "full_descriptions": trimmed_domains.at[id_, "full_descriptions"],
-                "significance_scores": trimmed_domains.at[id_, "significance_scores"],
+        # Initialize an empty dictionary to store full descriptions and significance scores of domains
+        domain_info_map = {}
+        # Domain IDs are the index of the DataFrame (it's common for some IDs to be missing)
+        for domain_id in trimmed_domains.index:
+            # Sort full_descriptions and significance_scores by significance_scores in descending order
+            descriptions_and_scores = sorted(
+                zip(
+                    trimmed_domains.at[domain_id, "full_descriptions"],
+                    trimmed_domains.at[domain_id, "significance_scores"],
+                ),
+                key=lambda x: x[1],  # Sort by significance score
+                reverse=True,  # Descending order
+            )
+            # Unzip the sorted tuples back into separate lists
+            sorted_descriptions, sorted_scores = zip(*descriptions_and_scores)
+            # Assign to the domain info map
+            domain_info_map[int(domain_id)] = {
+                "full_descriptions": list(sorted_descriptions),
+                "significance_scores": list(sorted_scores),
             }
-            for id_ in trimmed_domains.index
-        }
+
+        return domain_info_map
 
     @staticmethod
     def _create_node_id_to_domain_ids_and_significances(domains: pd.DataFrame) -> Dict[int, Dict]:

risk/network/graph/summary.py

@@ -25,7 +25,7 @@ class AnalysisSummary:
         self,
         annotations: Dict[str, Any],
         neighborhoods: Dict[str, Any],
-        graph,  # Avoid type hinting NetworkGraph to avoid circular import
+        graph,  # Avoid type hinting NetworkGraph to prevent circular imports
     ):
         """Initialize the Results object with analysis components.
 
@@ -47,7 +47,7 @@ class AnalysisSummary:
         # Load results and export directly to CSV
         results = self.load()
         results.to_csv(filepath, index=False)
-        logger.info(f"Results summary exported to CSV file: {filepath}")
+        logger.info(f"Analysis summary exported to CSV file: {filepath}")
 
     def to_json(self, filepath: str) -> None:
         """Export significance results to a JSON file.
@@ -58,7 +58,7 @@ class AnalysisSummary:
         # Load results and export directly to JSON
         results = self.load()
         results.to_json(filepath, orient="records", indent=4)
-        logger.info(f"Results summary exported to JSON file: {filepath}")
+        logger.info(f"Analysis summary exported to JSON file: {filepath}")
 
     def to_txt(self, filepath: str) -> None:
         """Export significance results to a text file.
@@ -71,15 +71,11 @@ class AnalysisSummary:
         with open(filepath, "w") as txt_file:
             txt_file.write(results.to_string(index=False))
 
-        logger.info(f"Results summary exported to text file: {filepath}")
+        logger.info(f"Analysis summary exported to text file: {filepath}")
 
     def load(self) -> pd.DataFrame:
         """Load and process domain and annotation data into a DataFrame with significance metrics.
 
-        Args:
-            graph (Any): Graph object containing domain-to-node and node-to-label mappings.
-            annotations (Dict[str, Any]): Annotation details, including ordered annotations and matrix.
-
         Returns:
             pd.DataFrame: Processed DataFrame containing significance scores, p-values, q-values,
                 and annotation member information.
@@ -128,7 +124,7 @@ class AnalysisSummary:
         results["Annotation Members in Network"] = results["Annotation"].apply(
             lambda desc: self._get_annotation_members(desc)
         )
-        results["Annotation Member in Network Count"] = results[
+        results["Annotation Members in Network Count"] = results[
             "Annotation Members in Network"
         ].apply(lambda x: len(x.split(";")) if x else 0)
 
@@ -139,7 +135,7 @@ class AnalysisSummary:
                     "Domain ID",
                     "Annotation",
                     "Annotation Members in Network",
-                    "Annotation Member in Network Count",
+                    "Annotation Members in Network Count",
                     "Summed Significance Score",
                     "Enrichment P-value",
                     "Enrichment Q-value",

risk/network/plot/contour.py

@@ -3,7 +3,7 @@ risk/network/plot/contour
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
-from typing import List, Tuple, Union
+from typing import Any, Dict, List, Tuple, Union
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -63,6 +63,8 @@ class Contour:
             contour_color=(
                 "custom" if isinstance(color, np.ndarray) else color
             ),  # np.ndarray usually indicates custom colors
+            contour_linestyle=linestyle,
+            contour_linewidth=linewidth,
             contour_alpha=alpha,
             contour_fill_alpha=fill_alpha,
         )
@@ -280,6 +282,7 @@ class Contour:
         min_scale: float = 0.8,
         max_scale: float = 1.0,
         scale_factor: float = 1.0,
+        ids_to_colors: Union[Dict[int, Any], None] = None,
         random_seed: int = 888,
     ) -> np.ndarray:
         """Get colors for the contours based on node annotations or a specified colormap.
@@ -296,6 +299,7 @@ class Contour:
                 Controls the brightest colors. Defaults to 1.0.
             scale_factor (float, optional): Exponent for adjusting color scaling based on significance scores.
                 A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
+            ids_to_colors (Dict[int, Any], None, optional): Mapping of domain IDs to specific colors. Defaults to None.
             random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
 
         Returns:
@@ -310,6 +314,7 @@ class Contour:
             min_scale=min_scale,
             max_scale=max_scale,
             scale_factor=scale_factor,
+            ids_to_colors=ids_to_colors,
             random_seed=random_seed,
         )
 

risk/network/plot/labels.py

@@ -54,7 +54,7 @@ class Labels:
         words_to_omit: Union[List, None] = None,
         overlay_ids: bool = False,
         ids_to_keep: Union[List, Tuple, np.ndarray, None] = None,
-        ids_to_replace: Union[Dict, None] = None,
+        ids_to_labels: Union[Dict[int, str], None] = None,
     ) -> None:
         """Annotate the network graph with labels for different domains, positioned around the network for clarity.
 
@@ -62,7 +62,7 @@ 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 (Union[str, Dict[str, str], None]): Defines how to transform the case of words.
+            fontcase (str, Dict[str, str], or None, optional): 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.
@@ -87,7 +87,7 @@ class Labels:
             overlay_ids (bool, optional): Whether to overlay domain IDs in the center of the centroids. Defaults to False.
             ids_to_keep (List, Tuple, np.ndarray, or None, optional): IDs of domains that must be labeled. To discover domain IDs,
                 you can set `overlay_ids=True`. Defaults to None.
-            ids_to_replace (Dict, optional): A dictionary mapping domain IDs to custom labels (strings). The labels should be
+            ids_to_labels (Dict[int, str], optional): A dictionary mapping domain IDs to custom labels (strings). The labels should be
                 space-separated words. If provided, the custom labels will replace the default domain terms. To discover domain IDs, you
                 can set `overlay_ids=True`. Defaults to None.
 
@@ -119,7 +119,7 @@ class Labels:
             label_words_to_omit=words_to_omit,
             label_overlay_ids=overlay_ids,
             label_ids_to_keep=ids_to_keep,
-            label_ids_to_replace=ids_to_replace,
+            label_ids_to_labels=ids_to_labels,
         )
 
         # Convert ids_to_keep to a tuple if it is not None
@@ -152,7 +152,7 @@ class Labels:
             self._process_ids_to_keep(
                 domain_id_to_centroid_map=domain_id_to_centroid_map,
                 ids_to_keep=ids_to_keep,
-                ids_to_replace=ids_to_replace,
+                ids_to_labels=ids_to_labels,
                 words_to_omit=words_to_omit,
                 max_labels=max_labels,
                 min_label_lines=min_label_lines,
@@ -173,7 +173,7 @@ class Labels:
             self._process_remaining_domains(
                 domain_id_to_centroid_map=domain_id_to_centroid_map,
                 ids_to_keep=ids_to_keep,
-                ids_to_replace=ids_to_replace,
+                ids_to_labels=ids_to_labels,
                 words_to_omit=words_to_omit,
                 remaining_labels=remaining_labels,
                 min_chars_per_line=min_chars_per_line,
@@ -368,7 +368,7 @@ class Labels:
         self,
         domain_id_to_centroid_map: Dict[str, np.ndarray],
         ids_to_keep: Union[List[str], Tuple[str], np.ndarray],
-        ids_to_replace: Union[Dict[str, str], None],
+        ids_to_labels: Union[Dict[int, str], None],
         words_to_omit: Union[List[str], None],
         max_labels: Union[int, None],
         min_label_lines: int,
@@ -384,7 +384,7 @@ class Labels:
         Args:
             domain_id_to_centroid_map (Dict[str, np.ndarray]): Mapping of domain IDs to their centroids.
             ids_to_keep (List, Tuple, or np.ndarray, optional): IDs of domains that must be labeled.
-            ids_to_replace (Dict[str, str], optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
+            ids_to_labels (Dict[int, str], None, optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
             words_to_omit (List, optional): List of words to omit from the labels. Defaults to None.
             max_labels (int, optional): Maximum number of labels allowed.
             min_label_lines (int): Minimum number of lines in a label.
@@ -419,7 +419,7 @@ class Labels:
                     domain=domain,
                     domain_centroid=domain_centroid,
                     domain_id_to_centroid_map=domain_id_to_centroid_map,
-                    ids_to_replace=ids_to_replace,
+                    ids_to_labels=ids_to_labels,
                     words_to_omit=words_to_omit,
                     min_label_lines=min_label_lines,
                     max_label_lines=max_label_lines,
@@ -434,7 +434,7 @@ class Labels:
         self,
         domain_id_to_centroid_map: Dict[str, np.ndarray],
         ids_to_keep: Union[List[str], Tuple[str], np.ndarray],
-        ids_to_replace: Union[Dict[str, str], None],
+        ids_to_labels: Union[Dict[int, str], None],
         words_to_omit: Union[List[str], None],
         remaining_labels: int,
         min_label_lines: int,
@@ -450,7 +450,7 @@ class Labels:
         Args:
             domain_id_to_centroid_map (Dict[str, np.ndarray]): Mapping of domain IDs to their centroids.
             ids_to_keep (List, Tuple, or np.ndarray, optional): IDs of domains that must be labeled.
-            ids_to_replace (Dict[str, str], optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
+            ids_to_labels (Dict[int, str], None, optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
             words_to_omit (List, optional): List of words to omit from the labels. Defaults to None.
             remaining_labels (int): The remaining number of labels that can be generated.
             min_label_lines (int): Minimum number of lines in a label.
@@ -515,7 +515,7 @@ class Labels:
                 domain=domain,
                 domain_centroid=domain_centroid,
                 domain_id_to_centroid_map=domain_id_to_centroid_map,
-                ids_to_replace=ids_to_replace,
+                ids_to_labels=ids_to_labels,
                 words_to_omit=words_to_omit,
                 min_label_lines=min_label_lines,
                 max_label_lines=max_label_lines,
@@ -536,7 +536,7 @@ class Labels:
         domain: str,
         domain_centroid: np.ndarray,
         domain_id_to_centroid_map: Dict[str, np.ndarray],
-        ids_to_replace: Union[Dict[str, str], None],
+        ids_to_labels: Union[Dict[int, str], None],
         words_to_omit: Union[List[str], None],
         min_label_lines: int,
         max_label_lines: int,
@@ -552,7 +552,7 @@ class Labels:
             domain (str): Domain ID to process.
             domain_centroid (np.ndarray): Centroid position of the domain.
             domain_id_to_centroid_map (Dict[str, np.ndarray]): Mapping of domain IDs to their centroids.
-            ids_to_replace (Dict[str, str], None, optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
+            ids_to_labels (Dict[int, str], None, optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
             words_to_omit (List[str], None, optional): List of words to omit from the labels. Defaults to None.
             min_label_lines (int): Minimum number of lines required in a label.
             max_label_lines (int): Maximum number of lines allowed in a label.
@@ -571,7 +571,7 @@ class Labels:
         # Process the domain terms
         domain_terms = self._process_terms(
             domain=domain,
-            ids_to_replace=ids_to_replace,
+            ids_to_labels=ids_to_labels,
             words_to_omit=words_to_omit,
             max_label_lines=max_label_lines,
             min_chars_per_line=min_chars_per_line,
@@ -596,7 +596,7 @@ class Labels:
     def _process_terms(
         self,
         domain: str,
-        ids_to_replace: Union[Dict[str, str], None],
+        ids_to_labels: Union[Dict[int, str], None],
         words_to_omit: Union[List[str], None],
         max_label_lines: int,
         min_chars_per_line: int,
@@ -606,8 +606,8 @@ class Labels:
 
         Args:
             domain (str): The domain being processed.
-            ids_to_replace (Dict[str, str], optional): Dictionary mapping domain IDs to custom labels.
-            words_to_omit (List, optional): List of words to omit from the labels.
+            ids_to_labels (Dict[int, str], None): Dictionary mapping domain IDs to custom labels.
+            words_to_omit (List[str], None): List of words to omit from the labels.
             max_label_lines (int): Maximum number of lines in a label.
             min_chars_per_line (int): Minimum number of characters in a line to display.
             max_chars_per_line (int): Maximum number of characters in a line to display.
@@ -615,9 +615,9 @@ class Labels:
         Returns:
             str: Processed terms separated by TERM_DELIMITER, with words combined if necessary to fit within constraints.
         """
-        # Return custom labels if domain is in ids_to_replace
-        if ids_to_replace and domain in ids_to_replace:
-            terms = ids_to_replace[domain].replace(" ", TERM_DELIMITER)
+        # Return custom labels if domain is in ids_to_labels
+        if ids_to_labels and domain in ids_to_labels:
+            terms = ids_to_labels[domain].replace(" ", TERM_DELIMITER)
             return terms
 
         else:
@@ -645,6 +645,7 @@ class Labels:
         min_scale: float = 0.8,
         max_scale: float = 1.0,
         scale_factor: float = 1.0,
+        ids_to_colors: Union[Dict[int, Any], None] = None,
         random_seed: int = 888,
     ) -> np.ndarray:
         """Get colors for the labels based on node annotations or a specified colormap.
@@ -661,6 +662,7 @@ class Labels:
                 Controls the brightest colors. Defaults to 1.0.
             scale_factor (float, optional): Exponent for adjusting color scaling based on significance scores.
                 A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
+            ids_to_colors (Dict[int, Any], None, optional): Mapping of domain IDs to specific colors. Defaults to None.
             random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
 
         Returns:
@@ -675,6 +677,7 @@ class Labels:
             min_scale=min_scale,
             max_scale=max_scale,
             scale_factor=scale_factor,
+            ids_to_colors=ids_to_colors,
             random_seed=random_seed,
         )
 

risk/network/plot/network.py

@@ -3,7 +3,7 @@ risk/network/plot/network
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
-from typing import Any, List, Tuple, Union
+from typing import Any, Dict, List, Tuple, Union
 
 import networkx as nx
 import numpy as np
@@ -205,6 +205,7 @@ class Network:
         alpha: Union[float, None] = 1.0,
         nonsignificant_color: Union[str, List, Tuple, np.ndarray] = "white",
         nonsignificant_alpha: Union[float, None] = 1.0,
+        ids_to_colors: Union[Dict[int, Any], None] = None,
         random_seed: int = 888,
     ) -> np.ndarray:
         """Adjust the colors of nodes in the network graph based on significance.
@@ -224,6 +225,7 @@ class Network:
                 Defaults to "white".
             nonsignificant_alpha (float, None, optional): Alpha value for non-significant nodes. If provided, it overrides any existing alpha values found
                 in `nonsignificant_color`. Defaults to 1.0.
+            ids_to_colors (Dict[int, Any], None, optional): Mapping of domain IDs to specific colors. Defaults to None.
             random_seed (int, optional): Seed for random number generation. Defaults to 888.
 
         Returns:
@@ -239,6 +241,7 @@ class Network:
             min_scale=min_scale,
             max_scale=max_scale,
             scale_factor=scale_factor,
+            ids_to_colors=ids_to_colors,
             random_seed=random_seed,
         )
         # Apply the alpha value for significant nodes

risk/network/plot/utils/color.py

@@ -7,6 +7,7 @@ from typing import Any, Dict, List, Tuple, Union
 
 import matplotlib
 import matplotlib.colors as mcolors
+import networkx as nx
 import numpy as np
 
 from risk.network.graph import NetworkGraph
@@ -22,6 +23,7 @@ def get_annotated_domain_colors(
     min_scale: float = 0.8,
     max_scale: float = 1.0,
     scale_factor: float = 1.0,
+    ids_to_colors: Union[Dict[int, Any], None] = None,
     random_seed: int = 888,
 ) -> np.ndarray:
     """Get colors for the domains based on node annotations, or use a specified color.
@@ -37,6 +39,7 @@ def get_annotated_domain_colors(
         max_scale (float, optional): Maximum scale for color intensity when generating domain colors. Defaults to 1.0.
         scale_factor (float, optional): Factor for adjusting the contrast in the colors generated based on significance. Higher values
             increase the contrast. Defaults to 1.0.
+        ids_to_colors (Dict[int, Any], None, optional): Mapping of domain IDs to specific colors. Defaults to None.
         random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
 
     Returns:
@@ -52,6 +55,7 @@ def get_annotated_domain_colors(
         min_scale=min_scale,
         max_scale=max_scale,
         scale_factor=scale_factor,
+        ids_to_colors=ids_to_colors,
         random_seed=random_seed,
     )
     annotated_colors = []
@@ -59,14 +63,12 @@ def get_annotated_domain_colors(
         if len(node_ids) > 1:
             # For multi-node domains, choose the brightest color based on RGB sum
             domain_colors = np.array([node_colors[node] for node in node_ids])
-            brightest_color = domain_colors[
-                np.argmax(domain_colors[:, :3].sum(axis=1))  # Sum the RGB values
-            ]
-            annotated_colors.append(brightest_color)
+            color = domain_colors[np.argmax(domain_colors[:, :3].sum(axis=1))]  # Sum the RGB values
         else:
             # Single-node domains default to white (RGBA)
-            default_color = np.array([1.0, 1.0, 1.0, 1.0])
-            annotated_colors.append(default_color)
+            color = np.array([1.0, 1.0, 1.0, 1.0])
+
+        annotated_colors.append(color)
 
     return np.array(annotated_colors)
 
@@ -80,6 +82,7 @@ def get_domain_colors(
     min_scale: float = 0.8,
     max_scale: float = 1.0,
     scale_factor: float = 1.0,
+    ids_to_colors: Union[Dict[int, Any], None] = None,
     random_seed: int = 888,
 ) -> np.ndarray:
     """Generate composite colors for domains based on significance or specified colors.
@@ -97,16 +100,22 @@ def get_domain_colors(
             Defaults to 1.0.
         scale_factor (float, optional): Exponent for adjusting the color scaling based on significance scores. Higher values increase
             contrast by dimming lower scores more. Defaults to 1.0.
+        ids_to_colors (Dict[int, Any], None, optional): Mapping of domain IDs to specific colors. Defaults to None.
         random_seed (int, optional): Seed for random number generation to ensure reproducibility of color assignments. Defaults to 888.
 
     Returns:
         np.ndarray: Array of RGBA colors generated for each domain, based on significance or the specified color.
     """
     # Get colors for each domain
-    domain_colors = _get_domain_colors(graph=graph, cmap=cmap, color=color, random_seed=random_seed)
+    domain_ids_to_colors = _get_domain_ids_to_colors(
+        graph=graph, cmap=cmap, color=color, ids_to_colors=ids_to_colors, random_seed=random_seed
+    )
     # Generate composite colors for nodes
     node_colors = _get_composite_node_colors(
-        graph=graph, domain_colors=domain_colors, blend_colors=blend_colors, blend_gamma=blend_gamma
+        graph=graph,
+        domain_ids_to_colors=domain_ids_to_colors,
+        blend_colors=blend_colors,
+        blend_gamma=blend_gamma,
     )
     # Transform colors to ensure proper alpha values and intensity
     transformed_colors = _transform_colors(
@@ -119,10 +128,11 @@ def get_domain_colors(
     return transformed_colors
 
 
-def _get_domain_colors(
+def _get_domain_ids_to_colors(
     graph: NetworkGraph,
     cmap: str = "gist_rainbow",
     color: Union[str, List, Tuple, np.ndarray, None] = None,
+    ids_to_colors: Union[Dict[int, Any], None] = None,
     random_seed: int = 888,
 ) -> Dict[int, Any]:
     """Get colors for each domain.
@@ -132,6 +142,7 @@ def _get_domain_colors(
         cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
         color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for the domains.
             If None, the colormap will be used. Defaults to None.
+        ids_to_colors (Dict[int, Any], None, optional): Mapping of domain IDs to specific colors. Defaults to None.
         random_seed (int, optional): Seed for random number generation. Defaults to 888.
 
     Returns:
@@ -145,17 +156,30 @@ def _get_domain_colors(
         color=color,
         random_seed=random_seed,
     )
-    return dict(zip(graph.domain_id_to_node_ids_map.keys(), domain_colors))
+    # Assign colors to domains either based on the generated colormap or the user-specified colors
+    domain_ids_to_colors = {}
+    for domain_id, domain_color in zip(graph.domain_id_to_node_ids_map.keys(), domain_colors):
+        if ids_to_colors and domain_id in ids_to_colors:
+            # Convert user-specified colors to RGBA format
+            user_rgba = to_rgba(ids_to_colors[domain_id])
+            domain_ids_to_colors[domain_id] = user_rgba
+        else:
+            domain_ids_to_colors[domain_id] = domain_color
+
+    return domain_ids_to_colors
 
 
 def _get_composite_node_colors(
-    graph, domain_colors: np.ndarray, blend_colors: bool = False, blend_gamma: float = 2.2
+    graph: NetworkGraph,
+    domain_ids_to_colors: Dict[int, Any],
+    blend_colors: bool = False,
+    blend_gamma: float = 2.2,
 ) -> np.ndarray:
     """Generate composite colors for nodes based on domain colors and significance values, with optional color blending.
 
     Args:
         graph (NetworkGraph): The network data and attributes to be visualized.
-        domain_colors (np.ndarray): Array or list of RGBA colors corresponding to each domain.
+        domain_ids_to_colors (Dict[int, Any]): Mapping of domain IDs to RGBA colors.
         blend_colors (bool): Whether to blend colors for nodes with multiple domains. Defaults to False.
         blend_gamma (float, optional): Gamma correction factor to be used for perceptual color blending.
             This parameter is only relevant if blend_colors is True. Defaults to 2.2.
@@ -167,11 +191,10 @@ def _get_composite_node_colors(
     num_nodes = len(graph.node_coordinates)
     # Initialize composite colors array with shape (number of nodes, 4) for RGBA
     composite_colors = np.zeros((num_nodes, 4))
-
     # If blending is not required, directly assign domain colors to nodes
     if not blend_colors:
         for domain_id, nodes in graph.domain_id_to_node_ids_map.items():
-            color = domain_colors[domain_id]
+            color = domain_ids_to_colors[domain_id]
             for node in nodes:
                 composite_colors[node] = color
 
@@ -180,11 +203,11 @@ def _get_composite_node_colors(
         for node, node_info in graph.node_id_to_domain_ids_and_significance_map.items():
             domains = node_info["domains"]  # List of domain IDs
             significances = node_info["significances"]  # List of significance values
-            # Filter domains and significances to keep only those with corresponding colors in domain_colors
+            # Filter domains and significances to keep only those with corresponding colors in domain_ids_to_colors
             filtered_domains_significances = [
                 (domain_id, significance)
                 for domain_id, significance in zip(domains, significances)
-                if domain_id in domain_colors
+                if domain_id in domain_ids_to_colors
             ]
             # If no valid domains exist, skip this node
             if not filtered_domains_significances:
@@ -193,7 +216,7 @@ def _get_composite_node_colors(
             # Unpack filtered domains and significances
             filtered_domains, filtered_significances = zip(*filtered_domains_significances)
             # Get the colors corresponding to the valid filtered domains
-            colors = [domain_colors[domain_id] for domain_id in filtered_domains]
+            colors = [domain_ids_to_colors[domain_id] for domain_id in filtered_domains]
             # Blend the colors using the given gamma (default is 2.2 if None)
             gamma = blend_gamma if blend_gamma is not None else 2.2
             composite_color = _blend_colors_perceptually(colors, filtered_significances, gamma)
@@ -204,8 +227,8 @@ def _get_composite_node_colors(
 
 
 def _get_colors(
-    network,
-    domain_id_to_node_ids_map,
+    network: nx.Graph,
+    domain_id_to_node_ids_map: Dict[int, Any],
     cmap: str = "gist_rainbow",
     color: Union[str, List, Tuple, np.ndarray, None] = None,
     random_seed: int = 888,
@@ -214,7 +237,7 @@ def _get_colors(
     close in space get maximally separated colors, while keeping some randomness.
 
     Args:
-        network (NetworkX graph): The graph representing the network.
+        network (nx.Graph): The graph representing the network.
         domain_id_to_node_ids_map (Dict[int, Any]): Mapping from domain IDs to lists of node IDs.
         cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
         color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for the domains.
@@ -252,7 +275,7 @@ def _get_colors(
     return [colormap(pos) for pos in color_positions]
 
 
-def _assign_distant_colors(dist_matrix, num_colors_to_generate):
+def _assign_distant_colors(dist_matrix: np.ndarray, num_colors_to_generate: int) -> np.ndarray:
     """Assign colors to centroids that are close in space, ensuring stark color differences.
 
     Args:
@@ -404,7 +427,8 @@ def to_rgba(
             return np.tile(
                 rgba_color, (num_repeats, 1)
             )  # Repeat the color if num_repeats is provided
-        return np.array([rgba_color])  # Return a single color wrapped in a numpy array
+
+        return rgba_color
 
     # Handle a list/array of colors
     elif isinstance(color, (list, tuple, np.ndarray)):
@@ -421,4 +445,4 @@ def to_rgba(
         return rgba_colors
 
     else:
-        raise ValueError("Color must be a valid RGB/RGBA or array of RGB/RGBA colors.")
+        raise ValueError("Color must be a valid string, RGB/RGBA, or array of RGB/RGBA colors.")

risk/network/plot/utils/layout.py

@@ -3,8 +3,9 @@ risk/network/plot/utils/layout
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
-from typing import Tuple
+from typing import Any, Dict, List, Tuple
 
+import networkx as nx
 import numpy as np
 
 
@@ -68,11 +69,13 @@ def refine_center_iteratively(
     return center, new_radius
 
 
-def calculate_centroids(network, domain_id_to_node_ids_map):
+def calculate_centroids(
+    network: nx.Graph, domain_id_to_node_ids_map: Dict[int, Any]
+) -> List[Tuple[float, float]]:
     """Calculate the centroid for each domain based on node x and y coordinates in the network.
 
     Args:
-        network (NetworkX graph): The graph representing the network.
+        network (nx.Graph): The graph representing the network.
         domain_id_to_node_ids_map (Dict[int, Any]): Mapping from domain IDs to lists of node IDs.
 
     Returns:

{risk_network-0.0.9b3.dist-info → risk_network-0.0.9b5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b3
+Version: 0.0.9b5
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b3.dist-info → risk_network-0.0.9b5.dist-info}/RECORD

@@ -1,8 +1,8 @@
-risk/__init__.py,sha256=japxenqMvqgfrLH-PHOulkDBiW_CZRMVUaDbR92setc,112
+risk/__init__.py,sha256=xpU4eFf8OBGeA2fxuMCAFmBEQO6YlnDSVL09OvyHThs,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=De1vn8Xc-TKz6aTL0bvJI-SVrIqU3k0IWAbKc7dde1c,23618
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
-risk/annotations/annotations.py,sha256=m3WeCdE1a2undpSl_Q2I17drD95r2McKtpzhiiSdxHY,13143
+risk/annotations/annotations.py,sha256=aC30M-wdd72ZjOfn8RZKAsGM7Yti0Wl_4CHTvayoPvY,13312
 risk/annotations/io.py,sha256=eOkPD9G6KzkhGRc_ZW2McxQ8665o-H3uDG8bmKlzQ80,9591
 risk/log/__init__.py,sha256=gy7C5L6D222AYUChq5lkc0LsCJ_QMQPaFiBJKbecdac,201
 risk/log/console.py,sha256=C52s3FgQ2e9kQWcXL8m7rs_pnKXt5Yy8PBHmQkOTiNo,4537
@@ -15,16 +15,16 @@ risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=gFtYUj9j9aul4paKq_qSGJn39Nazxu_MXv8m-tYYtrk,6840
 risk/network/io.py,sha256=AWSbZGLZHtl72KSlafQlcYoG00YLSznG7UYDi_wDT7M,22958
 risk/network/graph/__init__.py,sha256=H0YEiwqZ02LBTkH4blPwUjQ-DOUnhaTTNHM0BcXii6U,81
-risk/network/graph/network.py,sha256=o7Rdp2S8cxYiT90IvGLqsn93wq9YA1vKRZ7fedLUir0,10208
-risk/network/graph/summary.py,sha256=f4j-ERlddzAhd9qEELiGdzmPqpzgoRODyHNe9QuRT7k,9190
+risk/network/graph/network.py,sha256=j75Lfwd5VGIDv0GlVoYIgN6RRua7i-PNg5D-ssgRhfo,11190
+risk/network/graph/summary.py,sha256=h2bpUjfwI1NMflkKwplGQEGPswfAtunormdTIEQYbvs,8987
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
 risk/network/plot/canvas.py,sha256=TlCpNtvoceizAumNr9I02JcBrBO6FiAFAa2ZC0bx3SU,13356
-risk/network/plot/contour.py,sha256=2ZVOlduo4Y4yIpXDJMIKO-v7eULcJ2QacQyOc7pUAxE,15267
-risk/network/plot/labels.py,sha256=YqeOhE7nah16kK3L88JnOJVqE6WWj7lm23niVdEc8cU,45504
-risk/network/plot/network.py,sha256=_yyOUoxJ_jelZV3TMCCTcGnt014TBYMUfecSLOiUb7E,13788
+risk/network/plot/contour.py,sha256=91-K9jlV3K82Ax13BoLdDeZkBR5_8AnZujAblHBK-3A,15580
+risk/network/plot/labels.py,sha256=S1UOYUB1WbsaQEVkEr5cUKQbUuebKJPKILqhL8zmQWM,45733
+risk/network/plot/network.py,sha256=vcm53MlaWd-wmaPDo8-Ap2gJPAp0SNEGZ2NiGamkJKo,14014
 risk/network/plot/plotter.py,sha256=iTPMiTnTTatM_-q1Ox_bjt5Pvv-Lo8gceiYB6TVzDcw,5770
-risk/network/plot/utils/color.py,sha256=rGOx4WAdjyaeWFALybkKzJabm9VSmsWb5_hsb__pcNg,19701
-risk/network/plot/utils/layout.py,sha256=RnJq0yODpoheZnDl7KKFPQeXrnrsS3FLIdxupoYVZq4,3553
+risk/network/plot/utils/color.py,sha256=T5qOlPhHzgLwileaVqT8Vq9A1ZQvaSMWvsCTnauAgTs,20802
+risk/network/plot/utils/layout.py,sha256=6o7idoWQnyzujSWOFXQykUvyPy8NuRtJV04TnlbXXBo,3647
 risk/stats/__init__.py,sha256=WcgoETQ-hS0LQqKRsAMIPtP15xZ-4eul6VUBuUx4Wzc,220
 risk/stats/hypergeom.py,sha256=oc39f02ViB1vQ-uaDrxG_tzAT6dxQBRjc88EK2EGn78,2282
 risk/stats/poisson.py,sha256=polLgwS08MTCNzupYdmMUoEUYrJOjAbcYtYwjlfeE5Y,1803
@@ -32,8 +32,8 @@ risk/stats/stats.py,sha256=z8NrhiVj4BzJ250bVLfytpmfC7RzYu7mBuIZD_l0aCA,7222
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=meBNSrbRa9P8WJ54n485l0H7VQJlMSfHqdN4aCKYCtQ,10105
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.9b3.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b3.dist-info/METADATA,sha256=nUhDrkDb3ZbsCcKRxKOgx6yL6t1FHK4SRbrQNjdktII,47497
-risk_network-0.0.9b3.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-risk_network-0.0.9b3.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b3.dist-info/RECORD,,
+risk_network-0.0.9b5.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b5.dist-info/METADATA,sha256=Oc_07HiBSedyTbbiP-2a-xeLgEH-3zzNdXYzV6FSdQY,47497
+risk_network-0.0.9b5.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+risk_network-0.0.9b5.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b5.dist-info/RECORD,,