risk-network 0.0.9b5__py3-none-any.whl → 0.0.9b7__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.5"
+__version__ = "0.0.9-beta.7"

risk/annotations/annotations.py

@@ -15,6 +15,8 @@ import pandas as pd
 from nltk.tokenize import word_tokenize
 from nltk.corpus import stopwords
 
+from risk.log import logger
+
 
 def _setup_nltk():
     """Ensure necessary NLTK data is downloaded."""
@@ -35,15 +37,23 @@ _setup_nltk()
 stop_words = set(stopwords.words("english"))
 
 
-def load_annotations(network: nx.Graph, annotations_input: Dict[str, Any]) -> Dict[str, Any]:
+def load_annotations(
+    network: nx.Graph, annotations_input: Dict[str, Any], min_nodes_per_term: int = 2
+) -> Dict[str, Any]:
     """Convert annotations input to a DataFrame and reindex based on the network's node labels.
 
     Args:
         network (nx.Graph): The network graph.
         annotations_input (Dict[str, Any]): A dictionary with annotations.
+        min_nodes_per_term (int, optional): The minimum number of network nodes required for each annotation
+            term to be included. Defaults to 2.
 
     Returns:
         Dict[str, Any]: A dictionary containing ordered nodes, ordered annotations, and the binary annotations matrix.
+
+    Raises:
+        ValueError: If no annotations are found for the nodes in the network.
+        ValueError: If no annotations have at least min_nodes_per_term nodes in the network.
     """
     # Flatten the dictionary to a list of tuples for easier DataFrame creation
     flattened_annotations = [
@@ -61,13 +71,24 @@ def load_annotations(network: nx.Graph, annotations_input: Dict[str, Any]) -> Di
     annotations_pivot = annotations_pivot.reindex(index=node_label_order)
     # Raise an error if no valid annotations are found for the nodes in the network
     if annotations_pivot.notnull().sum().sum() == 0:
+        raise ValueError("No terms found in the annotation file for the nodes in the network.")
+
+    # Filter out annotations with fewer than min_nodes_per_term occurrences
+    # This assists in reducing noise and focusing on more relevant annotations for statistical analysis
+    num_terms_before_filtering = annotations_pivot.shape[1]
+    annotations_pivot = annotations_pivot.loc[
+        :, (annotations_pivot.sum(axis=0) >= min_nodes_per_term)
+    ]
+    num_terms_after_filtering = annotations_pivot.shape[1]
+    # Log the number of annotations before and after filtering
+    logger.info(f"Minimum number of nodes per annotation term: {min_nodes_per_term}")
+    logger.info(f"Number of input annotation terms: {num_terms_before_filtering}")
+    logger.info(f"Number of remaining annotation terms: {num_terms_after_filtering}")
+    if num_terms_after_filtering == 0:
         raise ValueError(
-            "No annotations found in the annotations file for the nodes in the network."
+            f"No annotation terms found with at least {min_nodes_per_term} nodes in the network."
         )
 
-    # 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/annotations/io.py

@@ -25,27 +25,32 @@ class AnnotationsIO:
     def __init__(self):
         pass
 
-    def load_json_annotation(self, network: nx.Graph, filepath: str) -> Dict[str, Any]:
+    def load_json_annotation(
+        self, network: nx.Graph, filepath: str, min_nodes_per_term: int = 2
+    ) -> Dict[str, Any]:
         """Load annotations from a JSON file and convert them to a DataFrame.
 
         Args:
             network (NetworkX graph): The network to which the annotations are related.
             filepath (str): Path to the JSON annotations file.
+            min_nodes_per_term (int, optional): The minimum number of network nodes required for each annotation
+                term to be included. Defaults to 2.
 
         Returns:
             Dict[str, Any]: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
         """
         filetype = "JSON"
         # Log the loading of the JSON file
-        params.log_annotations(filepath=filepath, filetype=filetype)
+        params.log_annotations(
+            filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
+        )
         _log_loading(filetype, filepath=filepath)
 
-        # Open and read the JSON file
+        # Load the JSON file into a dictionary
         with open(filepath, "r") as file:
             annotations_input = json.load(file)
 
-        # Load the annotations into the provided network
-        return load_annotations(network, annotations_input)
+        return load_annotations(network, annotations_input, min_nodes_per_term)
 
     def load_excel_annotation(
         self,
@@ -55,6 +60,7 @@ class AnnotationsIO:
         nodes_colname: str = "nodes",
         sheet_name: str = "Sheet1",
         nodes_delimiter: str = ";",
+        min_nodes_per_term: int = 2,
     ) -> Dict[str, Any]:
         """Load annotations from an Excel file and associate them with the network.
 
@@ -65,6 +71,8 @@ class AnnotationsIO:
             nodes_colname (str): Name of the column containing the nodes associated with each label.
             sheet_name (str, optional): The name of the Excel sheet to load (default is 'Sheet1').
             nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
+            min_nodes_per_term (int, optional): The minimum number of network nodes required for each annotation
+                term to be included. Defaults to 2.
 
         Returns:
             Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes,
@@ -72,7 +80,9 @@ class AnnotationsIO:
         """
         filetype = "Excel"
         # Log the loading of the Excel file
-        params.log_annotations(filepath=filepath, filetype=filetype)
+        params.log_annotations(
+            filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
+        )
         _log_loading(filetype, filepath=filepath)
 
         # Load the specified sheet from the Excel file
@@ -82,10 +92,9 @@ class AnnotationsIO:
             lambda x: x.split(nodes_delimiter)
         )
         # Convert the DataFrame to a dictionary pairing labels with their corresponding nodes
-        label_node_dict = annotation.set_index(label_colname)[nodes_colname].to_dict()
+        annotations_input = annotation.set_index(label_colname)[nodes_colname].to_dict()
 
-        # Load the annotations into the provided network
-        return load_annotations(network, label_node_dict)
+        return load_annotations(network, annotations_input, min_nodes_per_term)
 
     def load_csv_annotation(
         self,
@@ -94,6 +103,7 @@ class AnnotationsIO:
         label_colname: str = "label",
         nodes_colname: str = "nodes",
         nodes_delimiter: str = ";",
+        min_nodes_per_term: int = 2,
     ) -> Dict[str, Any]:
         """Load annotations from a CSV file and associate them with the network.
 
@@ -103,6 +113,8 @@ class AnnotationsIO:
             label_colname (str): Name of the column containing the labels (e.g., GO terms).
             nodes_colname (str): Name of the column containing the nodes associated with each label.
             nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
+            min_nodes_per_term (int, optional): The minimum number of network nodes required for each annotation
+                term to be included. Defaults to 2.
 
         Returns:
             Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes,
@@ -110,7 +122,9 @@ class AnnotationsIO:
         """
         filetype = "CSV"
         # Log the loading of the CSV file
-        params.log_annotations(filepath=filepath, filetype=filetype)
+        params.log_annotations(
+            filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
+        )
         _log_loading(filetype, filepath=filepath)
 
         # Load the CSV file into a dictionary
@@ -118,8 +132,7 @@ class AnnotationsIO:
             filepath, label_colname, nodes_colname, delimiter=",", nodes_delimiter=nodes_delimiter
         )
 
-        # Load the annotations into the provided network
-        return load_annotations(network, annotations_input)
+        return load_annotations(network, annotations_input, min_nodes_per_term)
 
     def load_tsv_annotation(
         self,
@@ -128,6 +141,7 @@ class AnnotationsIO:
         label_colname: str = "label",
         nodes_colname: str = "nodes",
         nodes_delimiter: str = ";",
+        min_nodes_per_term: int = 2,
     ) -> Dict[str, Any]:
         """Load annotations from a TSV file and associate them with the network.
 
@@ -137,6 +151,8 @@ class AnnotationsIO:
             label_colname (str): Name of the column containing the labels (e.g., GO terms).
             nodes_colname (str): Name of the column containing the nodes associated with each label.
             nodes_delimiter (str, optional): Delimiter used to separate multiple nodes within the nodes column (default is ';').
+            min_nodes_per_term (int, optional): The minimum number of network nodes required for each annotation
+                term to be included. Defaults to 2.
 
         Returns:
             Dict[str, Any]: A dictionary where each label is paired with its respective list of nodes,
@@ -144,7 +160,9 @@ class AnnotationsIO:
         """
         filetype = "TSV"
         # Log the loading of the TSV file
-        params.log_annotations(filepath=filepath, filetype=filetype)
+        params.log_annotations(
+            filetype=filetype, filepath=filepath, min_nodes_per_term=min_nodes_per_term
+        )
         _log_loading(filetype, filepath=filepath)
 
         # Load the TSV file into a dictionary
@@ -152,15 +170,18 @@ class AnnotationsIO:
             filepath, label_colname, nodes_colname, delimiter="\t", nodes_delimiter=nodes_delimiter
         )
 
-        # Load the annotations into the provided network
-        return load_annotations(network, annotations_input)
+        return load_annotations(network, annotations_input, min_nodes_per_term)
 
-    def load_dict_annotation(self, network: nx.Graph, content: Dict[str, Any]) -> Dict[str, Any]:
+    def load_dict_annotation(
+        self, network: nx.Graph, content: Dict[str, Any], min_nodes_per_term: int = 2
+    ) -> Dict[str, Any]:
         """Load annotations from a provided dictionary and convert them to a dictionary annotation.
 
         Args:
             network (NetworkX graph): The network to which the annotations are related.
             content (Dict[str, Any]): The annotations dictionary to load.
+            min_nodes_per_term (int, optional): The minimum number of network nodes required for each annotation
+                term to be included. Defaults to 2.
 
         Returns:
             Dict[str, Any]: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
@@ -176,13 +197,8 @@ class AnnotationsIO:
         params.log_annotations(filepath="In-memory dictionary", filetype=filetype)
         _log_loading(filetype, "In-memory dictionary")
 
-        # Load the annotations into the provided network
-        annotations_dict = load_annotations(network, content)
-        # Ensure the output is a dictionary
-        if not isinstance(annotations_dict, dict):
-            raise ValueError("Expected output to be a dictionary")
-
-        return annotations_dict
+        # Load the annotations as a dictionary from the provided dictionary
+        return load_annotations(network, content, min_nodes_per_term)
 
 
 def _load_matrix_file(

risk/neighborhoods/__init__.py

@@ -3,7 +3,7 @@ risk/neighborhoods
 ~~~~~~~~~~~~~~~~~~
 """
 
-from .domains import define_domains, trim_domains_and_top_annotations
+from .domains import define_domains, trim_domains
 from .neighborhoods import (
     get_network_neighborhoods,
     process_neighborhoods,

risk/neighborhoods/domains.py

@@ -86,13 +86,13 @@ def define_domains(
     return node_to_domain
 
 
-def trim_domains_and_top_annotations(
+def trim_domains(
     domains: pd.DataFrame,
     top_annotations: pd.DataFrame,
     min_cluster_size: int = 5,
     max_cluster_size: int = 1000,
 ) -> Tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame]:
-    """Trim domains and top annotations that do not meet size criteria and find outliers.
+    """Trim domains that do not meet size criteria and find outliers.
 
     Args:
         domains (pd.DataFrame): DataFrame of domain data for the network nodes.
@@ -101,8 +101,7 @@ def trim_domains_and_top_annotations(
         max_cluster_size (int, optional): Maximum size of a cluster to be retained. Defaults to 1000.
 
     Returns:
-        Tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame]:
-            - Trimmed annotations (pd.DataFrame)
+        Tuple[pd.DataFrame, pd.DataFrame]:
             - Trimmed domains (pd.DataFrame)
             - A DataFrame with domain labels (pd.DataFrame)
     """
@@ -155,14 +154,11 @@ def trim_domains_and_top_annotations(
     ).set_index("id")
 
     # Remove invalid domains
-    valid_annotations = top_annotations[~top_annotations["domain"].isin(invalid_domain_ids)].drop(
-        columns=["normalized_value"]
-    )
     valid_domains = domains[~domains["primary_domain"].isin(invalid_domain_ids)]
     valid_trimmed_domains_matrix = trimmed_domains_matrix[
         ~trimmed_domains_matrix.index.isin(invalid_domain_ids)
     ]
-    return valid_annotations, valid_domains, valid_trimmed_domains_matrix
+    return valid_domains, valid_trimmed_domains_matrix
 
 
 def _optimize_silhouette_across_linkage_and_metrics(

risk/network/graph/network.py

@@ -27,7 +27,6 @@ class NetworkGraph:
         network: nx.Graph,
         annotations: Dict[str, Any],
         neighborhoods: Dict[str, Any],
-        top_annotations: pd.DataFrame,
         domains: pd.DataFrame,
         trimmed_domains: pd.DataFrame,
         node_label_to_node_id_map: Dict[str, Any],
@@ -39,24 +38,20 @@ class NetworkGraph:
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
             neighborhoods (Dict[str, Any]): Neighborhood significance data.
-            top_annotations (pd.DataFrame): DataFrame containing annotations data for the network nodes.
             domains (pd.DataFrame): DataFrame containing domain data for the network nodes.
             trimmed_domains (pd.DataFrame): DataFrame containing trimmed domain data for the network nodes.
             node_label_to_node_id_map (Dict[str, Any]): A dictionary mapping node labels to their corresponding IDs.
             node_significance_sums (np.ndarray): Array containing the significant sums for the nodes.
         """
         # Initialize self.network downstream of the other attributes
-        self.top_annotations = top_annotations
+        # All public attributes can be accessed after initialization
         self.domain_id_to_node_ids_map = self._create_domain_id_to_node_ids_map(domains)
-        self.domains = domains
         self.domain_id_to_domain_terms_map = self._create_domain_id_to_domain_terms_map(
             trimmed_domains
         )
         self.domain_id_to_domain_info_map = self._create_domain_id_to_domain_info_map(
             trimmed_domains
         )
-        self.trimmed_domains = trimmed_domains
-        self.node_significance_sums = node_significance_sums
         self.node_id_to_domain_ids_and_significance_map = (
             self._create_node_id_to_domain_ids_and_significances(domains)
         )
@@ -64,6 +59,7 @@ class NetworkGraph:
         self.node_label_to_significance_map = dict(
             zip(node_label_to_node_id_map.keys(), node_significance_sums)
         )
+        self.node_significance_sums = node_significance_sums
         self.node_label_to_node_id_map = node_label_to_node_id_map
 
         # NOTE: Below this point, instance attributes (i.e., self) will be used!
@@ -75,6 +71,32 @@ class NetworkGraph:
         # NOTE: Only after the above attributes are initialized, we can create the summary
         self.summary = AnalysisSummary(annotations, neighborhoods, self)
 
+    def pop(self, domain_id: str) -> None:
+        """Remove domain ID from instance domain ID mappings. This can be useful for cleaning up
+        domain-specific mappings based on a given criterion, as domain attributes are stored and
+        accessed only in dictionaries modified by this method.
+
+        Args:
+            key (str): The domain ID key to be removed from each mapping.
+        """
+        # Define the domain mappings to be updated
+        domain_mappings = [
+            self.domain_id_to_node_ids_map,
+            self.domain_id_to_domain_terms_map,
+            self.domain_id_to_domain_info_map,
+            self.domain_id_to_node_labels_map,
+        ]
+        # Remove the specified domain_id key from each mapping if it exists
+        for mapping in domain_mappings:
+            if domain_id in mapping:
+                mapping.pop(domain_id)
+
+        # Remove the domain_id from the node_id_to_domain_ids_and_significance_map
+        for node_id, domain_info in self.node_id_to_domain_ids_and_significance_map.items():
+            if domain_id in domain_info["domains"]:
+                domain_info["domains"].remove(domain_id)
+                domain_info["significances"].pop(domain_id)
+
     @staticmethod
     def _create_domain_id_to_node_ids_map(domains: pd.DataFrame) -> Dict[int, Any]:
         """Create a mapping from domains to the list of node IDs belonging to each domain.

risk/network/plot/canvas.py

@@ -10,7 +10,7 @@ import numpy as np
 
 from risk.log import params
 from risk.network.graph import NetworkGraph
-from risk.network.plot.utils.color import to_rgba
+from risk.network.plot.utils.colors import to_rgba
 from risk.network.plot.utils.layout import calculate_bounding_box
 
 

risk/network/plot/contour.py

@@ -13,7 +13,7 @@ from scipy.stats import gaussian_kde
 
 from risk.log import params, logger
 from risk.network.graph import NetworkGraph
-from risk.network.plot.utils.color import get_annotated_domain_colors, to_rgba
+from risk.network.plot.utils.colors import get_annotated_domain_colors, to_rgba
 
 
 class Contour:

risk/network/plot/labels.py

@@ -12,7 +12,7 @@ import pandas as pd
 
 from risk.log import params
 from risk.network.graph import NetworkGraph
-from risk.network.plot.utils.color import get_annotated_domain_colors, to_rgba
+from risk.network.plot.utils.colors import get_annotated_domain_colors, to_rgba
 from risk.network.plot.utils.layout import calculate_bounding_box
 
 TERM_DELIMITER = "::::"  # String used to separate multiple domain terms when constructing composite domain labels

risk/network/plot/network.py

@@ -10,7 +10,7 @@ import numpy as np
 
 from risk.log import params
 from risk.network.graph import NetworkGraph
-from risk.network.plot.utils.color import get_domain_colors, to_rgba
+from risk.network.plot.utils.colors import get_domain_colors, to_rgba
 
 
 class Network:

risk/network/plot/plotter.py

@@ -14,7 +14,7 @@ from risk.network.plot.canvas import Canvas
 from risk.network.plot.contour import Contour
 from risk.network.plot.labels import Labels
 from risk.network.plot.network import Network
-from risk.network.plot.utils.color import to_rgba
+from risk.network.plot.utils.colors import to_rgba
 from risk.network.plot.utils.layout import calculate_bounding_box
 
 

risk/network/plot/utils/{color.py → colors.py}

@@ -410,6 +410,7 @@ def to_rgba(
 
         if alpha is not None:  # Override alpha if provided
             rgba[3] = alpha
+
         return rgba
 
     # If color is a 2D array of RGBA values, convert it to a list of lists

risk/risk.py

@@ -16,7 +16,7 @@ from risk.neighborhoods import (
     define_domains,
     get_network_neighborhoods,
     process_neighborhoods,
-    trim_domains_and_top_annotations,
+    trim_domains,
 )
 from risk.network import NetworkIO, NetworkGraph, NetworkPlotter
 from risk.stats import (
@@ -335,16 +335,20 @@ class RISK(NetworkIO, AnnotationsIO):
         )
 
         log_header("Optimizing distance threshold for domains")
+        # Extract the significant significance matrix from the neighborhoods data
+        significant_neighborhoods_significance = processed_neighborhoods[
+            "significant_significance_matrix"
+        ]
         # Define domains in the network using the specified clustering settings
-        domains = self._define_domains(
-            neighborhoods=processed_neighborhoods,
+        domains = define_domains(
             top_annotations=top_annotations,
+            significant_neighborhoods_significance=significant_neighborhoods_significance,
             linkage_criterion=linkage_criterion,
             linkage_method=linkage_method,
             linkage_metric=linkage_metric,
         )
         # Trim domains and top annotations based on cluster size constraints
-        top_annotations, domains, trimmed_domains = trim_domains_and_top_annotations(
+        domains, trimmed_domains = trim_domains(
             domains=domains,
             top_annotations=top_annotations,
             min_cluster_size=min_cluster_size,
@@ -361,7 +365,6 @@ class RISK(NetworkIO, AnnotationsIO):
             network=network,
             annotations=annotations,
             neighborhoods=neighborhoods,
-            top_annotations=top_annotations,
             domains=domains,
             trimmed_domains=trimmed_domains,
             node_label_to_node_id_map=node_label_to_id,
@@ -484,34 +487,3 @@ class RISK(NetworkIO, AnnotationsIO):
             min_cluster_size=min_cluster_size,
             max_cluster_size=max_cluster_size,
         )
-
-    def _define_domains(
-        self,
-        neighborhoods: Dict[str, Any],
-        top_annotations: pd.DataFrame,
-        linkage_criterion: str,
-        linkage_method: str,
-        linkage_metric: str,
-    ) -> pd.DataFrame:
-        """Define domains in the network based on significance data.
-
-        Args:
-            neighborhoods (Dict[str, Any]): Enrichment data for neighborhoods.
-            top_annotations (pd.DataFrame): Enrichment matrix for top annotations.
-            linkage_criterion (str): Clustering criterion for defining domains.
-            linkage_method (str): Clustering method to use.
-            linkage_metric (str): Metric to use for calculating distances.
-
-        Returns:
-            pd.DataFrame: Matrix of defined domains.
-        """
-        # Extract the significant significance matrix from the neighborhoods data
-        significant_neighborhoods_significance = neighborhoods["significant_significance_matrix"]
-        # Call external function to define domains based on the extracted data
-        return define_domains(
-            top_annotations=top_annotations,
-            significant_neighborhoods_significance=significant_neighborhoods_significance,
-            linkage_criterion=linkage_criterion,
-            linkage_method=linkage_method,
-            linkage_metric=linkage_metric,
-        )

{risk_network-0.0.9b5.dist-info → risk_network-0.0.9b7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b5
+Version: 0.0.9b7
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b5.dist-info → risk_network-0.0.9b7.dist-info}/RECORD

@@ -1,29 +1,29 @@
-risk/__init__.py,sha256=xpU4eFf8OBGeA2fxuMCAFmBEQO6YlnDSVL09OvyHThs,112
+risk/__init__.py,sha256=qkmHFIeApkRQEVhb6MctmvmD84ri0SRmooehDAeIV2k,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=De1vn8Xc-TKz6aTL0bvJI-SVrIqU3k0IWAbKc7dde1c,23618
+risk/risk.py,sha256=kntBxYwAEpoAjXN_l6BM3yxFKyuAKmd8OMGl2P00pZ4,22416
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
-risk/annotations/annotations.py,sha256=aC30M-wdd72ZjOfn8RZKAsGM7Yti0Wl_4CHTvayoPvY,13312
-risk/annotations/io.py,sha256=eOkPD9G6KzkhGRc_ZW2McxQ8665o-H3uDG8bmKlzQ80,9591
+risk/annotations/annotations.py,sha256=WVT9wzTm8lTpMw_3SnbyljWR77yExo0rb1zVgJza8nw,14284
+risk/annotations/io.py,sha256=tk1dAsxIwW5oLxB294ppiuZd4__Y5pj8se8KhitRSNA,10554
 risk/log/__init__.py,sha256=gy7C5L6D222AYUChq5lkc0LsCJ_QMQPaFiBJKbecdac,201
 risk/log/console.py,sha256=C52s3FgQ2e9kQWcXL8m7rs_pnKXt5Yy8PBHmQkOTiNo,4537
 risk/log/parameters.py,sha256=o4StqYCa0kt7_Ht4mKa1DwwvhGUwkC_dGBaiUIc0GB0,5683
-risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
+risk/neighborhoods/__init__.py,sha256=C-SD0G-9skSLjLFdAB6v6lAjO8la2v6Fqy63h2MY28k,186
 risk/neighborhoods/community.py,sha256=MAgIblbuisEPwVU6mFZd4Yd9NUKlaHK99suw51r1Is0,7065
-risk/neighborhoods/domains.py,sha256=cMp2McuaSxRp7lQvzjgZnlt5dzxwyj6HAWKyT9u2sng,11662
+risk/neighborhoods/domains.py,sha256=t91xSpx9Ty9hSlhRq2_XwyPpBP7sjKhovcPPvkwWtf0,11398
 risk/neighborhoods/neighborhoods.py,sha256=0TAP-xi4hgtnrK0cKQPHQHq9IVGHOMF1wYEcx6tsxRA,22241
 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=j75Lfwd5VGIDv0GlVoYIgN6RRua7i-PNg5D-ssgRhfo,11190
+risk/network/graph/network.py,sha256=JzYbrgJLiNWFyPIR6_qNSjMtmXmfzRv2FwWSdyg8HjY,12205
 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=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=T5qOlPhHzgLwileaVqT8Vq9A1ZQvaSMWvsCTnauAgTs,20802
+risk/network/plot/canvas.py,sha256=W8dFv4XYTzCWXBchgsc0esOQRn4usM4LkwNGPSDMobE,13357
+risk/network/plot/contour.py,sha256=VONX9l6owrZvWtR0mWQ6z2GSd1YXIv5wV_sf5ROQLT4,15581
+risk/network/plot/labels.py,sha256=eorP80CmAbHmt7de2qHna1tHGKL8YiHknwFW2R3tvjI,45734
+risk/network/plot/network.py,sha256=_K8Am2y6zSGrm3fAgMbXxzgspbugJi3uK4_tG8qqGoI,14015
+risk/network/plot/plotter.py,sha256=eS1vHqvOA2O001Rq7WiDcgqcehJ3fg4OPfvkezH4erw,5771
+risk/network/plot/utils/colors.py,sha256=k_461yoLgE7OxFYnpjU-Am1XFUbnOogiPqlVFYlwViQ,20803
 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
@@ -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-0.0.9b5.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,,
+risk_network-0.0.9b7.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b7.dist-info/METADATA,sha256=Ss2U9ENOyI2wMdGcSPG0KVcE41sigd_hZZL0XosvpWM,47497
+risk_network-0.0.9b7.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+risk_network-0.0.9b7.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b7.dist-info/RECORD,,