risk-network 0.0.8b27__py3-none-any.whl → 0.0.9b2__py3-none-any.whl

risk/risk.py

@@ -42,19 +42,10 @@ class RISK(NetworkIO, AnnotationsIO):
         """
         # Set global verbosity for logging
         set_global_verbosity(verbose)
-        # Initialize and log network parameters
-        params.initialize()
+        # Provide public access to the logged network parameters
+        self.params = params
         super().__init__()
 
-    @property
-    def params(self) -> params:
-        """Access the logged network parameters.
-
-        Returns:
-            Params: An instance of the Params class with logged parameters and methods to access or update them.
-        """
-        return params
-
     def load_neighborhoods_by_hypergeom(
         self,
         network: nx.Graph,
@@ -259,9 +250,9 @@ class RISK(NetworkIO, AnnotationsIO):
         network: nx.Graph,
         annotations: Dict[str, Any],
         neighborhoods: Dict[str, Any],
-        tail: str = "right",  # OPTIONS: "right" (enrichment), "left" (depletion), "both"
-        pval_cutoff: float = 0.01,  # OPTIONS: Any value between 0 to 1
-        fdr_cutoff: float = 0.9999,  # OPTIONS: Any value between 0 to 1
+        tail: str = "right",
+        pval_cutoff: float = 0.01,
+        fdr_cutoff: float = 0.9999,
         impute_depth: int = 0,
         prune_threshold: float = 0.0,
         linkage_criterion: str = "distance",
@@ -274,8 +265,8 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (pd.DataFrame): DataFrame containing annotation data for the network.
-            neighborhoods (Dict[str, Any]): Neighborhood enrichment data.
+            annotations (Dict[str, Any]): The annotations associated with the network.
+            neighborhoods (Dict[str, Any]): Neighborhood significance data.
             tail (str, optional): Type of significance tail ("right", "left", "both"). Defaults to "right".
             pval_cutoff (float, optional): p-value cutoff for significance. Defaults to 0.01.
             fdr_cutoff (float, optional): FDR cutoff for significance. Defaults to 0.9999.
@@ -360,19 +351,21 @@ class RISK(NetworkIO, AnnotationsIO):
             max_cluster_size=max_cluster_size,
         )
 
-        # Prepare node mapping and enrichment sums for the final NetworkGraph object
+        # Prepare node mapping and significance sums for the final NetworkGraph object
         ordered_nodes = annotations["ordered_nodes"]
         node_label_to_id = dict(zip(ordered_nodes, range(len(ordered_nodes))))
-        node_enrichment_sums = processed_neighborhoods["node_enrichment_sums"]
+        node_significance_sums = processed_neighborhoods["node_significance_sums"]
 
         # Return the fully initialized NetworkGraph object
         return NetworkGraph(
             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,
-            node_enrichment_sums=node_enrichment_sums,
+            node_significance_sums=node_significance_sums,
         )
 
     def load_plotter(
@@ -467,7 +460,7 @@ class RISK(NetworkIO, AnnotationsIO):
         Args:
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): Annotations data for the network.
-            neighborhoods (Dict[str, Any]): Neighborhood enrichment data.
+            neighborhoods (Dict[str, Any]): Neighborhood significance data.
             min_cluster_size (int, optional): Minimum size for clusters. Defaults to 5.
             max_cluster_size (int, optional): Maximum size for clusters. Defaults to 1000.
 
@@ -476,16 +469,18 @@ class RISK(NetworkIO, AnnotationsIO):
         """
         # Extract necessary data from annotations and neighborhoods
         ordered_annotations = annotations["ordered_annotations"]
-        neighborhood_enrichment_sums = neighborhoods["neighborhood_enrichment_counts"]
-        significant_enrichment_matrix = neighborhoods["significant_enrichment_matrix"]
-        significant_binary_enrichment_matrix = neighborhoods["significant_binary_enrichment_matrix"]
+        neighborhood_significance_sums = neighborhoods["neighborhood_significance_counts"]
+        significant_significance_matrix = neighborhoods["significant_significance_matrix"]
+        significant_binary_significance_matrix = neighborhoods[
+            "significant_binary_significance_matrix"
+        ]
         # Call external function to define top annotations
         return define_top_annotations(
             network=network,
             ordered_annotation_labels=ordered_annotations,
-            neighborhood_enrichment_sums=neighborhood_enrichment_sums,
-            significant_enrichment_matrix=significant_enrichment_matrix,
-            significant_binary_enrichment_matrix=significant_binary_enrichment_matrix,
+            neighborhood_significance_sums=neighborhood_significance_sums,
+            significant_significance_matrix=significant_significance_matrix,
+            significant_binary_significance_matrix=significant_binary_significance_matrix,
             min_cluster_size=min_cluster_size,
             max_cluster_size=max_cluster_size,
         )
@@ -498,7 +493,7 @@ class RISK(NetworkIO, AnnotationsIO):
         linkage_method: str,
         linkage_metric: str,
     ) -> pd.DataFrame:
-        """Define domains in the network based on enrichment data.
+        """Define domains in the network based on significance data.
 
         Args:
             neighborhoods (Dict[str, Any]): Enrichment data for neighborhoods.
@@ -510,12 +505,12 @@ class RISK(NetworkIO, AnnotationsIO):
         Returns:
             pd.DataFrame: Matrix of defined domains.
         """
-        # Extract the significant enrichment matrix from the neighborhoods data
-        significant_neighborhoods_enrichment = neighborhoods["significant_enrichment_matrix"]
+        # 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_enrichment=significant_neighborhoods_enrichment,
+            significant_neighborhoods_significance=significant_neighborhoods_significance,
             linkage_criterion=linkage_criterion,
             linkage_method=linkage_method,
             linkage_metric=linkage_metric,

risk/stats/stats.py

@@ -44,7 +44,7 @@ def calculate_significance_matrices(
             enrichment_pvals, enrichment_qvals, pval_cutoff=pval_cutoff, fdr_cutoff=fdr_cutoff
         )
         # Compute the enrichment matrix using both q-values and p-values
-        enrichment_matrix = (enrichment_qvals**2) * (enrichment_pvals**0.5)
+        enrichment_matrix = (enrichment_pvals**0.5) * (enrichment_qvals**2)
     else:
         # Compute threshold matrices based on p-value cutoffs only
         depletion_alpha_threshold_matrix = _compute_threshold_matrix(
@@ -62,7 +62,7 @@ def calculate_significance_matrices(
     log_enrichment_matrix = -np.log10(enrichment_matrix)
 
     # Select the appropriate significance matrices based on the specified tail
-    enrichment_matrix, significant_binary_enrichment_matrix = _select_significance_matrices(
+    significance_matrix, significant_binary_significance_matrix = _select_significance_matrices(
         tail,
         log_depletion_matrix,
         depletion_alpha_threshold_matrix,
@@ -71,14 +71,14 @@ def calculate_significance_matrices(
     )
 
     # Filter the enrichment matrix using the binary significance matrix
-    significant_enrichment_matrix = np.where(
-        significant_binary_enrichment_matrix == 1, enrichment_matrix, 0
+    significant_significance_matrix = np.where(
+        significant_binary_significance_matrix == 1, significance_matrix, 0
     )
 
     return {
-        "enrichment_matrix": enrichment_matrix,
-        "significant_binary_enrichment_matrix": significant_binary_enrichment_matrix,
-        "significant_enrichment_matrix": significant_enrichment_matrix,
+        "significance_matrix": significance_matrix,
+        "significant_significance_matrix": significant_significance_matrix,
+        "significant_binary_significance_matrix": significant_binary_significance_matrix,
     }
 
 
@@ -109,15 +109,15 @@ def _select_significance_matrices(
 
     if tail == "left":
         # Select depletion matrix and corresponding alpha threshold for left-tail analysis
-        enrichment_matrix = -log_depletion_matrix
+        significance_matrix = -log_depletion_matrix
         alpha_threshold_matrix = depletion_alpha_threshold_matrix
     elif tail == "right":
         # Select enrichment matrix and corresponding alpha threshold for right-tail analysis
-        enrichment_matrix = log_enrichment_matrix
+        significance_matrix = log_enrichment_matrix
         alpha_threshold_matrix = enrichment_alpha_threshold_matrix
     elif tail == "both":
         # Select the matrix with the highest absolute values while preserving the sign
-        enrichment_matrix = np.where(
+        significance_matrix = np.where(
             np.abs(log_depletion_matrix) >= np.abs(log_enrichment_matrix),
             -log_depletion_matrix,
             log_enrichment_matrix,
@@ -129,10 +129,10 @@ def _select_significance_matrices(
 
     # Create a binary significance matrix where valid indices meet the alpha threshold
     valid_idxs = ~np.isnan(alpha_threshold_matrix)
-    significant_binary_enrichment_matrix = np.zeros(alpha_threshold_matrix.shape)
-    significant_binary_enrichment_matrix[valid_idxs] = alpha_threshold_matrix[valid_idxs]
+    significant_binary_significance_matrix = np.zeros(alpha_threshold_matrix.shape)
+    significant_binary_significance_matrix[valid_idxs] = alpha_threshold_matrix[valid_idxs]
 
-    return enrichment_matrix, significant_binary_enrichment_matrix
+    return significance_matrix, significant_binary_significance_matrix
 
 
 def _compute_threshold_matrix(

{risk_network-0.0.8b27.dist-info → risk_network-0.0.9b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b27
+Version: 0.0.9b2
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

risk_network-0.0.9b2.dist-info/RECORD

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risk_network-0.0.8b27.dist-info/RECORD

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