risk-network 0.0.9b6__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.6"
+__version__ = "0.0.9-beta.7"

risk/annotations/io.py

@@ -41,7 +41,9 @@ class AnnotationsIO:
         """
         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)
 
         # Load the JSON file into a dictionary
@@ -78,7 +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
@@ -118,7 +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
@@ -154,7 +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

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-0.0.9b6.dist-info → risk_network-0.0.9b7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b6
+Version: 0.0.9b7
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b6.dist-info → risk_network-0.0.9b7.dist-info}/RECORD

@@ -1,29 +1,29 @@
-risk/__init__.py,sha256=fpCtulKZFHI4Je7dm4qBJHyP9InK9uDRYmYYgog9BGQ,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=WVT9wzTm8lTpMw_3SnbyljWR77yExo0rb1zVgJza8nw,14284
-risk/annotations/io.py,sha256=Nj_RPmn-WM1zMsssm9bVGR94SHytkEBK-wcBJ3WhqkU,10310
+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-0.0.9b6.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b6.dist-info/METADATA,sha256=0YZ5Rd4bqOid3nSHpa-S6fBBtBhYPoAQ1SlACtmDVaw,47497
-risk_network-0.0.9b6.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-risk_network-0.0.9b6.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b6.dist-info/RECORD,,
+risk_network-0.0.9b7.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
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+risk_network-0.0.9b7.dist-info/RECORD,,