risk-network 0.0.9b33__py3-none-any.whl → 0.0.9b35__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.33"
+__version__ = "0.0.9-beta.35"

risk/neighborhoods/api.py

@@ -280,7 +280,7 @@ class NeighborhoodsAPI:
         null_distribution: str = "network",
         random_seed: int = 888,
     ) -> Dict[str, Any]:
-        """Load significant neighborhoods for the network using the Z-score test.
+        """Load significant neighborhoods for the network using the z-score test.
 
         Args:
             network (nx.Graph): The network graph.
@@ -299,8 +299,8 @@ class NeighborhoodsAPI:
         Returns:
             Dict[str, Any]: Computed significance of neighborhoods.
         """
-        log_header("Running Z-score test")
-        # Compute neighborhood significance using the Z-score test
+        log_header("Running z-score test")
+        # Compute neighborhood significance using the z-score test
         return self._load_neighborhoods_by_statistical_test(
             network=network,
             annotations=annotations,

risk/network/graph/summary.py

@@ -103,9 +103,9 @@ class Summary:
         # Add minimum p-values and q-values to DataFrame
         results[
             [
-                "Enrichment P-value",
+                "Enrichment P-Value",
                 "Enrichment Q-value",
-                "Depletion P-value",
+                "Depletion P-Value",
                 "Depletion Q-value",
             ]
         ] = results.apply(
@@ -137,9 +137,9 @@ class Summary:
                     "Annotation Members in Network",
                     "Annotation Members in Network Count",
                     "Summed Significance Score",
-                    "Enrichment P-value",
+                    "Enrichment P-Value",
                     "Enrichment Q-value",
-                    "Depletion P-value",
+                    "Depletion P-Value",
                     "Depletion Q-value",
                 ]
             ]
@@ -156,9 +156,9 @@ class Summary:
                 "Annotation Members in Network": "",
                 "Annotation Members in Network Count": 0,
                 "Summed Significance Score": 0.0,
-                "Enrichment P-value": 1.0,
+                "Enrichment P-Value": 1.0,
                 "Enrichment Q-value": 1.0,
-                "Depletion P-value": 1.0,
+                "Depletion P-Value": 1.0,
                 "Depletion Q-value": 1.0,
             }
         )

risk/network/io.py

@@ -262,8 +262,25 @@ class NetworkIO:
             attribute_table.columns = attribute_table.iloc[0]
             # Skip first four rows, select source and target columns, and reset index
             attribute_table = attribute_table.iloc[4:, :]
-            attribute_table = attribute_table[[source_label, target_label]]
+            try:
+                # Attempt to filter the attribute_table with the given labels
+                attribute_table = attribute_table[[source_label, target_label]]
+            except KeyError as e:
+                # Find which key(s) caused the issue
+                missing_keys = [
+                    key
+                    for key in [source_label, target_label]
+                    if key not in attribute_table.columns
+                ]
+                # Raise the KeyError with details about the issue and available options
+                available_columns = ", ".join(attribute_table.columns)
+                raise KeyError(
+                    f"The column(s) '{', '.join(missing_keys)}' do not exist in the table. "
+                    f"Available columns are: {available_columns}."
+                ) from e
+
             attribute_table = attribute_table.dropna().reset_index(drop=True)
+
             # Create a graph
             G = nx.Graph()
             # Add edges and nodes
@@ -271,7 +288,6 @@ class NetworkIO:
                 source = row[source_label]
                 target = row[target_label]
                 G.add_edge(source, target)
-
                 if source not in G:
                     G.add_node(source)  # Optionally add x, y coordinates here if available
                 if target not in G:

risk/stats/stat_tests.py

@@ -215,7 +215,7 @@ def compute_zscore_test(
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
     """
-    Compute Z-score test for enrichment and depletion in neighborhoods with selectable null distribution.
+    Compute z-score test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
@@ -257,10 +257,10 @@ def compute_zscore_test(
         * (1 - neighborhood_sums / background_population)
     )
     std_dev[std_dev == 0] = np.nan  # Avoid division by zero
-    # Compute Z-scores
+    # Compute z-scores
     z_scores = (observed - expected) / std_dev
 
-    # Convert Z-scores to depletion and enrichment p-values
+    # Convert z-scores to depletion and enrichment p-values
     enrichment_pvals = norm.sf(z_scores)  # Upper tail
     depletion_pvals = norm.cdf(z_scores)  # Lower tail
 

{risk_network-0.0.9b33.dist-info → risk_network-0.0.9b35.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b33
+Version: 0.0.9b35
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b33.dist-info → risk_network-0.0.9b35.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=tx937GNV-GVI2M_OD_HsV2h_fKyIPshKazJbidEHhC4,127
+risk/__init__.py,sha256=r0xnE00ojEe_XG3ZBNV_1n3-vl0XWYuOA9-na0o5v2w,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=s827_lRknFseOP9O4zW8sP-IcCd2EzrpV_tnVY_tz5s,1104
 risk/annotations/__init__.py,sha256=parsbcux1U4urpUqh9AdzbDWuLj9HlMidycMPkpSQFo,179
@@ -8,17 +8,17 @@ risk/log/__init__.py,sha256=7LxDysQu7doi0LAvlY2YbjN6iJH0fNknqy8lSLgeljo,217
 risk/log/console.py,sha256=PgjyEvyhYLUSHXPUKEqOmxsDsfrjPICIgqo_cAHq0N8,4575
 risk/log/parameters.py,sha256=VtwfMzLU1xI4yji3-Ch5vHjH-KdwTfwaEMmi7hFQTs0,5716
 risk/neighborhoods/__init__.py,sha256=Q74HwTH7okI-vaskJPy2bYwb5sNjGASTzJ6m8V8arCU,234
-risk/neighborhoods/api.py,sha256=TjIMVnSPC702zMlwyaz2i0ofNx-d9L9g3P-TTSBMx90,23341
+risk/neighborhoods/api.py,sha256=ywngw2TQVV27gYlWDXcs8-qnmeepnvb-W9ov6J6VEPM,23341
 risk/neighborhoods/community.py,sha256=5Q_-VAJC-5SY5EUsB8gIlemeDoAL85uLjyl16pItHiQ,16699
 risk/neighborhoods/domains.py,sha256=jMJ4-Qzwgmo6Hya8h0E2_IcMaLpbuH_FWlmSjJl2ikc,12832
 risk/neighborhoods/neighborhoods.py,sha256=l9FhADB1C-OxM8E9QXOcA4osUDgA1vs4ud-OCGKKybc,21457
 risk/network/__init__.py,sha256=oVi3FA1XXKD84014Cykq-9bpX4_s0F3aAUfNOU-07Qw,73
 risk/network/geometry.py,sha256=eVtGHMgBf9fEqQZUFdHWjw-zFYYpfUONoHFSAxoRkug,6219
-risk/network/io.py,sha256=V90Me_qZ5Rt584q4qVGaLZ7I_Po5EJC544y9Vjqycnw,20917
+risk/network/io.py,sha256=RCH4nQdgYDXcNwMfpSz7qEmPO0pJ1p9fL0rNQptsQrc,21673
 risk/network/graph/__init__.py,sha256=ziGJew3yhtqvrb9LUuneDu_LwW2Wa9vd4UuhoL5l1CA,91
 risk/network/graph/api.py,sha256=t5Mh5_lD2uTLioEJFfCRe7ncc5iLNYzxd6r05wSiv7s,8169
 risk/network/graph/graph.py,sha256=qEWyZvuaGT_vvjhreBdmRPX3gst2wQFaXhFAvikPSqw,12158
-risk/network/graph/summary.py,sha256=eYJP78EHxu3ZhKoDCFshNxuEIB3dvH0PUg2T7qNkjC8,10289
+risk/network/graph/summary.py,sha256=Y_0rL2C1UoQeZQIPVe5LbaCO356Mcc8HisnrXwQsRm8,10289
 risk/network/plotter/__init__.py,sha256=4gWtQHGzQVNHmEBXi31Zf0tX0y2sTcE66J_yGnn7268,99
 risk/network/plotter/api.py,sha256=oJIj7vYv-3VpfN41ndCNtxcWIuhT2ULwAaPPU2f4oeM,1785
 risk/network/plotter/canvas.py,sha256=ifyTMyXYRzlcdSYy6C23k3dmwtbLDrOfdMvEjkW2gLg,13460
@@ -30,12 +30,12 @@ risk/network/plotter/utils/colors.py,sha256=EaiKsNPy_lcjrPp-QTNy3LnQdAZMjz2Legbe
 risk/network/plotter/utils/layout.py,sha256=OPqV8jzV9dpnOhYU4SYMSfsIXalVzESrlBSI_Y43OGU,3640
 risk/stats/__init__.py,sha256=2zdLv3tUHKyAjwAo7LprVXRaak1cHgrpYMVMSik6JM4,324
 risk/stats/significance.py,sha256=6cKv2xBQXWTHZ6HpNWIqlNfKKS5pG_BcCUdMM3r_zw4,7336
-risk/stats/stat_tests.py,sha256=MR59l5k0i5AiEIjPFPKIKHcj_nQ2wxvwW4eqYV7jOa0,11776
+risk/stats/stat_tests.py,sha256=tj0ri9w89_1fsjGLuafTWpfBEwZXpSLn7Ej2aAQ5lxk,11776
 risk/stats/permutation/__init__.py,sha256=OLmYLm2uj96hPsSaUs0vUqFYw6Thwch_aHtpL7L0ZFw,127
 risk/stats/permutation/permutation.py,sha256=BWjgdBpLVcHvmwHy0bmD4aJFccxifNBSrrCBPppyKf4,10569
 risk/stats/permutation/test_functions.py,sha256=KlECWTz1EZ6EPF_OAgHb0uznaIhopiVYb_AKUKuC4no,3120
-risk_network-0.0.9b33.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b33.dist-info/METADATA,sha256=StXA3M84MbWRUp_6g1654AQ0rg4PirZ4HKBmGs6V_ug,47627
-risk_network-0.0.9b33.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-risk_network-0.0.9b33.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b33.dist-info/RECORD,,
+risk_network-0.0.9b35.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b35.dist-info/METADATA,sha256=0rVbcV_Dh2DepCIKj-AbFry3t8J1yPNLyY_Kluq141A,47627
+risk_network-0.0.9b35.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b35.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b35.dist-info/RECORD,,