risk-network 0.0.9b29__py3-none-any.whl → 0.0.9b30__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.29"
+__version__ = "0.0.9-beta.30"

risk/stats/stat_tests.py

@@ -152,31 +152,49 @@ def compute_hypergeom_test(
 
     # Sparse matrix multiplication for observed counts
     annotated_in_neighborhood = neighborhoods.T @ annotations  # Result is sparse
-
-    def compute_pvals_for_column(col_idx: int):
-        """Compute depletion and enrichment p-values for a single annotation column."""
-        observed_counts = annotated_in_neighborhood[:, col_idx].toarray().flatten()
-        ann_total = annotation_sums[col_idx]
-        # Compute depletion and enrichment p-values
-        depletion_pvals = hypergeom.cdf(
-            observed_counts, background_population, ann_total, neighborhood_sums
-        )
-        enrichment_pvals = hypergeom.sf(
-            observed_counts - 1, background_population, ann_total, neighborhood_sums
-        )
-        return col_idx, depletion_pvals, enrichment_pvals
-
-    # Use ThreadPoolExecutor to process columns in parallel
-    num_columns = annotations.shape[1]
-    depletion_pvals = np.empty((annotated_in_neighborhood.shape[0], num_columns), dtype=np.float64)
-    enrichment_pvals = np.empty((annotated_in_neighborhood.shape[0], num_columns), dtype=np.float64)
+    # Determine the axis with fewer vectors
+    axis_to_process = 0 if annotations.shape[0] < annotations.shape[1] else 1
+
+    # Initialize p-value arrays
+    depletion_pvals = np.empty(annotated_in_neighborhood.shape, dtype=np.float64)
+    enrichment_pvals = np.empty(annotated_in_neighborhood.shape, dtype=np.float64)
+
+    def compute_pvals_for_index(idx: int):
+        """Compute p-values for a given index."""
+        if axis_to_process == 0:  # Process rows
+            observed_counts = annotated_in_neighborhood[idx, :].toarray().flatten()
+            neigh_total = neighborhood_sums[idx]
+            return (
+                idx,
+                hypergeom.cdf(observed_counts, background_population, annotation_sums, neigh_total),
+                hypergeom.sf(
+                    observed_counts - 1, background_population, annotation_sums, neigh_total
+                ),
+            )
+        else:  # Process columns
+            observed_counts = annotated_in_neighborhood[:, idx].toarray().flatten()
+            ann_total = annotation_sums[idx]
+            return (
+                idx,
+                hypergeom.cdf(observed_counts, background_population, ann_total, neighborhood_sums),
+                hypergeom.sf(
+                    observed_counts - 1, background_population, ann_total, neighborhood_sums
+                ),
+            )
+
+    # Use ThreadPoolExecutor to process indices in parallel
+    num_indices = annotations.shape[axis_to_process]
     with ThreadPoolExecutor() as executor:
-        results = executor.map(compute_pvals_for_column, range(num_columns))
+        results = executor.map(compute_pvals_for_index, range(num_indices))
 
     # Collect results
-    for col_idx, dep_pval, enr_pval in results:
-        depletion_pvals[:, col_idx] = dep_pval
-        enrichment_pvals[:, col_idx] = enr_pval
+    for idx, dep_pval, enr_pval in results:
+        if axis_to_process == 0:  # Rows
+            depletion_pvals[idx, :] = dep_pval
+            enrichment_pvals[idx, :] = enr_pval
+        else:  # Columns
+            depletion_pvals[:, idx] = dep_pval
+            enrichment_pvals[:, idx] = enr_pval
 
     return {"depletion_pvals": depletion_pvals, "enrichment_pvals": enrichment_pvals}
 

{risk_network-0.0.9b29.dist-info → risk_network-0.0.9b30.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b29
+Version: 0.0.9b30
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b29.dist-info → risk_network-0.0.9b30.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=zxCDSH8dgk6s0jbXYvLcOxAb7IGjNoZoOCoCwQ1Vd7g,127
+risk/__init__.py,sha256=fTPZhSt0RrpQ6uKRXrk-CSsXCmnWnq5_hfufVq6Bu-0,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=s827_lRknFseOP9O4zW8sP-IcCd2EzrpV_tnVY_tz5s,1104
 risk/annotations/__init__.py,sha256=parsbcux1U4urpUqh9AdzbDWuLj9HlMidycMPkpSQFo,179
@@ -30,12 +30,12 @@ risk/network/plotter/utils/colors.py,sha256=VU1sLPRC99ll6EGK4vRNgLMUXU8lja1vjiXU
 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=kZu48JPDneMwAZGVci2i_oaJUPLUKwiYTT3c4pKhr-0,12490
+risk/stats/stat_tests.py,sha256=e6Ep_cedc-JIK6Ap-YimX-X2oCxfFFmT5rHw99mYfYk,13171
 risk/stats/permutation/__init__.py,sha256=OLmYLm2uj96hPsSaUs0vUqFYw6Thwch_aHtpL7L0ZFw,127
 risk/stats/permutation/permutation.py,sha256=BWjgdBpLVcHvmwHy0bmD4aJFccxifNBSrrCBPppyKf4,10569
 risk/stats/permutation/test_functions.py,sha256=D3XMPM8CasUNytWSRce22TI6KK6XulYn5uGG4lWxaHs,3120
-risk_network-0.0.9b29.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b29.dist-info/METADATA,sha256=K9e3VRGdXrMUzmhtpX0PLQBFCdakxyBgKbW88xpIVYw,47627
-risk_network-0.0.9b29.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-risk_network-0.0.9b29.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b29.dist-info/RECORD,,
+risk_network-0.0.9b30.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b30.dist-info/METADATA,sha256=BtXlxahgmGpryFSTVXLOOliVwQ5HG3_WNdDwStbkcgo,47627
+risk_network-0.0.9b30.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b30.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b30.dist-info/RECORD,,