added filter for truth annotations to support CellProfiler benchmarki…

…ng (#95) * added filter for truth annotations to support CellProfiler benchmarking * removed print bc it pollutes logs
recursionpharma · Jan 28, 2025 · 60df3eb · 60df3eb
1 parent f0988d2
commit 60df3eb
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/efaar_benchmarking/benchmarking.py b/efaar_benchmarking/benchmarking.py
@@ -911,6 +911,10 @@ def compound_gene_benchmark(
     """
     config = config or BenchmarkConfig()
     truth = truth_data if truth_data is not None else load_truth_data(benchmark_data_dir)
+    # filter truth relationships for genes & compounds in [filtered] metadata
+    truth = truth[
+        truth.gene_symbol.isin(map_data.metadata.perturbation) & truth.treatment.isin(map_data.metadata.perturbation)
+    ]
     similarities = compute_similarities(truth, map_data, pert_col, randomize=check_random)
 
     thresholds = (activity_threshold, inactivity_threshold)