pythonflex 0.3.1__tar.gz → 0.3.3__tar.gz

{pythonflex-0.3.1 → pythonflex-0.3.3}/PKG-INFO

@@ -1,8 +1,14 @@
 Metadata-Version: 2.4
 Name: pythonflex
-Version: 0.3.1
+Version: 0.3.3
 Summary: pythonFLEX is a benchmarking toolkit for evaluating CRISPR screen results against biological gold standards. The toolkit computes gene-level and complex-level performance metrics, helping researchers systematically assess the biological relevance and resolution of their CRISPR screening data.
 Author-email: Yasir Demirtaş <tyasird@hotmail.com>
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.9
 Requires-Dist: adjusttext
 Requires-Dist: art

{pythonflex-0.3.1 → pythonflex-0.3.3}/pyproject.toml

@@ -1,13 +1,20 @@
 [project]
 name = "pythonflex"
-version = "0.3.1"
+version = "0.3.3"
 description = "pythonFLEX is a benchmarking toolkit for evaluating CRISPR screen results against biological gold standards. The toolkit computes gene-level and complex-level performance metrics, helping researchers systematically assess the biological relevance and resolution of their CRISPR screening data."
 readme = "README.md"
 authors = [
     { name = "Yasir Demirtaş", email = "tyasird@hotmail.com" }
 ]
 requires-python = ">=3.9"
-
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
 
 # Exclude the input folder
 exclude = ["src/pythonflex/input/*", "src/pythonflex/output/*", "src/pythonflex/examples/output/*", 
@@ -67,3 +74,4 @@ pythonflex = { workspace = true }
 dev = [
     "pythonflex",
 ]
+

{pythonflex-0.3.1 → pythonflex-0.3.3}/src/pythonflex/__init__.py

@@ -3,9 +3,9 @@ from .utils import dsave, dload
 from .preprocessing import get_example_data_path, load_datasets,  get_common_genes, filter_matrix_by_genes, load_gold_standard, filter_duplicate_terms
 from .analysis import initialize, pra, pra_percomplex, fast_corr, perform_corr, is_symmetric, binary, has_mirror_of_first_pair, convert_full_to_half_matrix, drop_mirror_pairs, quick_sort, complex_contributions, save_results_to_csv, update_matploblib_config, mpr_prepare
 from .plotting import (
-    adjust_text_positions, plot_precision_recall_curve, plot_percomplex_scatter,
+    adjust_text_positions, plot_precision_recall_curve, plot_aggregated_pra, plot_iqr_pra, plot_all_runs_pra, plot_percomplex_scatter,
     plot_percomplex_scatter_bysize, plot_complex_contributions, plot_significant_complexes, plot_auc_scores,
-    plot_mpr_tp, plot_mpr_complexes, plot_mpr_tp_multi, plot_mpr_complexes_multi
+    plot_mpr_tp, plot_mpr_complexes, plot_mpr_tp_multi, plot_mpr_complexes_multi, plot_mpr_complexes_auc_scores
 )
 
 __all__ = [ "log", "get_example_data_path", "fast_corr",
@@ -13,8 +13,8 @@ __all__ = [ "log", "get_example_data_path", "fast_corr",
     "filter_matrix_by_genes", "load_gold_standard", "filter_duplicate_terms", "pra", "pra_percomplex",
     "perform_corr", "is_symmetric", "binary", "has_mirror_of_first_pair", "convert_full_to_half_matrix",
     "drop_mirror_pairs", "quick_sort", "complex_contributions", "adjust_text_positions", "plot_precision_recall_curve",
-    "plot_percomplex_scatter", "plot_percomplex_scatter_bysize", "plot_complex_contributions",
-    "plot_significant_complexes", "plot_auc_scores", "save_results_to_csv", "update_matploblib_config",
+    "plot_aggregated_pra", "plot_iqr_pra", "plot_all_runs_pra", "plot_percomplex_scatter", "plot_percomplex_scatter_bysize", "plot_complex_contributions",
+    "plot_significant_complexes", "plot_auc_scores", "plot_mpr_complexes_auc_scores", "save_results_to_csv", "update_matploblib_config",
     "mpr_prepare", "plot_mpr_tp", "plot_mpr_complexes",
     "plot_mpr_tp_multi", "plot_mpr_complexes_multi"
 ]

{pythonflex-0.3.1 → pythonflex-0.3.3}/src/pythonflex/analysis.py

@@ -844,7 +844,7 @@ def quick_sort(df, ascending=False):
     log.done("Pair-wise matrix sorting.")
     return sorted_df
 
-def save_results_to_csv(categories = ["complex_contributions", "pr_auc", "pra_percomplex"]):
+def save_results_to_csv(categories = ["complex_contributions", "pr_auc", "pra_percomplex", "mpr_complexes_auc"]):
 
     config = dload("config")  # Load config to get output folder
     output_folder = Path(config.get("output_folder", "output"))
@@ -856,6 +856,18 @@ def save_results_to_csv(categories = ["complex_contributions", "pr_auc", "pra_pe
         if data is None:
             log.warning(f"No data found for category '{category}'. Skipping save.")
             continue
+
+        if category == "mpr_complexes_auc" and isinstance(data, dict):
+            # Dict[dataset_name -> Dict[filter_key -> auc]]
+            try:
+                df = pd.DataFrame.from_dict(data, orient="index")
+                df.index.name = "Dataset"
+                csv_path = output_folder / f"{category}.csv"
+                df.to_csv(csv_path, index=True)
+                log.info(f"Saved '{category}' to {csv_path}")
+            except Exception as e:
+                log.warning(f"Failed to convert and save '{category}': {e}")
+            continue
         
         if category == "pr_auc" and isinstance(data, dict):
             # Special handling: Convert dict to DataFrame (assuming keys are indices, values are data)
@@ -1312,6 +1324,64 @@ def _mpr_module_coverage(contrib_df, terms, tp_th=1, percent_th=0.1):
     return coverage
 
 
+def _mpr_complexes_auc(
+    coverage: np.ndarray,
+    precision_cutoffs: np.ndarray,
+    max_complexes: float = 200.0,
+) -> float:
+    """Compute AUC for the Fig. 1F-style mPR curve (#complexes vs precision).
+
+    The plot uses:
+      x = #covered complexes (capped at `max_complexes`, shown on a log axis)
+      y = precision cutoff
+
+    We compute a normalized AUC by integrating precision over the *normalized*
+    coverage axis:
+        AUC = \int y \, d(x/max_complexes)
+
+    This yields a score in [0, 1] (or NaN if insufficient data).
+    """
+    cov = np.asarray(coverage, dtype=float)
+    prec = np.asarray(precision_cutoffs, dtype=float)
+
+    if cov.size == 0 or prec.size == 0:
+        return 0.0
+
+    # Match plot_mpr_complexes_multi(): only count cov>0 (log-x cannot show 0)
+    mask = (
+        np.isfinite(cov)
+        & np.isfinite(prec)
+        & (cov > 0)
+        & (cov <= max_complexes)
+        & (prec >= 0)
+        & (prec <= 1.0)
+    )
+    if not np.any(mask):
+        return 0.0
+
+    x_cov = cov[mask]
+    y = prec[mask]
+
+    # x-axis is log-scaled in the plot; normalize so cov=1 -> 0, cov=max_complexes -> 1
+    # (This matches the plot's tick hack where 1 is labeled as "0".)
+    x = np.log10(x_cov) / np.log10(float(max_complexes))
+
+    # Sort by x and collapse duplicate x values by taking max y (upper envelope)
+    order = np.argsort(x)
+    x = x[order]
+    y = y[order]
+
+    x_unique = np.unique(x)
+    if x_unique.size != x.size:
+        y = np.array([float(np.nanmax(y[x == xv])) for xv in x_unique], dtype=float)
+        x = x_unique
+
+    if x.size < 2:
+        return 0.0
+
+    return float(np.trapz(y, x))
+
+
 
 
 
@@ -1379,6 +1449,7 @@ def mpr_prepare(
 
     tp_curves = {}
     coverage_curves = {}
+    complexes_auc = {}
     precision_cutoffs = None
 
     for label, removed in filter_sets.items():
@@ -1393,6 +1464,7 @@ def mpr_prepare(
                 "precision": np.array([], dtype=float),
             }
             coverage_curves[label] = np.zeros(0, dtype=float)
+            complexes_auc[label] = float("nan")
             continue
 
         tp_cum = true.cumsum()
@@ -1417,11 +1489,17 @@ def mpr_prepare(
             percent_th=percent_th,
         )
         coverage_curves[label] = cov
+        complexes_auc[label] = _mpr_complexes_auc(
+            cov,
+            precision_cutoffs,
+            max_complexes=200.0,
+        )
 
     mpr_data = {
         "precision_cutoffs": precision_cutoffs,
         "tp_curves": tp_curves,
         "coverage_curves": coverage_curves,
+        "complexes_auc": complexes_auc,
         "filters": {
             "no_mtRibo_ETCI": sorted(mtRibo_ids),
             "no_small_highAUPRC": sorted(small_hi_ids),
@@ -1435,6 +1513,9 @@ def mpr_prepare(
 
     dsave(mpr_data, "mpr", name)
 
+    # Convenience: store AUCs as their own category for easy export / plotting.
+    dsave(complexes_auc, "mpr_complexes_auc", name)
+
 
 
 ### OLD FUNCTIONS

{pythonflex-0.3.1 → pythonflex-0.3.3}/src/pythonflex/examples/basic_usage.py

@@ -8,32 +8,34 @@ import pythonflex as flex
 inputs = {
     "Melanoma (63 Screens)": {
         "path": flex.get_example_data_path("melanoma_cell_lines_500_genes.csv"), 
-        "sort": "high"
+        "sort": "high",
+        "color": "#FF0000"
     },
     "Liver (24 Screens)": {
         "path": flex.get_example_data_path("liver_cell_lines_500_genes.csv"), 
-        "sort": "high"
+        "sort": "high",
+        "color": "#FFDD00"
     },
     "Neuroblastoma (37 Screens)": {
         "path": flex.get_example_data_path("neuroblastoma_cell_lines_500_genes.csv"), 
-        "sort": "high"
+        "sort": "high",
+        "color": "#FFDDDD"
     },
 }
 
 
 
-#%%
 default_config = {
     "min_genes_in_complex": 0,
     "min_genes_per_complex_analysis": 3,
-    "output_folder": "output",
+    "output_folder": "CORUM",
     "gold_standard": "CORUM",
-    "color_map": "RdYlBu",
-    "jaccard": True,
+    "color_map": "BuGn",
+    "jaccard": False,
     "use_common_genes": False,  # Set to False for individual dataset-gold standard intersections
     "plotting": {
         "save_plot": True,
-        "output_type": "pdf",
+        "output_type": "png",
     },
     "preprocessing": {
         "fill_na": True,
@@ -41,7 +43,8 @@ default_config = {
     },
     "corr_function": "numpy",
     "logging": {  
-        "visible_levels": ["DONE","STARTED"]  # "PROGRESS", "STARTED", ,"INFO","WARNING"
+        "visible_levels": ["DONE"]  
+        # "PROGRESS", "STARTED", ,"INFO","WARNING"
     }
 }
 
@@ -52,26 +55,33 @@ flex.initialize(default_config)
 data, _ = flex.load_datasets(inputs)
 terms, genes_in_terms = flex.load_gold_standard()
 
-
-#%%
 # Run analysis
 for name, dataset in data.items():
     pra = flex.pra(name, dataset, is_corr=False)
     fpc = flex.pra_percomplex(name, dataset, is_corr=False) 
     cc = flex.complex_contributions(name)
-    
+    flex.mpr_prepare(name)  
+
+
 
 
 #%%
 # Generate plots
-flex.plot_auc_scores()
-flex.plot_precision_recall_curve()
-flex.plot_percomplex_scatter(n_top=20)
-flex.plot_percomplex_scatter_bysize()
-flex.plot_significant_complexes()
-flex.plot_complex_contributions()
-
+# flex.plot_precision_recall_curve()
+# flex.plot_auc_scores()
+# flex.plot_significant_complexes()
+# flex.plot_percomplex_scatter(n_top=20)
+# flex.plot_percomplex_scatter_bysize()
+# flex.plot_complex_contributions()
+#%%
+#flex.plot_mpr_tp_multi(show_filters="all")
+flex.plot_mpr_complexes_multi(show_filters="all")
 
 #%%
 # Save results to CSV
 flex.save_results_to_csv()
+
+
+# %%
+flex.plot_mpr_complexes_auc_scores("all")
+# %%

pythonflex-0.3.3/src/pythonflex/examples/manuscript.py

@@ -0,0 +1,111 @@
+"""
+Basic usage example of the pythonFLEX package.
+Demonstrates initialization, data loading, analysis, and plotting.
+"""
+#%%
+import pythonflex as flex
+import pandas as pd
+
+gene_effect = pd.read_csv('C:/Users/yd/Desktop/projects/_datasets/depmap/25Q2/gene_effect.csv', index_col=0)
+
+skin = pd.read_csv('C:/Users/yd/Desktop/projects/_datasets/depmap/25Q2/subset/skin_cell_lines.csv', index_col=0)
+
+soft = pd.read_csv('C:/Users/yd/Desktop/projects/_datasets/depmap/25Q2/subset/soft_tissue_cell_lines.csv', index_col=0)
+
+
+cholesky = pd.read_csv('C:/Users/yd/Desktop/projects/_datasets/depmap/25Q2/25Q2_chronos_whitened_Cholesky.csv', index_col=0).T
+
+# inputs = {
+#     "All Screens": {
+#         "path": gene_effect, 
+#         "sort": "high",
+#         "color": "#000000"
+#     },
+#     "Skin": {
+#         "path": skin, 
+#         "sort": "high",
+#         "color": "#FF0000"
+#     },
+#     "Soft Tissue": {
+#         "path": soft, 
+#         "sort": "high",
+#         "color": "#FFFF00"
+#     },
+# }
+
+
+inputs = {
+    "DM All Screens": {
+        "path": gene_effect, 
+        "sort": "high",
+        "color": "#000000"
+    },
+    "DM Cholesky Whitening": {
+        "path": cholesky, 
+        "sort": "high",
+        "color": "#FF0000"
+    },
+   
+}
+
+
+
+
+default_config = {
+    "min_genes_in_complex": 2,
+    "min_genes_per_complex_analysis": 3,
+    "output_folder": "CORUM_DMvsCholesky",
+    "gold_standard": "CORUM",
+    "color_map": "BuGn",
+    "jaccard": False,
+    "use_common_genes": False,  # Set to False for individual dataset-gold standard intersections
+    "plotting": {
+        "save_plot": True,
+        "output_type": "pdf",
+    },
+    "preprocessing": {
+        "fill_na": True,
+        "normalize": False,
+    },
+    "corr_function": "numpy",
+    "logging": {  
+        "visible_levels": ["DONE"]  
+        # "PROGRESS", "STARTED", ,"INFO","WARNING"
+    }
+}
+
+# Initialize logger, config, and output folder
+flex.initialize(default_config)
+
+# Load datasets and gold standard terms
+data, _ = flex.load_datasets(inputs)
+terms, genes_in_terms = flex.load_gold_standard()
+
+# Run analysis
+for name, dataset in data.items():
+    pra = flex.pra(name, dataset, is_corr=False)
+    fpc = flex.pra_percomplex(name, dataset, is_corr=False) 
+    cc = flex.complex_contributions(name)
+    flex.mpr_prepare(name)  
+
+
+
+
+#%%
+# Generate plots
+flex.plot_precision_recall_curve()
+flex.plot_auc_scores()
+flex.plot_significant_complexes()
+flex.plot_percomplex_scatter(n_top=20)
+flex.plot_percomplex_scatter_bysize()
+flex.plot_complex_contributions()
+##
+#%%
+flex.plot_mpr_tp_multi(show_filters="all")
+flex.plot_mpr_complexes_multi(show_filters="all")
+
+# Save results to CSV
+flex.save_results_to_csv()
+
+# %%
+# %%