pythonflex 0.3__tar.gz → 0.3.2__tar.gz

{pythonflex-0.3 → pythonflex-0.3.2}/PKG-INFO

@@ -1,8 +1,14 @@
 Metadata-Version: 2.4
 Name: pythonflex
-Version: 0.3
+Version: 0.3.2
 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 → pythonflex-0.3.2}/pyproject.toml

@@ -1,13 +1,20 @@
 [project]
 name = "pythonflex"
-version = "0.3"
+version = "0.3.2"
 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 → pythonflex-0.3.2}/src/pythonflex/__init__.py

@@ -3,7 +3,7 @@ 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
 )
@@ -13,7 +13,7 @@ __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_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", "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 → pythonflex-0.3.2}/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 +55,32 @@ 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_auc_scores()
+flex.plot_significant_complexes()
 flex.plot_percomplex_scatter(n_top=20)
 flex.plot_percomplex_scatter_bysize()
-flex.plot_significant_complexes()
 flex.plot_complex_contributions()
-
+##
+flex.plot_mpr_tp_multi()
+flex.plot_mpr_complexes_multi()
 
 #%%
 # Save results to CSV
 flex.save_results_to_csv()
+
+# %%
+flex.plot_mpr_complexes_multi(show_filters="no_mtRibo_ETCI")
+# %%

{pythonflex-0.3 → pythonflex-0.3.2}/src/pythonflex/plotting.py

@@ -58,7 +58,12 @@ def plot_precision_recall_curve(line_width=2.0, hide_minor_ticks=True):
         log.warning(f"Color map '{cmap_name}' not found. Falling back to 'tab10'.")
         cmap = get_cmap("tab10")
 
-    fig, ax = plt.subplots()
+    # Increase figure width to accommodate external legend without squashing axes
+    fig, ax = plt.subplots(figsize=(6, 4))
+    
+    # Adjust layout to make room for legend on the right
+    plt.subplots_adjust(right=0.7)
+    
     ax.set_xscale("log")
 
     # optionally hide minor ticks on the log axis
@@ -92,7 +97,7 @@ def plot_precision_recall_curve(line_width=2.0, hide_minor_ticks=True):
     ax.set(title="",
            xlabel="Number of True Positives (TP)",
            ylabel="Precision")
-    ax.legend(loc="upper right", frameon=False)
+    ax.legend(loc="upper left", bbox_to_anchor=(1.05, 1), frameon=False)
     ax.set_ylim(0, 1)
 
     # Nature style: no grid, open top/right spines
@@ -109,6 +114,171 @@ def plot_precision_recall_curve(line_width=2.0, hide_minor_ticks=True):
         plt.show()
     plt.close(fig)
 
+def plot_aggregated_pra(agg_df, line_width=2.0, hide_minor_ticks=True):
+    """
+    Plots an aggregated Precision-Recall curve with mean line and min-max shading.
+    agg_df should be indexed by 'tp' and contain 'mean', 'min', 'max' columns for precision.
+    """
+    config = dload("config")
+    plot_config = config["plotting"]
+    
+    # Increase figure width to accommodate external legend without squashing axes
+    fig, ax = plt.subplots(figsize=(6, 4))
+    
+    # Adjust layout to make room for legend on the right
+    plt.subplots_adjust(right=0.7)
+    
+    ax.set_xscale("log")
+
+    # optionally hide minor ticks on the log axis
+    if hide_minor_ticks:
+        ax.xaxis.set_minor_locator(NullLocator())
+        ax.xaxis.set_minor_formatter(NullFormatter())
+
+    # Filter out very low TP counts if necessary, similar to plot_precision_recall_curve
+    agg_df = agg_df[agg_df.index > 10]
+    
+    tp = agg_df.index
+    mean_prec = agg_df['mean']
+    min_prec = agg_df['min']
+    max_prec = agg_df['max']
+
+    # Plot shading
+    ax.fill_between(tp, min_prec, max_prec, color='gray', alpha=0.3, label='Range (Min-Max)')
+    
+    # Plot mean line
+    ax.plot(tp, mean_prec, c="black", label="Mean Precision", linewidth=line_width, alpha=0.9)
+
+    ax.set(title="",
+           xlabel="Number of True Positives (TP)",
+           ylabel="Precision")
+    ax.legend(loc="upper left", bbox_to_anchor=(1.05, 1), frameon=False)
+    ax.set_ylim(0, 1)
+
+    # Nature style: no grid, open top/right spines
+    ax.grid(False)
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+
+    if plot_config["save_plot"]:
+        output_type = plot_config["output_type"]
+        output_path = Path(config["output_folder"]) / f"aggregated_precision_recall_curve.{output_type}"
+        fig.savefig(output_path, bbox_inches="tight", format=output_type)
+
+    if plot_config.get("show_plot", True):
+        plt.show()
+    plt.close(fig)
+
+def plot_iqr_pra(agg_df, line_width=2.0, hide_minor_ticks=True):
+    """
+    Plots an aggregated Precision-Recall curve with mean line and IQR (25-75%) shading.
+    agg_df should be indexed by 'tp' and contain 'mean', '25%', '75%' columns for precision.
+    """
+    config = dload("config")
+    plot_config = config["plotting"]
+    
+    # Increase figure width to accommodate external legend without squashing axes
+    fig, ax = plt.subplots(figsize=(6, 4))
+    
+    # Adjust layout to make room for legend on the right
+    plt.subplots_adjust(right=0.7)
+    
+    ax.set_xscale("log")
+
+    # optionally hide minor ticks on the log axis
+    if hide_minor_ticks:
+        ax.xaxis.set_minor_locator(NullLocator())
+        ax.xaxis.set_minor_formatter(NullFormatter())
+
+    # Filter out very low TP counts
+    agg_df = agg_df[agg_df.index > 10]
+    
+    tp = agg_df.index
+    mean_prec = agg_df['mean']
+    q25_prec = agg_df['25%']
+    q75_prec = agg_df['75%']
+
+    # Plot shading
+    ax.fill_between(tp, q25_prec, q75_prec, color='gray', alpha=0.3, label='IQR (25-75%)')
+    
+    # Plot mean line
+    ax.plot(tp, mean_prec, c="black", label="Mean Precision", linewidth=line_width, alpha=0.9)
+
+    ax.set(title="Precision-Recall (IQR)",
+           xlabel="Number of True Positives (TP)",
+           ylabel="Precision")
+    ax.legend(loc="upper left", bbox_to_anchor=(1.05, 1), frameon=False)
+    ax.set_ylim(0, 1)
+
+    # Nature style
+    ax.grid(False)
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+
+    if plot_config["save_plot"]:
+        output_type = plot_config["output_type"]
+        output_path = Path(config["output_folder"]) / f"aggregated_iqr_precision_recall_curve.{output_type}"
+        fig.savefig(output_path, bbox_inches="tight", format=output_type)
+
+    if plot_config.get("show_plot", True):
+        plt.show()
+    plt.close(fig)
+
+def plot_all_runs_pra(pra_list, mean_df=None, line_width=2.0, hide_minor_ticks=True):
+    """
+    Plots all individual Precision-Recall curves faintly, with an optional mean line.
+    pra_list: list of dataframes (each with 'tp' and 'precision' columns) OR list of Series (if index is tp)
+    mean_df: optional dataframe with 'mean' column indexed by tp
+    """
+    config = dload("config")
+    plot_config = config["plotting"]
+    
+    fig, ax = plt.subplots(figsize=(6, 4))
+    plt.subplots_adjust(right=0.7)
+    
+    ax.set_xscale("log")
+
+    if hide_minor_ticks:
+        ax.xaxis.set_minor_locator(NullLocator())
+        ax.xaxis.set_minor_formatter(NullFormatter())
+
+    # Plot individual lines
+    for i, df in enumerate(pra_list):
+        # Ensure we filter low TPs same as others
+        df_filtered = df[df['tp'] > 10] if 'tp' in df.columns else df[df.index > 10]
+        
+        x = df_filtered['tp'] if 'tp' in df_filtered.columns else df_filtered.index
+        y = df_filtered['precision'] if 'precision' in df_filtered.columns else df_filtered.values
+        
+        # Only add label for the first line to avoid cluttering legend
+        lbl = "Individual Runs" if i == 0 else None
+        ax.plot(x, y, c="gray", linewidth=0.5, alpha=0.3, label=lbl)
+
+    # Plot mean line if provided
+    if mean_df is not None:
+        mean_df = mean_df[mean_df.index > 10]
+        ax.plot(mean_df.index, mean_df['mean'], c="black", label="Mean Precision", linewidth=line_width, alpha=0.9)
+
+    ax.set(title="Precision-Recall (All Runs)",
+           xlabel="Number of True Positives (TP)",
+           ylabel="Precision")
+    ax.legend(loc="upper left", bbox_to_anchor=(1.05, 1), frameon=False)
+    ax.set_ylim(0, 1)
+
+    # Nature style
+    ax.grid(False)
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+
+    if plot_config["save_plot"]:
+        output_type = plot_config["output_type"]
+        output_path = Path(config["output_folder"]) / f"aggregated_all_runs_precision_recall_curve.{output_type}"
+        fig.savefig(output_path, bbox_inches="tight", format=output_type)
+
+    if plot_config.get("show_plot", True):
+        plt.show()
+    plt.close(fig)
+
 def plot_percomplex_scatter(n_top=10, sig_color='#B71A2A', nonsig_color='#DBDDDD', label_color='black', border_color='black', border_width=1.0, show_text_background=True):
     config = dload("config")
     plot_config = config["plotting"]
@@ -1050,14 +1220,10 @@ def plot_auc_scores():
     plt.close(fig)
     return pra_dict
 
-
-
-
 # -----------------------------------------------------------------------------
 # mPR plots (Fig. 1E and Fig. 1F)
 # -----------------------------------------------------------------------------
 
-
 def plot_mpr_complexes(name, ax=None, save=True, outname=None):
     """
     Fig. 1F-style module-level PR:
@@ -1208,7 +1374,6 @@ def plot_mpr_tp(name, ax=None, save=True, outname=None):
 
     return ax
 
-
 """
 Multi-dataset mPR plotting functions.
 
@@ -1229,7 +1394,6 @@ from pathlib import Path
 from .utils import dload
 from .logging_config import log
 
-
 # Default color palette (colorblind-friendly)
 DEFAULT_COLORS = [
     "#4E79A7",  # blue
@@ -1252,6 +1416,21 @@ FILTER_STYLES = {
 }
 
 
+def _normalize_show_filters(show_filters):
+    """Normalize show_filters to an ordered tuple of filter keys.
+
+    Common footgun: passing a single string (e.g. "no_mtRibo_ETCI") is iterable,
+    which would otherwise be treated as a sequence of characters.
+    """
+    if show_filters is None:
+        return tuple(FILTER_STYLES.keys())
+    if isinstance(show_filters, str):
+        return (show_filters,)
+    try:
+        return tuple(show_filters)
+    except TypeError:
+        return (show_filters,)
+
 def plot_mpr_tp_multi(
     dataset_names=None,
     colors=None,
@@ -1292,6 +1471,8 @@ def plot_mpr_tp_multi(
     config = dload("config")
     plot_config = config["plotting"]
     input_colors = dload("input", "colors")
+
+    show_filters = _normalize_show_filters(show_filters)
     
     # Sanitize color keys
     if input_colors:
@@ -1335,7 +1516,10 @@ def plot_mpr_tp_multi(
         colors = final_colors
     
     if ax is None:
-        fig, ax = plt.subplots(figsize=(5, 4))
+        # Increase width slightly
+        fig, ax = plt.subplots(figsize=(6, 4))
+        # Reserve space for legend on right
+        plt.subplots_adjust(right=0.7)
     else:
         fig = ax.figure
     
@@ -1413,14 +1597,21 @@ def plot_mpr_tp_multi(
     
     # Save
     if save:
+        output_type = plot_config.get("output_type", "pdf")
         if outname is None:
-            outname = "mpr_tp_multi.pdf"
+            outname = f"mpr_tp_multi.{output_type}"
+        
+        # Check if outname is just a filename or a full path
+        outpath = Path(outname)
+        if len(outpath.parts) == 1:
+             # Just a filename, prepend configured output folder
+             outpath = Path(config["output_folder"]) / outname
+
         fig.tight_layout()
-        fig.savefig(outname, bbox_inches="tight")
+        fig.savefig(outpath, bbox_inches="tight", format=output_type)
     
     return ax
 
-
 def plot_mpr_complexes_multi(
     dataset_names=None,
     colors=None,
@@ -1461,6 +1652,8 @@ def plot_mpr_complexes_multi(
     config = dload("config")
     plot_config = config["plotting"]
     input_colors = dload("input", "colors")
+
+    show_filters = _normalize_show_filters(show_filters)
     
     # Sanitize color keys
     if input_colors:
@@ -1504,7 +1697,10 @@ def plot_mpr_complexes_multi(
         colors = final_colors
     
     if ax is None:
-        fig, ax = plt.subplots(figsize=(5, 4))
+        # Increase width slightly
+        fig, ax = plt.subplots(figsize=(6, 4))
+        # Reserve space for legend on right
+        plt.subplots_adjust(right=0.7)
     else:
         fig = ax.figure
     
@@ -1564,18 +1760,26 @@ def plot_mpr_complexes_multi(
     
     # Save
     if save:
+        output_type = plot_config.get("output_type", "pdf")
         if outname is None:
-            outname = "mpr_complexes_multi.pdf"
+            outname = f"mpr_complexes_multi.{output_type}"
+        
+        # Check if outname is just a filename or a full path
+        outpath = Path(outname)
+        if len(outpath.parts) == 1:
+             # Just a filename, prepend configured output folder
+             outpath = Path(config["output_folder"]) / outname
+
         fig.tight_layout()
-        fig.savefig(outname, bbox_inches="tight")
+        fig.savefig(outpath, bbox_inches="tight", format=output_type)
     
     return ax
 
-
 def _add_vertical_legend(ax, dataset_names, colors, show_filters, linewidth):
     """
     Add vertically stacked legends: Dataset on top, Filter below.
     """
+    show_filters = _normalize_show_filters(show_filters)
     # Legend 1: Datasets (colors) - solid lines
     dataset_handles = []
     for i, name in enumerate(dataset_names):
@@ -1602,12 +1806,12 @@ def _add_vertical_legend(ax, dataset_names, colors, show_filters, linewidth):
     legend1 = ax.legend(
         dataset_handles, 
         dataset_names, 
-        loc="upper right",
+        loc="upper left",
         frameon=False,
         title="Dataset",
         fontsize=7,
         title_fontsize=8,
-        bbox_to_anchor=(1.0, 1.0)
+        bbox_to_anchor=(1.05, 1.0)
     )
     ax.add_artist(legend1)
     
@@ -1615,17 +1819,17 @@ def _add_vertical_legend(ax, dataset_names, colors, show_filters, linewidth):
     legend2 = ax.legend(
         filter_handles,
         filter_labels,
-        loc="upper right",
+        loc="upper left",
         frameon=False,
         fontsize=7,
-        bbox_to_anchor=(1.0, 1.0 - len(dataset_names) * 0.04 - 0.08)
+        bbox_to_anchor=(1.05, 1.0 - len(dataset_names) * 0.06 - 0.1)
     )
 
-
 def _add_dual_legend(ax, dataset_names, colors, show_filters, linewidth):
     """
     Add two legends: one for datasets (colors), one for filters (line styles).
     """
+    show_filters = _normalize_show_filters(show_filters)
     # Legend 1: Datasets (colors) - solid lines
     dataset_handles = []
     for i, name in enumerate(dataset_names):
@@ -1671,7 +1875,6 @@ def _add_dual_legend(ax, dataset_names, colors, show_filters, linewidth):
         title_fontsize=8,
     )
 
-
 # ============================================================================
 # Single dataset functions are now obsolete
 # ============================================================================

{pythonflex-0.3 → pythonflex-0.3.2}/src/pythonflex/preprocessing.py

@@ -13,28 +13,36 @@ from pathlib import Path
 
 
 def return_package_dir():
-
-    # Get the distribution
-    dist = distribution('pythonflex')
-
-    # Check for direct_url.json
-    direct_url_text = dist.read_text('direct_url.json')
-
-    if direct_url_text:
-        direct_url = json.loads(direct_url_text)
-        if direct_url.get('dir_info', {}).get('editable'):
-            # Editable install detected
-            project_url = direct_url['url']
-            # Remove 'file:///' prefix and handle Windows paths
-            project_root = project_url.removeprefix('file:///').replace('/', os.sep)
-            # Assuming src layout: project_root/src/pythonflex
-            package_dir = os.path.join(project_root, 'src', 'pythonflex')
+    try:
+        # Get the distribution
+        dist = distribution('pythonflex')
+
+        # Check for direct_url.json
+        try:
+            direct_url_text = dist.read_text('direct_url.json')
+        except FileNotFoundError:
+            direct_url_text = None
+
+        if direct_url_text:
+            direct_url = json.loads(direct_url_text)
+            if direct_url.get('dir_info', {}).get('editable'):
+                # Editable install detected
+                project_url = direct_url['url']
+                # Remove 'file:///' prefix and handle Windows paths
+                project_root = project_url.removeprefix('file:///').replace('/', os.sep)
+                # Assuming src layout: project_root/src/pythonflex
+                package_dir = os.path.join(project_root, 'src', 'pythonflex')
+            else:
+                # Non-editable
+                package_dir = str(files('pythonflex'))
         else:
-            # Non-editable
+            # No direct_url, assume non-editable
             package_dir = str(files('pythonflex'))
-    else:
-        # No direct_url, assume non-editable
-        package_dir = str(files('pythonflex'))
+            
+    except Exception: # PackageNotFoundError or other issues
+        # Fallback to local directory relative to this file
+        # precise location: src/pythonflex/preprocessing.py -> package dir is parent
+        package_dir = str(Path(__file__).parent)
 
     return package_dir
 
@@ -190,7 +198,6 @@ def load_gold_standard():
         "PATHWAY": "gold_standard/PATHWAY.parquet"
     }
     
-   
     if gold_standard_source in gold_standard_files:
         # Load predefined gold standard from package resources
         filename = gold_standard_files[gold_standard_source] 

pythonflex-0.3/src/pythonflex/examples/comparison.py

@@ -1,78 +0,0 @@
-"""
-Basic usage example of the pythonFLEX package.
-Demonstrates initialization, data loading, analysis, and plotting.
-"""
-#%%
-import pythonflex as flex
-import pandas as pd
-
-depmap = pd.read_csv('../../../../_datasets/depmap/25Q2/gene_effect.csv', index_col=0)
-white = pd.read_csv('../../../../_datasets/depmap/25Q2/25Q2_chronos_whitened_PCA.csv', index_col=0).T
-
-inputs = {
-    "25Q2": {
-        "path": depmap, 
-        "sort": "high",
-        "color": "#fff000"  # Black
-    },
-
-    "25Q2 white": {
-        "path": white,
-        "sort": "high",
-        "color": "#ff0000"  # Orange
-    },
-}
-
-default_config = {
-    "min_genes_in_complex": 0,
-    "min_genes_per_complex_analysis": 3,
-    "output_folder": "CORUM_25Q2_comparison2",
-    "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": "png",
-    },
-    "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) 
-    flex.mpr_prepare(name)  # Add this line
-    cc = flex.complex_contributions(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()
-flex.plot_mpr_complexes_multi()
-# Save results to CSV
-# flex.save_results_to_csv()
-
-# %%

pythonflex-0.3/src/pythonflex/examples/dataset_filtering.py

@@ -1,42 +0,0 @@
-
-# %%
-import pandas as pd
-
-df = pd.read_csv("../../../../datasets/depmap/24Q4/CRISPRGeneEffect.csv",index_col=0)
-model = pd.read_csv("../../../../datasets/depmap/24Q4/Model.csv",index_col=0)
-
-df.columns = df.columns.str.split(" \\(").str[0]
-df = df.T
-
-#%%
-
-# %%
-# get ModelID of selected disease for example OncotreePrimaryDisease==Melanoma
-melanoma = model[model.OncotreePrimaryDisease=="Melanoma"].index.unique().values
-liver = model[model.OncotreeLineage=="Liver"].index.unique().values
-neuroblastoma = model[model.OncotreePrimaryDisease=="Neuroblastoma"].index.unique().values
-
-# %%
-# mel.index is model ids, filter that ids in the columns of df
-mel_df = df.loc[:,df.columns.isin(melanoma)]
-liver_df = df.loc[:,df.columns.isin(liver)]
-neuro_df = df.loc[:,df.columns.isin(neuroblastoma)]
-
-
-# %%
-mel_df.to_csv("melanoma.csv")
-liver_df.to_csv("liver.csv")
-neuro_df.to_csv("neuroblastoma.csv")
-df.to_csv("depmap_geneeffect_all_cellines.csv")
-
-
-# %%
-import pandas as pd
-df = pd.read_csv('../../../../_datasets/depmap/19Q2/Achilles_gene_effect.csv', index_col=0)
-df.columns = df.columns.str.split(" \\(").str[0]
-df = df.T
-
-# %%
-df.to_csv("../../../../_datasets/depmap/19Q2/gene_effect.csv") 
-
-# %%

pythonflex-0.3/src/pythonflex/examples/diag.py

@@ -1,106 +0,0 @@
-#%%
-# Run this in Jupyter to test the two approaches
-
-import numpy as np
-import pandas as pd
-from pythonflex.utils import dload
-
-dataset_name = "[CORUM] 19Q2"
-
-pra = dload("pra", dataset_name)
-mpr = dload("mpr", dataset_name)
-
-filter_ids = set(mpr["filters"]["no_mtRibo_ETCI"])
-print(f"Filter IDs: {filter_ids}")
-
-cid_col = "complex_id" if "complex_id" in pra.columns else "complex_ids"
-
-# Sort by score descending
-pra_sorted = pra.sort_values("score", ascending=False).reset_index(drop=True)
-
-def has_filter_id(cids, filter_ids):
-    """Check if any complex ID is in filter_ids"""
-    if isinstance(cids, (np.ndarray, list)):
-        ids = [int(x) for x in cids if pd.notnull(x)]
-    else:
-        return False
-    return any(c in filter_ids for c in ids)
-
-# Mark which pairs should be filtered
-pra_sorted["should_filter"] = pra_sorted[cid_col].apply(lambda x: has_filter_id(x, filter_ids))
-
-print(f"\nTotal pairs: {len(pra_sorted)}")
-print(f"Pairs to filter: {pra_sorted['should_filter'].sum()}")
-print(f"TPs to filter: {(pra_sorted['should_filter'] & (pra_sorted['prediction']==1)).sum()}")
-
-# APPROACH 1: Mark as negative (what your Python does)
-# Keep all rows, but filtered TPs become FPs
-print("\n" + "=" * 70)
-print("APPROACH 1: Mark filtered TPs as negatives (keep rows)")
-print("=" * 70)
-
-df1 = pra_sorted.copy()
-df1["true_filtered"] = df1["prediction"].copy()
-df1.loc[df1["should_filter"] & (df1["prediction"]==1), "true_filtered"] = 0
-
-tp_cum_1 = df1["true_filtered"].cumsum()
-prec_1 = tp_cum_1 / (np.arange(len(df1)) + 1)
-
-# Show precision at key TP counts
-print("\nPrecision at key TP counts:")
-for target_tp in [10, 50, 100, 500, 1000]:
-    if target_tp <= tp_cum_1.max():
-        idx = np.where(tp_cum_1 >= target_tp)[0][0]
-        print(f"   TP={target_tp}: precision={prec_1.iloc[idx]:.3f} (at rank {idx+1})")
-
-# APPROACH 2: Remove rows entirely (what R does with replace=FALSE)
-print("\n" + "=" * 70)
-print("APPROACH 2: Remove filtered rows entirely")
-print("=" * 70)
-
-df2 = pra_sorted[~pra_sorted["should_filter"]].copy().reset_index(drop=True)
-
-tp_cum_2 = df2["prediction"].cumsum()
-prec_2 = tp_cum_2 / (np.arange(len(df2)) + 1)
-
-print(f"\nRows remaining after removal: {len(df2)}")
-print(f"TPs remaining: {df2['prediction'].sum()}")
-
-print("\nPrecision at key TP counts:")
-for target_tp in [10, 50, 100, 500, 1000]:
-    if target_tp <= tp_cum_2.max():
-        idx = np.where(tp_cum_2 >= target_tp)[0][0]
-        print(f"   TP={target_tp}: precision={prec_2.iloc[idx]:.3f} (at rank {idx+1})")
-
-# APPROACH 3: Only remove filtered POSITIVE pairs, keep negatives
-print("\n" + "=" * 70)
-print("APPROACH 3: Remove only filtered TPs (keep filtered negatives)")
-print("=" * 70)
-
-# This removes TP rows that contain filter IDs, but keeps negative rows
-remove_mask = pra_sorted["should_filter"] & (pra_sorted["prediction"] == 1)
-df3 = pra_sorted[~remove_mask].copy().reset_index(drop=True)
-
-tp_cum_3 = df3["prediction"].cumsum()
-prec_3 = tp_cum_3 / (np.arange(len(df3)) + 1)
-
-print(f"\nRows remaining: {len(df3)}")
-print(f"TPs remaining: {df3['prediction'].sum()}")
-
-print("\nPrecision at key TP counts:")
-for target_tp in [10, 50, 100, 500, 1000]:
-    if target_tp <= tp_cum_3.max():
-        idx = np.where(tp_cum_3 >= target_tp)[0][0]
-        print(f"   TP={target_tp}: precision={prec_3.iloc[idx]:.3f} (at rank {idx+1})")
-
-print("\n" + "=" * 70)
-print("COMPARISON")
-print("=" * 70)
-print("""
-Approach 1 (mark as negative): Filtered TPs become FPs, lowering precision
-Approach 2 (remove all filtered): Both TPs and negatives removed
-Approach 3 (remove only TPs): Only filtered TPs removed, negatives kept
-
-The R code uses Approach 3 (remove positive pairs that contain the filter ID).
-""")
-# %%

pythonflex-0.3/src/pythonflex/examples/test.py

@@ -1,104 +0,0 @@
-#%%
-import pythonflex as flex
-import os
-
-# # Define specific cell line types you're interested in
-DATA_DIR = "C:/Users/yd/Desktop/projects/_datasets/depmap/25Q2/subset/"
-
-# Specific cell lines of interest with "_cell_lines" suffix removed
-cell_line_files = [
-    "soft_tissue_cell_lines.csv",
-    "skin_cell_lines.csv", 
-    # "lung_cell_lines.csv",
-    # "head_and_neck_cell_lines.csv",
-    # "esophagus_stomach_cell_lines.csv",
-]
-
-inputs = {}
-
-# Create inputs dict with shortened names (removing "_cell_lines" suffix)
-for filename in cell_line_files:
-    # Remove .csv extension and _cell_lines suffix
-    key = filename.replace("_cell_lines.csv", "")
-    full_path = os.path.join(DATA_DIR, filename)
-    
-    inputs[key] = {
-        "path": full_path,
-        "sort": "high"
-    }
-
-inputs['depmap'] = {
-    "path": "C:/Users/yd/Desktop/projects/_datasets/depmap/25Q2/gene_effect.csv",
-    "sort": "high"
-}
-
-# Print the resulting inputs dictionary
-print("Configured inputs:")
-for key, value in inputs.items():
-    print(f"  {key}: {value['path']}")
-
-
-
-default_config = {
-    "min_genes_in_complex": 2,
-    "min_genes_per_complex_analysis": 2,
-    "output_folder": "25q2_min_genes_2",
-    "gold_standard": "CORUM",
-    "color_map": "RdYlBu",
-    "jaccard": True,
-    "plotting": {
-        "save_plot": True,
-        "output_type": "pdf",
-    },
-    "preprocessing": {
-        "fill_na": True,
-        "normalize": False,
-    },
-    "corr_function": "numpy",
-    "logging": {  
-        "visible_levels": ["DONE","STARTED"]  # "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)
-    
-
-
-#%%
-# Generate plots
-flex.plot_auc_scores()
-flex.plot_precision_recall_curve()
-flex.plot_percomplex_scatter()
-flex.plot_percomplex_scatter_bysize()
-flex.plot_significant_complexes()
-flex.plot_complex_contributions()
-
-
-#%%
-# Save results to CSV
-flex.save_results_to_csv()
-
-
-
-
-
-
-
-
-
-#%%
-
-