pythonflex 0.1.6__tar.gz → 0.2.1__tar.gz

{pythonflex-0.1.6 → pythonflex-0.2.1}/.gitignore

@@ -15,3 +15,4 @@ bfg-*.jar
 examples/output/
 src/benchmarkcr/examples/output/
 .aider*
+.vscode

{pythonflex-0.1.6 → pythonflex-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonflex
-Version: 0.1.6
+Version: 0.2.1
 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>
 Requires-Python: >=3.9

{pythonflex-0.1.6 → pythonflex-0.2.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pythonflex"
-version = "0.1.6"
+version = "0.2.1"
 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 = [

{pythonflex-0.1.6 → pythonflex-0.2.1}/src/pythonflex/__init__.py

@@ -2,7 +2,7 @@
 from .logging_config import log
 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
+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
 from .plotting import (
     adjust_text_positions, plot_precision_recall_curve, plot_percomplex_scatter,
     plot_percomplex_scatter_bysize, plot_complex_contributions, plot_significant_complexes, plot_auc_scores
@@ -14,5 +14,5 @@ __all__ = [ "log", "get_example_data_path", "fast_corr",
     "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"
+    "plot_significant_complexes", "plot_auc_scores", "save_results_to_csv", "update_matploblib_config"
 ]

{pythonflex-0.1.6 → pythonflex-0.2.1}/src/pythonflex/analysis.py

@@ -23,7 +23,7 @@ from .logging_config import log
 from .preprocessing import filter_matrix_by_genes
 from .utils import dsave, dload, _sanitize
 
-
+import matplotlib as mpl
 
 def deep_update(source, overrides):
     """Recursively update the source dict with the overrides."""
@@ -40,7 +40,7 @@ def initialize(config={}):
 
     default_config = {
         "min_genes_in_complex": 3,
-        "min_genes_per_complex_analysis": 3,
+        "min_genes_per_complex_analysis": 2,
         "output_folder": "output",
         "gold_standard": "CORUM",
         "color_map": "RdYlBu",
@@ -48,7 +48,7 @@ def initialize(config={}):
         "plotting": {
             "save_plot": True,
             "show_plot": True,
-            "output_type": "png",
+            "output_type": "pdf",
         },
         "preprocessing": {
             "normalize": False,
@@ -95,31 +95,105 @@ def initialize(config={}):
 
 
 
-def update_matploblib_config(config={}):
-    log.progress("Updating matplotlib settings.")
-    plt.rcParams.update({
-        "font.family": "DejaVu Sans",        # ← change if you prefer Arial, etc.
-        "mathtext.fontset": "dejavusans",
-        'font.size': 7,                # General font size
-        'axes.titlesize': 10,          # Title size
-        'axes.labelsize': 7,           # Axis labels (xlabel/ylabel)
-        'legend.fontsize': 7,          # Legend text
-        'xtick.labelsize': 6,          # X-axis tick labels
-        'ytick.labelsize': 6,          # Y-axis tick labels
-        'lines.linewidth': 1.5,        # Line width for plots
-        'figure.dpi': 300,             # Figure resolution
-        'figure.figsize': (8, 6),      # Default figure size
-        'grid.linestyle': '--',        # Grid line style
-        'grid.linewidth': 0.5,         # Grid line width
-        'grid.alpha': 0.2,             # Grid transparency
-        'axes.spines.right': False,    # Hide right spine
-        'axes.spines.top': False,      # Hide top spine
-        'image.cmap': config['color_map'],        # Default colormap
-        'axes.edgecolor': 'black',                # Axis edge color
-        'axes.facecolor': 'none',                 # Transparent axes background
-        'text.usetex': False                # Ensure LaTeX is off
+
+
+def update_matploblib_config(config=None, font_family="Arial", layout="single"):
+    """
+    Configure matplotlib settings optimized for Nature journal figures:
+      - 7 pt fonts (labels, ticks, legend), 9 pt titles
+      - Thin spines (0.5 pt), ticks out (left/bottom only), no minor ticks
+      - No grid, clean minimalist look
+      - Colorblind-friendly Tableau 10 color cycle
+      - Illustrator-safe PDF export (Type 42)
+      - Figure sizes: "single" (~89 mm), "double" (~183 mm), or custom (width, height) in inches
+    
+    Args:
+        config (dict, optional): Configuration dict (e.g., {'color_map': 'RdYlBu'}).
+        font_family (str): Preferred font (e.g., 'Arial', falls back to 'Helvetica').
+        layout (str or tuple): 'single' (~89 mm), 'double' (~183 mm), or (width, height) in inches.
+    """
+    if config is None:
+        config = {}
+    # Fallback if chosen font missing
+    try:
+        from matplotlib.font_manager import findfont, FontProperties
+        findfont(FontProperties(family=font_family))
+    except Exception:
+        font_family = "Helvetica"  # Nature prefers Helvetica if Arial unavailable
+        print(f"Warning: '{font_family}' not found, falling back to 'Helvetica'.")
+    
+    # Figure size presets (Nature: single ≈ 89 mm, double ≈ 183 mm at 25.4 mm/inch)
+    if isinstance(layout, tuple):
+        fig_w, fig_h = layout
+    else:
+        if layout == "double":
+            fig_w = 7.2  # ~183 mm
+            fig_h = 5.4  # Adjusted aspect
+        else:  # "single"
+            fig_w = 4.0  # Increased from 3.5" for more space (~102 mm)
+            fig_h = 3.0  # Increased from 2.6" for better aspect (~76 mm)
+    # Colorblind-friendly cycle (Tableau 10 adapted)
+    cb_cycle = [
+        "#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F",
+        "#EDC948", "#B07AA1", "#FF9DA7", "#9C755F", "#BAB0AC"
+    ]
+    mpl.rcParams.update({
+        # --- Text & Fonts ---
+        "text.usetex": False,  # Avoid LaTeX
+        "font.family": [font_family],  # Explicit font
+        "mathtext.fontset": "dejavusans",  # Disable mathtext
+        "mathtext.default": "regular",  # Plain text
+        "axes.unicode_minus": True,  # Proper minus signs
+        # --- Sizes (7 pt baseline, adjusted for space) ---
+        "font.size": 7,  # Reduced from 8 pt
+        "axes.titlesize": 9,  # Reduced from 10 pt
+        "axes.labelsize": 7,
+        "legend.fontsize": 7,
+        "xtick.labelsize": 7,
+        "ytick.labelsize": 7,
+        # --- Lines & Markers ---
+        "lines.linewidth": 1.5,  # Kept for data visibility
+        "lines.markersize": 4.0,
+        "patch.linewidth": 0.5,
+        "errorbar.capsize": 2,
+        # --- Axes, Spines, Ticks ---
+        "axes.linewidth": 0.5,
+        "axes.edgecolor": "black",
+        "axes.facecolor": "none",
+        "axes.titlepad": 3.0,
+        "axes.labelpad": 2.0,
+        "axes.prop_cycle": mpl.cycler(color=cb_cycle),
+        "xtick.direction": "out",
+        "ytick.direction": "out",
+        "xtick.major.size": 2.5,
+        "ytick.major.size": 2.5,
+        "xtick.minor.visible": False,
+        "ytick.minor.visible": False,
+        "xtick.major.width": 0.5,
+        "ytick.major.width": 0.5,
+        "xtick.top": False,
+        "ytick.right": False,
+        # --- Grid ---
+        "axes.grid": False,
+        # --- Legend ---
+        "legend.frameon": False,
+        "legend.handlelength": 1.6,  # Slightly adjusted
+        "legend.handletextpad": 0.4,
+        "legend.borderaxespad": 0.3,
+        "legend.loc": "best",  # Dynamic placement to avoid overlap
+        # --- Figure & Save ---
+        "figure.dpi": 600,
+        "figure.figsize": (fig_w, fig_h),
+        "savefig.dpi": 600,
+        "savefig.bbox": "tight",
+        "savefig.pad_inches": 0.1,  # Increased for spacing
+        "savefig.transparent": False,  # White background
+        # --- PDF/SVG Export ---
+        "pdf.fonttype": 42,
+        "ps.fonttype": 42,
+        "pdf.use14corefonts": False,
+        "svg.fonttype": "none",
     })
-    log.done("Matplotlib settings updated.")
 
 
 

{pythonflex-0.1.6 → pythonflex-0.2.1}/src/pythonflex/examples/basic_usage.py

@@ -22,7 +22,6 @@ inputs = {
 
 
 #%%
-
 default_config = {
     "min_genes_in_complex": 0,
     "min_genes_per_complex_analysis": 3,
@@ -32,7 +31,7 @@ default_config = {
     "jaccard": True,
     "plotting": {
         "save_plot": True,
-        "output_type": "PNG",
+        "output_type": "pdf",
     },
     "preprocessing": {
         "fill_na": True,
@@ -48,7 +47,6 @@ default_config = {
 flex.initialize(default_config)
 
 # Load datasets and gold standard terms
-
 data, _ = flex.load_datasets(inputs)
 terms, genes_in_terms = flex.load_gold_standard()
 
@@ -59,6 +57,7 @@ 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)
+    
 
 
 #%%

pythonflex-0.2.1/src/pythonflex/examples/test.py

@@ -0,0 +1,104 @@
+#%%
+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()
+
+
+
+
+
+
+
+
+
+#%%
+
+