comparison flexynesis_plot.py @ 8:9c91d13827ef draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad

7:9450286c42ab

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
import torch
from flexynesis import (
    build_cox_model,
    get_important_features,
    plot_dim_reduced,
    plot_hazard_ratios,
    plot_kaplan_meier_curves,
    plot_pr_curves,
    plot_roc_curves,

        if file_ext == '.csv':
            df = pd.read_csv(labels_input)
        elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
            df = pd.read_csv(labels_input, sep='\t')

        # Check if this is the specific format with sample_id, known_label, predicted_label
        required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
        if all(col in df.columns for col in required_cols):
            return df
        else:
            raise ValueError(f"Labels file {labels_input} does not contain required columns: {required_cols}")

    except Exception as e:
        raise ValueError(f"Error loading labels from {labels_input}: {e}") from e


def load_survival_data(survival_path):
    """Load survival data from a file. First column should be sample_id"""
    try:
        # Determine file extension
        file_ext = Path(survival_path).suffix.lower()

        if file_ext == '.csv':
            df = pd.read_csv(survival_path, index_col=0)
        elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
            df = pd.read_csv(survival_path, sep='\t', index_col=0)
        else:
            raise ValueError(f"Unsupported file extension: {file_ext}")
        return df

    except Exception as e:
        raise ValueError(f"Error loading survival data from {survival_path}: {e}") from e


def load_omics(omics_path):
    """Load omics data from a file. First column should be features"""
    try:

    except Exception as e:
        raise ValueError(f"Error loading omics data from {omics_path}: {e}") from e


def load_model(model_path):
    """Load flexynesis model from pickle file"""
    try:
        with open(model_path, 'rb') as f:
            model = torch.load(f, weights_only=False)
        return model
    except Exception as e:
        raise ValueError(f"Error loading model from {model_path}: {e}") from e


def match_samples_to_embeddings(sample_names, label_data):
    """Filter label data to match sample names in the embeddings"""
    df_matched = label_data[label_data['sample_id'].isin(sample_names)]
    return df_matched


def detect_color_type(labels_series):
    """Auto-detect whether target variables should be treated as categorical or numerical"""

def generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base):
    """Generate dimensionality reduction plots"""

    # Parse target values from comma-separated string
    if args.target_value:
        target_values = [val.strip() for val in args.target_value.split(',')]
    else:
        # If no target values specified, use all unique variables
        target_values = matched_labels['variable'].unique().tolist()

    print(f"Generating {args.method.upper()} plots for {len(target_values)} target variable(s): {', '.join(target_values)}")

    # Check variables
    available_vars = matched_labels['variable'].unique()
    missing_vars = [var for var in target_values if var not in available_vars]

    if missing_vars:
        print(f"Warning: The following target variables were not found in the data: {', '.join(missing_vars)}")
        print(f"Available variables: {', '.join(available_vars)}")

    # Filter to only process available variables
    valid_vars = [var for var in target_values if var in available_vars]

    if not valid_vars:
        raise ValueError(f"None of the specified target variables were found in the data. Available: {', '.join(available_vars)}")

    # Generate plots for each valid target variable
    for var in valid_vars:
        print(f"\nPlotting variable: {var}")

        # Filter matched labels for current variable
        var_labels = matched_labels[matched_labels['variable'] == var].copy()
        var_labels = var_labels.drop_duplicates(subset='sample_id')

        if var_labels.empty:
            print(f"Warning: No data found for variable '{var}', skipping...")
            continue

        # Auto-detect color type
        known_color_type = detect_color_type(var_labels['known_label'])
        predicted_color_type = detect_color_type(var_labels['predicted_label'])

        print(f"  Auto-detected color types - Known: {known_color_type}, Predicted: {predicted_color_type}")

        try:
            # Plot 1: Known labels
            print(f"  Creating known labels plot for {var}...")
            fig_known = plot_dim_reduced(
                matrix=embeddings,
                labels=var_labels['known_label'],
                method=args.method,
                color_type=known_color_type
            )

            output_path_known = output_dir / f"{output_name_base}_{var}_known.{args.format}"
            print(f"  Saving known labels plot to: {output_path_known.name}")
            fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')

            # Plot 2: Predicted labels
            print(f"  Creating predicted labels plot for {var}...")
            fig_predicted = plot_dim_reduced(
                matrix=embeddings,
                labels=var_labels['predicted_label'],
                method=args.method,
                color_type=predicted_color_type
            )

            output_path_predicted = output_dir / f"{output_name_base}_{var}_predicted.{args.format}"
            print(f"  Saving predicted labels plot to: {output_path_predicted.name}")
            fig_predicted.save(output_path_predicted, dpi=args.dpi, bbox_inches='tight')

            print(f"  ✓ Successfully created plots for variable '{var}'")

        except Exception as e:
            print(f"  ✗ Error creating plots for variable '{var}': {e}")
            continue

    print(f"\nDimensionality reduction plots completed for {len(valid_vars)} variable(s)!")


def generate_km_plots(survival_data, label_data, args, output_dir, output_name_base):
    """Generate Kaplan-Meier plots"""
    print("Generating Kaplan-Meier curves of risk subtypes...")

    # Reset index and rename the index column to sample_id
    survival_data = survival_data.reset_index()
    if survival_data.columns[0] != 'sample_id':
        survival_data = survival_data.rename(columns={survival_data.columns[0]: 'sample_id'})

    # Convert survival event column to binary (0/1) based on event_value
    # Check if the event column exists
    if args.surv_event_var not in survival_data.columns:
        raise ValueError(f"Column '{args.surv_event_var}' not found in survival data")

    # Convert to string for comparison to handle mixed types
    survival_data[args.surv_event_var] = survival_data[args.surv_event_var].astype(str)
    event_value_str = str(args.event_value)

    # Create binary event column (1 if matches event_value, 0 otherwise)
    survival_data[f'{args.surv_event_var}_binary'] = (
        survival_data[args.surv_event_var] == event_value_str
    ).astype(int)

    # Filter for survival category and class_label == '1:DECEASED'
    label_data['class_label'] = label_data['class_label'].astype(str)

    label_data = label_data[(label_data['variable'] == args.surv_event_var) & (label_data['class_label'] == event_value_str)]

    # check survival data
    for col in [args.surv_time_var, args.surv_event_var]:
        if col not in survival_data.columns:
            raise ValueError(f"Column '{col}' not found in survival data")

    # Merge survival data with labels
    df_deceased = pd.merge(survival_data, label_data, on='sample_id', how='inner')

    if df_deceased.empty:
        raise ValueError("No matching samples found after merging survival and label data.")

    # Get risk scores
    risk_scores = df_deceased['probability'].values

    # Compute groups (e.g., median split)
    quantiles = np.quantile(risk_scores, [0.5])
    groups = np.digitize(risk_scores, quantiles)
    group_labels = ['low_risk' if g == 0 else 'high_risk' for g in groups]

    fig_known = plot_kaplan_meier_curves(
        durations=df_deceased[args.surv_time_var],
        events=df_deceased[f'{args.surv_event_var}_binary'],
        categorical_variable=group_labels
    )

    output_path_known = output_dir / f"{output_name_base}_km_risk_subtypes.{args.format}"
    print(f"Saving Kaplan-Meier plot to: {output_path_known.absolute()}")
    fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')

    print("Kaplan-Meier plot saved successfully!")


def generate_cox_plots(model, clinical_train, clinical_test, omics_train, omics_test, args, output_dir, output_name_base):
    """Generate Cox proportional hazards plots"""
    print("Generating Cox proportional hazards analysis...")

    # Parse clinical variables
    clinical_vars = [var.strip() for var in args.clinical_variables.split(',')]

    # Validate that survival variables are included
    required_vars = [args.surv_time_var, args.surv_event_var]
    for var in required_vars:
        if var not in clinical_vars:

    df_clin = pd.concat([df_clin_train, df_clin_test], axis=0)

    # Get top survival markers
    print(f"Extracting top {args.top_features} important features for {args.surv_event_var}...")
    try:
        imp = get_important_features(model,
                                     var=args.surv_event_var,
                                     top=args.top_features
                                     )['name'].unique().tolist()
        print(f"Top features: {', '.join(imp)}")
    except Exception as e:
        raise ValueError(f"Error getting important features: {e}")

    # Extract feature data from omics datasets

    final_samples = len(df)
    print(f"Removed {initial_samples - final_samples} samples without survival data")

    if df.empty:
        raise ValueError("No samples remain after filtering for survival data")

    # Convert survival event column to binary (0/1) based on event_value
    # Convert to string for comparison to handle mixed types
    df[args.surv_event_var] = df[args.surv_event_var].astype(str)
    event_value_str = str(args.event_value)

    df[f'{args.surv_event_var}'] = (
        df[args.surv_event_var] == event_value_str
    ).astype(int)

    # Build Cox model
    print(f"Building Cox model with time variable: {args.surv_time_var}, event variable: {args.surv_event_var}")
    try:
        coxm = build_cox_model(df,

def generate_plot_scatter(labels, args, output_dir, output_name_base):
    """Generate scatter plot of known vs predicted labels"""
    print("Generating scatter plots of known vs predicted labels...")

    # Parse target values from comma-separated string
    if args.target_value:
        target_values = [val.strip() for val in args.target_value.split(',')]
    else:
        # If no target values specified, use all unique variables
        target_values = labels['variable'].unique().tolist()

    print(f"Processing target values: {target_values}")

    successful_plots = 0
    skipped_plots = 0

    for target_value in target_values:
        print(f"\nProcessing target value: '{target_value}'")

        # Filter labels for the current target value
        target_labels = labels[labels['variable'] == target_value]

        if target_labels.empty:
            print(f"  Warning: No data found for target value '{target_value}' - skipping")
            skipped_plots += 1
            continue

        # Check if labels are numeric and convert
        true_values = pd.to_numeric(target_labels['known_label'], errors='coerce')
        predicted_values = pd.to_numeric(target_labels['predicted_label'], errors='coerce')

        if true_values.isna().all() or predicted_values.isna().all():
            print(f"No valid numeric values found for known or predicted labels in '{target_value}'")
            skipped_plots += 1
            continue

        try:
            print(f"  Generating scatter plot for '{target_value}'...")
            fig = plot_scatter(true_values, predicted_values)

            # Create output filename with target value
            safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
            if len(target_values) > 1:
                output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
            else:
                output_filename = f"{output_name_base}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving scatter plot to: {output_path.absolute()}")
            fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

            successful_plots += 1
            print(f"  Scatter plot for '{target_value}' generated successfully!")

        except Exception as e:
            print(f"  Error generating plot for '{target_value}': {str(e)}")
            skipped_plots += 1

    # Summary
    print("  Summary:")
    print(f"  Successfully generated: {successful_plots} plots")
    print(f"  Skipped: {skipped_plots} plots")

    if successful_plots == 0:
        raise ValueError("No scatter plots could be generated. Check your data and target values.")

    print("Scatter plot generation completed!")


def generate_label_concordance_heatmap(labels, args, output_dir, output_name_base):
    """Generate label concordance heatmap"""
    print("Generating label concordance heatmaps...")

    # Parse target values from comma-separated string
    if args.target_value:
        target_values = [val.strip() for val in args.target_value.split(',')]
    else:

        print(f"\nProcessing target value: '{target_value}'")

        # Filter labels for the current target value
        target_labels = labels[labels['variable'] == target_value]

        if target_labels.empty:
            print(f"  Warning: No data found for target value '{target_value}' - skipping")
            continue

        true_values = target_labels['known_label'].tolist()
        predicted_values = target_labels['predicted_label'].tolist()

        try:
            print(f"  Generating heatmap for '{target_value}'...")
            fig = plot_label_concordance_heatmap(true_values, predicted_values)
            plt.close(fig)

            # Create output filename with target value
            safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
            if len(target_values) > 1:
                output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
            else:
                output_filename = f"{output_name_base}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving heatmap to: {output_path.absolute()}")
            fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')

        except Exception as e:
            print(f"  Error generating heatmap for '{target_value}': {str(e)}")
            continue

    print("Label concordance heatmap generated successfully!")


def generate_pr_curves(labels, args, output_dir, output_name_base):
    """Generate precision-recall curves"""
    print("Generating precision-recall curves...")

    # Parse target values from comma-separated string
    if args.target_value:
        target_values = [val.strip() for val in args.target_value.split(',')]
    else:
        # If no target values specified, use all unique variables
        target_values = labels['variable'].unique().tolist()

    print(f"Processing target values: {target_values}")

    for target_value in target_values:
        print(f"\nProcessing target value: '{target_value}'")

        # Filter labels for the current target value
        target_labels = labels[labels['variable'] == target_value]

        # Check if this is a regression problem (no class probabilities)
        prob_columns = target_labels['class_label'].unique()
        non_na_probs = target_labels['probability'].notna().sum()

        print(f"  Class labels found: {list(prob_columns)}")
        print(f"  Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")

        # If most probabilities are NaN, this is likely a regression problem
        if non_na_probs < len(target_labels) * 0.1:  # Less than 10% valid probabilities
            print("  Detected regression problem - precision-recall curves not applicable")
            print(f"  Skipping '{target_value}' (use regression evaluation metrics instead)")
            continue

        # Debug: Check data quality
        total_rows = len(target_labels)

            print(f"  Unmapped labels: {unmapped_labels}")
            print(f"  Available classes: {class_names}")
            continue

        try:
            print(f"  Generating precision-recall curve for '{target_value}'...")
            fig = plot_pr_curves(y_true_np, y_probs_np)

            # Create output filename with target value
            safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
            if len(target_values) > 1:
                output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
            else:
                output_filename = f"{output_name_base}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving precision-recall curve to: {output_path.absolute()}")
            fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

        except Exception as e:
            print(f"  Error generating precision-recall curve for '{target_value}': {str(e)}")
            print(f"  Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}")
            print(f"  Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}")
            continue

    print("Precision-recall curves generated successfully!")


def generate_roc_curves(labels, args, output_dir, output_name_base):
    """Generate ROC curves"""
    print("Generating ROC curves...")

    # Parse target values from comma-separated string
    if args.target_value:
        target_values = [val.strip() for val in args.target_value.split(',')]
    else:
        # If no target values specified, use all unique variables
        target_values = labels['variable'].unique().tolist()

    print(f"Processing target values: {target_values}")

    for target_value in target_values:
        print(f"\nProcessing target value: '{target_value}'")

        # Filter labels for the current target value
        target_labels = labels[labels['variable'] == target_value]

        # Check if this is a regression problem (no class probabilities)
        prob_columns = target_labels['class_label'].unique()
        non_na_probs = target_labels['probability'].notna().sum()

        print(f"  Class labels found: {list(prob_columns)}")
        print(f"  Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")

        # If most probabilities are NaN, this is likely a regression problem
        if non_na_probs < len(target_labels) * 0.1:  # Less than 10% valid probabilities
            print("  Detected regression problem - ROC curves not applicable")
            print(f"  Skipping '{target_value}' (use regression evaluation metrics instead)")
            continue

        # Debug: Check data quality
        total_rows = len(target_labels)
        missing_labels = target_labels['known_label'].isna().sum()
        missing_probs = target_labels['probability'].isna().sum()
        unique_samples = target_labels['sample_id'].nunique()
        unique_classes = target_labels['class_label'].nunique()

        print(f"  Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
        print(f"  Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")

        if missing_labels > 0:
            print(f"  Warning: Found {missing_labels} missing known_label values")
            missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
            print(f"  Sample IDs with missing known_label: {list(missing_samples)}")

            # Remove rows with missing known_label
            target_labels = target_labels.dropna(subset=['known_label'])
            if target_labels.empty:
                print(f"  Error: No valid known_label data remaining for '{target_value}' - skipping")
                continue

        # 1. Pivot to wide format
        prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability')

        print(f"  After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes")
        print(f"  Class columns: {list(prob_df.columns)}")

        # Check for NaN values in probability data
        nan_counts = prob_df.isna().sum()
        if nan_counts.any():
            print(f"  NaN counts per class: {dict(nan_counts)}")
            print(f"  Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}")

            # Drop only rows where ALL probabilities are NaN
            all_nan_rows = prob_df.isna().all(axis=1)
            if all_nan_rows.any():
                print(f"  Dropping {all_nan_rows.sum()} samples with all NaN probabilities")
                prob_df = prob_df[~all_nan_rows]

            remaining_nans = prob_df.isna().sum().sum()
            if remaining_nans > 0:
                print(f"  Warning: {remaining_nans} individual NaN values remain - filling with 0")
                prob_df = prob_df.fillna(0)

            if prob_df.empty:
                print(f"  Error: No valid probability data remaining for '{target_value}' - skipping")
                continue

        # 2. Get true labels
        true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id')

        # 3. Align indices - only keep samples that exist in both datasets
        common_indices = prob_df.index.intersection(true_labels_df.index)
        if len(common_indices) == 0:
            print(f"  Error: No common sample_ids between probability and true label data for '{target_value}' - skipping")
            continue

        print(f"  Found {len(common_indices)} samples with both probability and true label data")

        # Filter both datasets to common indices
        prob_df_aligned = prob_df.loc[common_indices]
        y_true = true_labels_df.loc[common_indices]['known_label']

        # 4. Final check for NaN values
        if y_true.isna().any():
            print(f"  Error: True labels still contain NaN after alignment for '{target_value}' - skipping")
            continue

        if prob_df_aligned.isna().any().any():
            print(f"  Error: Probability data still contains NaN after alignment for '{target_value}' - skipping")
            continue

        # 5. Convert categorical labels to integer labels
        # Create a mapping from class names to integers
        class_names = list(prob_df_aligned.columns)
        class_to_int = {class_name: i for i, class_name in enumerate(class_names)}

        print(f"  Class mapping: {class_to_int}")

        # Convert true labels to integers
        y_true_np = y_true.map(class_to_int).to_numpy()
        y_probs_np = prob_df_aligned.to_numpy()

        print(f"  Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}")
        print(f"  Unique true labels (integers): {set(y_true_np)}")
        print(f"  Class labels (columns): {class_names}")
        print(f"  Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}")

        # Check for any unmapped labels (will be NaN)
        if pd.isna(y_true_np).any():
            print("  Error: Some true labels could not be mapped to class columns")
            unmapped_labels = set(y_true[y_true.map(class_to_int).isna()])
            print(f"  Unmapped labels: {unmapped_labels}")
            print(f"  Available classes: {class_names}")
            continue

        try:
            print(f"  Generating ROC curve for '{target_value}'...")
            fig = plot_roc_curves(y_true_np, y_probs_np)

            # Create output filename with target value
            safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
            if len(target_values) > 1:
                output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
            else:
                output_filename = f"{output_name_base}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving ROC curve to: {output_path.absolute()}")
            fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

    print("ROC curves generated successfully!")


def generate_box_plots(labels, args, output_dir, output_name_base):
    """Generate box plots for model predictions"""

    print("Generating box plots...")

    # Parse target values from comma-separated string
    if args.target_value:

    # Arguments for dimensionality reduction
    parser.add_argument("--embeddings", type=str,
                        help="Path to input data embeddings file (CSV or tabular format). Required for dimred plots.")
    parser.add_argument("--method", type=str, default='pca', choices=['pca', 'umap'],
                        help="Transformation method ('pca' or 'umap'). Default is 'pca'. Used for dimred plots.")

    # Arguments for Kaplan-Meier
    parser.add_argument("--survival_data", type=str,
                        help="Path to survival data file with columns: duration and event. Required for kaplan_meier plots.")
    parser.add_argument("--surv_time_var", type=str, required=False,
                        help="Column name for survival time")
    parser.add_argument("--surv_event_var", type=str, required=False,
                        help="Column name for survival event")
    parser.add_argument("--event_value", type=str, required=False,
                        help="Value in event column that represents an event (e.g., 'DECEASED')")

    # Arguments for Cox analysis
    parser.add_argument("--model", type=str,
                        help="Path to trained flexynesis model (pickle file). Required for cox plots.")
    parser.add_argument("--clinical_train", type=str,
                        help="Path to training dataset (pickle file). Required for cox plots.")
    parser.add_argument("--clinical_test", type=str,
                        help="Path to test dataset (pickle file). Required for cox plots.")
    parser.add_argument("--omics_train", type=str, default=None,

                        help="If True, performs K-fold cross-validation and returns average C-index. Default is False")
    parser.add_argument("--n_splits", type=int, default=5,
                        help="Number of folds for cross-validation. Default is 5")
    parser.add_argument("--random_state", type=int, default=42,
                        help="Random seed for reproducibility. Default is 42")

    # Arguments for dimred, scatter plot, heatmap, PR curves, ROC curves, and box plots
    parser.add_argument("--target_value", type=str, default=None,
                        help="Target value for scatter plot.")

    # Common arguments
    parser.add_argument("--output_dir", type=str, default='output',
                        help="Output directory. Default is 'output'")
    parser.add_argument("--output_name", type=str, default=None,
                        help="Output filename base")

                raise ValueError("--method is required for dimensionality reduction plots")
            if not args.surv_time_var:
                raise ValueError("--surv_time_var is required for Kaplan-Meier plots")
            if not args.surv_event_var:
                raise ValueError("--surv_event_var is required for Kaplan-Meier plots")
            if not args.event_value:
                raise ValueError("--event_value is required for Kaplan-Meier plots")

        if args.plot_type in ['cox']:
            if not args.model:
                raise ValueError("--model is required when plot_type is 'cox'")
            if not os.path.isfile(args.model):
                raise FileNotFoundError(f"Model file not found: {args.model}")
            if not args.clinical_train:
                raise ValueError("--clinical_train is required when plot_type is 'cox'")
            if not os.path.isfile(args.clinical_train):
                raise FileNotFoundError(f"Training dataset file not found: {args.clinical_train}")
            if not args.clinical_test:

            if not args.surv_time_var:
                raise ValueError("--surv_time_var is required for Cox plots")
            if not args.surv_event_var:
                raise ValueError("--surv_event_var is required for Cox plots")
            if not args.clinical_variables:
                raise ValueError("--clinical_variables is required for Cox plots")
            if not isinstance(args.top_features, int) or args.top_features <= 0:
                raise ValueError("--top_features must be a positive integer")
            if not args.event_value:
                raise ValueError("--event_value is required for Kaplan-Meier plots")
            if not args.crossval:
                args.crossval = False
            if not isinstance(args.n_splits, int) or args.n_splits <= 0:
                raise ValueError("--n_splits must be a positive integer")
            if not isinstance(args.random_state, int):
                raise ValueError("--random_state must be an integer")

        if args.plot_type in ['scatter']:
            if not args.labels:
                raise ValueError("--labels is required for scatter plots")
            if not args.target_value:

                output_name_base = f"{embeddings_name}_{args.method}"
            elif args.plot_type == 'kaplan_meier':
                survival_name = Path(args.survival_data).stem
                output_name_base = f"{survival_name}_km"
            elif args.plot_type == 'cox':
                model_name = Path(args.model).stem
                output_name_base = f"{model_name}_cox"
            elif args.plot_type == 'scatter':
                labels_name = Path(args.labels).stem
                output_name_base = f"{labels_name}_scatter"
            elif args.plot_type == 'concordance_heatmap':

        # Generate plots based on type
        if args.plot_type in ['dimred']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            label_data = load_labels(args.labels)
            # Load embeddings data
            print(f"Loading embeddings from: {args.embeddings}")
            embeddings, sample_names = load_embeddings(args.embeddings)
            print(f"embeddings shape: {embeddings.shape}")

            # Match samples to embeddings
            matched_labels = match_samples_to_embeddings(sample_names, label_data)
            print(f"Successfully matched {len(matched_labels)} samples for dimensionality reduction")

            generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base)

        elif args.plot_type in ['kaplan_meier']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            label_data = load_labels(args.labels)
            # Load survival data
            print(f"Loading survival data from: {args.survival_data}")
            survival_data = load_survival_data(args.survival_data)
            print(f"Survival data shape: {survival_data.shape}")

            generate_km_plots(survival_data, label_data, args, output_dir, output_name_base)

        elif args.plot_type in ['cox']:
            # Load model and datasets
            print(f"Loading model from: {args.model}")
            model = load_model(args.model)
            print(f"Loading training dataset from: {args.clinical_train}")
            clinical_train = load_omics(args.clinical_train)
            print(f"Loading test dataset from: {args.clinical_test}")
            clinical_test = load_omics(args.clinical_test)
            print(f"Loading training omics dataset from: {args.omics_train}")
            omics_train = load_omics(args.omics_train)
            print(f"Loading test omics dataset from: {args.omics_test}")
            omics_test = load_omics(args.omics_test)

            generate_cox_plots(model, clinical_train, clinical_test, omics_test, omics_train, args, output_dir, output_name_base)

        elif args.plot_type in ['scatter']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            label_data = load_labels(args.labels)

            generate_plot_scatter(label_data, args, output_dir, output_name_base)

        elif args.plot_type in ['concordance_heatmap']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            label_data = load_labels(args.labels)

            generate_label_concordance_heatmap(label_data, args, output_dir, output_name_base)

        elif args.plot_type in ['pr_curve']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            label_data = load_labels(args.labels)

            generate_pr_curves(label_data, args, output_dir, output_name_base)

        elif args.plot_type in ['roc_curve']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            label_data = load_labels(args.labels)

            generate_roc_curves(label_data, args, output_dir, output_name_base)

        elif args.plot_type in ['box_plot']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            label_data = load_labels(args.labels)

            generate_box_plots(label_data, args, output_dir, output_name_base)

        print("All plots generated successfully!")

    except (FileNotFoundError, ValueError, pd.errors.ParserError) as e:
        print(f"Error: {e}")

8:9c91d13827ef

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from flexynesis import (
    build_cox_model,
    plot_dim_reduced,
    plot_hazard_ratios,
    plot_kaplan_meier_curves,
    plot_pr_curves,
    plot_roc_curves,

        if file_ext == '.csv':
            df = pd.read_csv(labels_input)
        elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
            df = pd.read_csv(labels_input, sep='\t')

        print(f"available columns: {df.columns.tolist()}")
        return df

    except Exception as e:
        raise ValueError(f"Error loading labels from {labels_input}: {e}") from e


def load_omics(omics_path):
    """Load omics data from a file. First column should be features"""
    try:

    except Exception as e:
        raise ValueError(f"Error loading omics data from {omics_path}: {e}") from e


def match_samples_to_embeddings(sample_names, labels):
    """Filter label data to match sample names in the embeddings"""
    # Create a DataFrame from sample_names to preserve order
    sample_df = pd.DataFrame({'sample_names': sample_names})

    # left_join
    first_column = labels.columns[0]
    df_matched = sample_df.merge(labels, left_on='sample_names', right_on=first_column, how='left')

    # remove sample_names to keep the initial structure
    df_matched = df_matched.drop('sample_names', axis=1)
    return df_matched


def detect_color_type(labels_series):
    """Auto-detect whether target variables should be treated as categorical or numerical"""

def generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base):
    """Generate dimensionality reduction plots"""

    # Check if this is the specific format with sample_id, known_label, predicted_label
    required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
    is_flexynesis_format = all(col in matched_labels.columns for col in required_cols)

    if not args.color:
        if is_flexynesis_format:
            print("Detected flexynesis labels format")
            print(f"Generating {args.method.upper()} plots for known and predicted labels...")
        else:
            print("Labels are not in flexynesis format (Custom labels), please specify a color variable with --color")

        # Parse target values from comma-separated string
        if args.target_value:
            target_values = [val.strip() for val in args.target_value.split(',')]
        else:
            # If no target values specified, use all unique variables
            target_values = matched_labels['variable'].unique().tolist()

        print(f"Generating {args.method.upper()} plots for {len(target_values)} target variable(s): {', '.join(target_values)}")

        # Check variables
        available_vars = matched_labels['variable'].unique()
        missing_vars = [var for var in target_values if var not in available_vars]

        if missing_vars:
            print(f"Warning: The following target variables were not found in the data: {', '.join(missing_vars)}")
            print(f"Available variables: {', '.join(available_vars)}")

        # Filter to only process available variables
        valid_vars = [var for var in target_values if var in available_vars]

        if not valid_vars:
            raise ValueError(f"None of the specified target variables were found in the data. Available: {', '.join(available_vars)}")

        # Generate plots for each valid target variable
        for var in valid_vars:
            print(f"\nPlotting variable: {var}")

            # Filter matched labels for current variable
            var_labels = matched_labels[matched_labels['variable'] == var].copy()
            var_labels = var_labels.drop_duplicates(subset='sample_id')

            if var_labels.empty:
                print(f"Warning: No data found for variable '{var}', skipping...")
                continue

            # Auto-detect color type
            known_color_type = detect_color_type(var_labels['known_label'])
            predicted_color_type = detect_color_type(var_labels['predicted_label'])

            print(f"  Auto-detected color types - Known: {known_color_type}, Predicted: {predicted_color_type}")

            try:
                # Plot 1: Known labels
                print(f"  Creating known labels plot for {var}...")
                fig_known = plot_dim_reduced(
                    matrix=embeddings,
                    labels=var_labels['known_label'],
                    method=args.method,
                    color_type=known_color_type
                )

                output_path_known = output_dir / f"{output_name_base}_{var}_known.{args.format}"
                print(f"  Saving known labels plot to: {output_path_known.name}")
                fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')

                # Plot 2: Predicted labels
                print(f"  Creating predicted labels plot for {var}...")
                fig_predicted = plot_dim_reduced(
                    matrix=embeddings,
                    labels=var_labels['predicted_label'],
                    method=args.method,
                    color_type=predicted_color_type
                )

                output_path_predicted = output_dir / f"{output_name_base}_{var}_predicted.{args.format}"
                print(f"  Saving predicted labels plot to: {output_path_predicted.name}")
                fig_predicted.save(output_path_predicted, dpi=args.dpi, bbox_inches='tight')

                print(f"  ✓ Successfully created plots for variable '{var}'")

            except Exception as e:
                print(f"  ✗ Error creating plots for variable '{var}': {e}")
                continue

        print(f"\nDimensionality reduction plots completed for {len(valid_vars)} variable(s)!")

    else:
        # check if the color variable exists in matched_labels
        if args.color not in matched_labels.columns:
            raise ValueError(f"Color variable '{args.color}' not found in matched labels. Available columns: {matched_labels.columns.tolist()}")

        # Auto-detect color type
        color_type = detect_color_type(matched_labels[args.color])

        print(f"  Auto-detected color type: {color_type}")

        # Plot: Specified color column
        print(f"  Creating plot for {args.color}...")
        fig = plot_dim_reduced(
            matrix=embeddings,
            labels=matched_labels[args.color],
            method=args.method,
            color_type=color_type
        )

        output_path = output_dir / f"{output_name_base}_{args.color}.{args.format}"
        print(f"  Saving plot to: {output_path.name}")
        fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

        print(f"  ✓ Successfully created plot for variable '{args.color}'")


def generate_km_plots(survival_data, labels, args, output_dir, output_name_base):
    """Generate Kaplan-Meier plots"""

    # Check if this is the specific format with sample_id, known_label, predicted_label
    required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
    is_flexynesis_format = all(col in labels.columns for col in required_cols)

    if not is_flexynesis_format:
        raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")

    print("Generating Kaplan-Meier curves of risk subtypes...")

    if survival_data.columns[0] != 'sample_id':
        survival_data = survival_data.rename(columns={survival_data.columns[0]: 'sample_id'})

    # Check if the event column exists
    if args.surv_event_var not in survival_data.columns:
        raise ValueError(f"Column '{args.surv_event_var}' not found in survival data")

    labels = labels[(labels['variable'] == args.surv_event_var)]

    # Merge survival data with labels
    df_deceased = pd.merge(survival_data, labels, on='sample_id', how='inner')
    df_deceased = df_deceased.dropna(subset=[args.surv_time_var, args.surv_event_var])

    if df_deceased.empty:
        raise ValueError("No matching samples found after merging survival and label data.")

    # Get risk scores
    risk_scores = df_deceased['predicted_label'].values

    # Compute groups (e.g., median split)
    quantiles = np.quantile(risk_scores, [0.5])
    groups = np.digitize(risk_scores, quantiles)
    group_labels = ['low_risk' if g == 0 else 'high_risk' for g in groups]

    fig_known = plot_kaplan_meier_curves(
        durations=df_deceased[args.surv_time_var],
        events=df_deceased[args.surv_event_var],
        categorical_variable=group_labels
    )

    output_path_known = output_dir / f"{output_name_base}_km_risk_subtypes.{args.format}"
    print(f"Saving Kaplan-Meier plot to: {output_path_known.absolute()}")
    fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')

    print("Kaplan-Meier plot saved successfully!")


def generate_cox_plots(important_features, clinical_train, clinical_test, omics_train, omics_test, args, output_dir, output_name_base):
    """Generate Cox proportional hazards plots"""
    print("Generating Cox proportional hazards analysis...")

    # Check if this is the specific format with target_variable, importance
    required_cols = ['target_variable', 'layer', 'importance']
    is_flexynesis_format = all(col in important_features.columns for col in required_cols)

    if not is_flexynesis_format:
        raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid important_features file with the required columns, {required_cols}.")

    # Parse clinical variables
    clinical_vars = []
    if args.clinical_variables:
        clinical_vars = [var.strip() for var in args.clinical_variables.split(',')]

    # Validate that survival variables are included
    required_vars = [args.surv_time_var, args.surv_event_var]
    for var in required_vars:
        if var not in clinical_vars:

    df_clin = pd.concat([df_clin_train, df_clin_test], axis=0)

    # Get top survival markers
    print(f"Extracting top {args.top_features} important features for {args.surv_event_var}...")
    try:
        print(f"Loading {args.top_features} important features from: {args.important_features}")
        imp_features = load_labels(args.important_features)
        imp_features = imp_features[imp_features['target_variable'] == args.surv_event_var]
        if args.layer not in imp_features['layer'].unique():
            print(f"Available class labels: {imp_features['layer'].unique()}")
            raise ValueError(f"Class label '{args.layer}' not found in important features data: {args.important_features}")
        imp_features = imp_features[imp_features['layer'] == args.layer]
        if imp_features.empty:
            raise ValueError(f"No important features found for target variable '{args.surv_event_var}' in {args.important_features}")
        imp_features = imp_features.sort_values(by='importance', ascending=False)

        if len(imp_features) < args.top_features:
            raise ValueError(f"Requested top {args.top_features} features, but only {len(imp_features)} available in {args.important_features}")

        imp = imp_features['name'].unique().tolist()[0:args.top_features]

        print(f"Top features: {', '.join(imp)}")
    except Exception as e:
        raise ValueError(f"Error getting important features: {e}")

    # Extract feature data from omics datasets

    final_samples = len(df)
    print(f"Removed {initial_samples - final_samples} samples without survival data")

    if df.empty:
        raise ValueError("No samples remain after filtering for survival data")

    # Build Cox model
    print(f"Building Cox model with time variable: {args.surv_time_var}, event variable: {args.surv_event_var}")
    try:
        coxm = build_cox_model(df,

def generate_plot_scatter(labels, args, output_dir, output_name_base):
    """Generate scatter plot of known vs predicted labels"""
    print("Generating scatter plots of known vs predicted labels...")

    # Check if this is the specific format with sample_id, known_label, predicted_label
    required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
    is_flexynesis_format = all(col in labels.columns for col in required_cols)

    if is_flexynesis_format:
        # Parse target values from comma-separated string
        if args.target_value:
            target_values = [val.strip() for val in args.target_value.split(',')]
        else:
            # If no target values specified, use all unique variables
            target_values = labels['variable'].unique().tolist()

        print(f"Processing target values: {target_values}")

        successful_plots = 0
        skipped_plots = 0

        for target_value in target_values:
            print(f"\nProcessing target value: '{target_value}'")

            # Filter labels for the current target value
            target_labels = labels[labels['variable'] == target_value]

            if target_labels.empty:
                print(f"  Warning: No data found for target value '{target_value}' - skipping")
                skipped_plots += 1
                continue

            # Check if labels are numeric and convert
            true_values = pd.to_numeric(target_labels['known_label'], errors='coerce')
            predicted_values = pd.to_numeric(target_labels['predicted_label'], errors='coerce')

            if true_values.isna().all() or predicted_values.isna().all():
                print(f"No valid numeric values found for known or predicted labels in '{target_value}'")
                skipped_plots += 1
                continue

            try:
                print(f"  Generating scatter plot for '{target_value}'...")
                fig = plot_scatter(true_values, predicted_values)

                # Create output filename with target value
                safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
                output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"

                output_path = output_dir / output_filename
                print(f"  Saving scatter plot to: {output_path.absolute()}")
                fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

                successful_plots += 1
                print(f"  Scatter plot for '{target_value}' generated successfully!")

            except Exception as e:
                print(f"  Error generating plot for '{target_value}': {str(e)}")
                skipped_plots += 1

        # Summary
        print("  Summary:")
        print(f"  Successfully generated: {successful_plots} plots")
        print(f"  Skipped: {skipped_plots} plots")

        if successful_plots == 0:
            raise ValueError("No scatter plots could be generated. Check your data and target values.")

        print("Scatter plot generation completed!")

    if not is_flexynesis_format:
        print("Labels are not in flexynesis format (Custom labels)")

        if not args.true_label or not args.predicted_label:
            raise ValueError("For custom labels, please specify --true_label and --predicted_label arguments.")

        # Check if labels are numeric and convert
        true_values = pd.to_numeric(labels[args.true_label], errors='coerce')
        predicted_values = pd.to_numeric(labels[args.predicted_label], errors='coerce')

        if true_values.isna().all() or predicted_values.isna().all():
            print("No valid numeric values found for known or predicted labels")

        try:
            print("  Generating scatter plot...")
            fig = plot_scatter(true_values, predicted_values)

            # Create output filename with target value
            output_filename = f"{output_name_base}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving scatter plot to: {output_path.absolute()}")
            fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

        except Exception as e:
            print(f"  Error generating plot: {str(e)}")

        print("Scatter plot generation completed!")


def generate_label_concordance_heatmap(labels, args, output_dir, output_name_base):
    """Generate label concordance heatmap"""
    print("Generating label concordance heatmaps...")

    # Check if this is the specific format with sample_id, known_label, predicted_label
    required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
    is_flexynesis_format = all(col in labels.columns for col in required_cols)

    if is_flexynesis_format:
        # Parse target values from comma-separated string
        if args.target_value:
            target_values = [val.strip() for val in args.target_value.split(',')]
        else:
            # If no target values specified, use all unique variables
            target_values = labels['variable'].unique().tolist()

        print(f"Processing target values: {target_values}")

        for target_value in target_values:
            print(f"\nProcessing target value: '{target_value}'")

            # Filter labels for the current target value
            target_labels = labels[labels['variable'] == target_value]

            if target_labels.empty:
                print(f"  Warning: No data found for target value '{target_value}' - skipping")
                continue

            true_values = target_labels['known_label'].tolist()
            predicted_values = target_labels['predicted_label'].tolist()

            try:
                print(f"  Generating heatmap for '{target_value}'...")
                fig = plot_label_concordance_heatmap(true_values, predicted_values)
                plt.close(fig)

                # Create output filename with target value
                safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
                output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"

                output_path = output_dir / output_filename
                print(f"  Saving heatmap to: {output_path.absolute()}")
                fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')

            except Exception as e:
                print(f"  Error generating heatmap for '{target_value}': {str(e)}")
                continue

        print("Label concordance heatmap generated successfully!")

    if not is_flexynesis_format:
        print("Labels are not in flexynesis format (Custom labels)")

        if not args.true_label or not args.predicted_label:
            raise ValueError("For custom labels, please specify --true_label and --predicted_label arguments.")

        true_values = labels[args.true_label].tolist()
        predicted_values = labels[args.predicted_label].tolist()

        try:
            print("  Generating heatmap for...")
            fig = plot_label_concordance_heatmap(true_values, predicted_values)
            plt.close(fig)

            # Create output filename with target value
            output_filename = f"{output_name_base}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving heatmap to: {output_path.absolute()}")
            fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')

        except Exception as e:
            print(f"  Error generating heatmap': {str(e)}")

        print("Label concordance heatmap generated successfully!")


def generate_pr_curves(labels, args, output_dir, output_name_base):
    """Generate precision-recall curves"""
    print("Generating precision-recall curves...")

    # Check if this is the specific format with sample_id, known_label, predicted_label
    required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
    is_flexynesis_format = all(col in labels.columns for col in required_cols)

    if not is_flexynesis_format:
        raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")

    # Parse target values from comma-separated string
    if args.target_value:
        target_values = [val.strip() for val in args.target_value.split(',')]
    else:
        # If no target values specified, use all unique variables
        target_values = labels['variable'].unique().tolist()

    print(f"Processing target values: {target_values}")

    for target_value in target_values:
        print(f"\nProcessing target value: '{target_value}'")

        # Filter labels for the current target value
        target_labels = labels[labels['variable'] == target_value]

        # Check if this is a regression problem (no class probabilities)
        prob_columns = target_labels['class_label'].unique()
        non_na_probs = target_labels['probability'].notna().sum()

        print(f"  Class labels found: {list(prob_columns)}")
        print(f"  Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")

        # If most probabilities are NaN, this is likely a regression problem
        if non_na_probs < len(target_labels) * 0.1:  # Less than 10% valid probabilities
            print("  Detected regression problem - precision-recall curves not applicable")
            print(f"  Skipping '{target_value}' (use regression evaluation metrics instead)")
            continue

        # Debug: Check data quality
        total_rows = len(target_labels)
        missing_labels = target_labels['known_label'].isna().sum()
        missing_probs = target_labels['probability'].isna().sum()
        unique_samples = target_labels['sample_id'].nunique()
        unique_classes = target_labels['class_label'].nunique()

        print(f"  Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
        print(f"  Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")

        if missing_labels > 0:
            print(f"  Warning: Found {missing_labels} missing known_label values")
            missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
            print(f"  Sample IDs with missing known_label: {list(missing_samples)}")

            # Remove rows with missing known_label
            target_labels = target_labels.dropna(subset=['known_label'])
            if target_labels.empty:
                print(f"  Error: No valid known_label data remaining for '{target_value}' - skipping")
                continue

        # 1. Pivot to wide format
        prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability')

        print(f"  After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes")
        print(f"  Class columns: {list(prob_df.columns)}")

        # Check for NaN values in probability data
        nan_counts = prob_df.isna().sum()
        if nan_counts.any():
            print(f"  NaN counts per class: {dict(nan_counts)}")
            print(f"  Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}")

            # Drop only rows where ALL probabilities are NaN
            all_nan_rows = prob_df.isna().all(axis=1)
            if all_nan_rows.any():
                print(f"  Dropping {all_nan_rows.sum()} samples with all NaN probabilities")
                prob_df = prob_df[~all_nan_rows]

            remaining_nans = prob_df.isna().sum().sum()
            if remaining_nans > 0:
                print(f"  Warning: {remaining_nans} individual NaN values remain - filling with 0")
                prob_df = prob_df.fillna(0)

            if prob_df.empty:
                print(f"  Error: No valid probability data remaining for '{target_value}' - skipping")
                continue

        # 2. Get true labels
        true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id')

        # 3. Align indices - only keep samples that exist in both datasets
        common_indices = prob_df.index.intersection(true_labels_df.index)
        if len(common_indices) == 0:
            print(f"  Error: No common sample_ids between probability and true label data for '{target_value}' - skipping")
            continue

        print(f"  Found {len(common_indices)} samples with both probability and true label data")

        # Filter both datasets to common indices
        prob_df_aligned = prob_df.loc[common_indices]
        y_true = true_labels_df.loc[common_indices]['known_label']

        # 4. Final check for NaN values
        if y_true.isna().any():
            print(f"  Error: True labels still contain NaN after alignment for '{target_value}' - skipping")
            continue

        if prob_df_aligned.isna().any().any():
            print(f"  Error: Probability data still contains NaN after alignment for '{target_value}' - skipping")
            continue

        # 5. Convert categorical labels to integer labels
        # Create a mapping from class names to integers
        class_names = list(prob_df_aligned.columns)
        class_to_int = {class_name: i for i, class_name in enumerate(class_names)}

        print(f"  Class mapping: {class_to_int}")

        # Convert true labels to integers
        y_true_np = y_true.map(class_to_int).to_numpy()
        y_probs_np = prob_df_aligned.to_numpy()

        print(f"  Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}")
        print(f"  Unique true labels (integers): {set(y_true_np)}")
        print(f"  Class labels (columns): {class_names}")
        print(f"  Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}")

        # Check for any unmapped labels (will be NaN)
        if pd.isna(y_true_np).any():
            print("  Error: Some true labels could not be mapped to class columns")
            unmapped_labels = set(y_true[y_true.map(class_to_int).isna()])
            print(f"  Unmapped labels: {unmapped_labels}")
            print(f"  Available classes: {class_names}")
            continue

        try:
            print(f"  Generating precision-recall curve for '{target_value}'...")
            fig = plot_pr_curves(y_true_np, y_probs_np)

            # Create output filename with target value
            safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
            output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving precision-recall curve to: {output_path.absolute()}")
            fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

        except Exception as e:
            print(f"  Error generating precision-recall curve for '{target_value}': {str(e)}")
            print(f"  Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}")
            print(f"  Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}")
            continue

    print("Precision-recall curves generated successfully!")


def generate_roc_curves(labels, args, output_dir, output_name_base):
    """Generate ROC curves"""
    print("Generating ROC curves...")

    # Check if this is the specific format with sample_id, known_label, predicted_label
    required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
    is_flexynesis_format = all(col in labels.columns for col in required_cols)

    if not is_flexynesis_format:
        raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")

    # Parse target values from comma-separated string
    if args.target_value:
        target_values = [val.strip() for val in args.target_value.split(',')]
    else:

        print(f"\nProcessing target value: '{target_value}'")

        # Filter labels for the current target value
        target_labels = labels[labels['variable'] == target_value]

        # Check if this is a regression problem (no class probabilities)
        prob_columns = target_labels['class_label'].unique()
        non_na_probs = target_labels['probability'].notna().sum()

        print(f"  Class labels found: {list(prob_columns)}")
        print(f"  Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")

        # If most probabilities are NaN, this is likely a regression problem
        if non_na_probs < len(target_labels) * 0.1:  # Less than 10% valid probabilities
            print("  Detected regression problem - ROC curves not applicable")
            print(f"  Skipping '{target_value}' (use regression evaluation metrics instead)")
            continue

        # Debug: Check data quality
        total_rows = len(target_labels)

            print(f"  Unmapped labels: {unmapped_labels}")
            print(f"  Available classes: {class_names}")
            continue

        try:
            print(f"  Generating ROC curve for '{target_value}'...")
            fig = plot_roc_curves(y_true_np, y_probs_np)

            # Create output filename with target value
            safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
            output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"

            output_path = output_dir / output_filename
            print(f"  Saving ROC curve to: {output_path.absolute()}")
            fig.save(output_path, dpi=args.dpi, bbox_inches='tight')

    print("ROC curves generated successfully!")


def generate_box_plots(labels, args, output_dir, output_name_base):
    """Generate box plots for model predictions"""

    # Check if this is the specific format with sample_id, known_label, predicted_label
    required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
    is_flexynesis_format = all(col in labels.columns for col in required_cols)

    if not is_flexynesis_format:
        raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")

    print("Generating box plots...")

    # Parse target values from comma-separated string
    if args.target_value:

    # Arguments for dimensionality reduction
    parser.add_argument("--embeddings", type=str,
                        help="Path to input data embeddings file (CSV or tabular format). Required for dimred plots.")
    parser.add_argument("--method", type=str, default='pca', choices=['pca', 'umap'],
                        help="Transformation method ('pca' or 'umap'). Default is 'pca'. Used for dimred plots.")
    parser.add_argument("--color", type=str, default=None,
                        help="User-defined color for the plot.")

    # Arguments for Kaplan-Meier
    parser.add_argument("--survival_data", type=str,
                        help="Path to survival data file with columns: duration and event. Required for kaplan_meier plots.")
    parser.add_argument("--surv_time_var", type=str, required=False,
                        help="Column name for survival time")
    parser.add_argument("--surv_event_var", type=str, required=False,
                        help="Column name for survival event")

    # Arguments for Cox analysis
    parser.add_argument("--important_features", type=str,
                        help="Path to calculated feature importance file. Required for cox plots.")
    parser.add_argument("--clinical_train", type=str,
                        help="Path to training dataset (pickle file). Required for cox plots.")
    parser.add_argument("--clinical_test", type=str,
                        help="Path to test dataset (pickle file). Required for cox plots.")
    parser.add_argument("--omics_train", type=str, default=None,

                        help="If True, performs K-fold cross-validation and returns average C-index. Default is False")
    parser.add_argument("--n_splits", type=int, default=5,
                        help="Number of folds for cross-validation. Default is 5")
    parser.add_argument("--random_state", type=int, default=42,
                        help="Random seed for reproducibility. Default is 42")
    parser.add_argument("--layer", type=str, default=None,
                        help="Class label for filtering important features.")

    # Arguments for dimred, scatter plot, heatmap, PR curves, ROC curves, and box plots
    parser.add_argument("--target_value", type=str, default=None,
                        help="Target value for scatter plot.")

    # Arguments for scatter plots and concordance heatmaps
    parser.add_argument("--true_label", type=str, default=None,
                        help="Column name for true labels in scatter plots and concordance heatmaps.")
    parser.add_argument("--predicted_label", type=str, default=None,
                        help="Column name for predicted labels in scatter plots and concordance heatmaps.")
    # Common arguments
    parser.add_argument("--output_dir", type=str, default='output',
                        help="Output directory. Default is 'output'")
    parser.add_argument("--output_name", type=str, default=None,
                        help="Output filename base")

                raise ValueError("--method is required for dimensionality reduction plots")
            if not args.surv_time_var:
                raise ValueError("--surv_time_var is required for Kaplan-Meier plots")
            if not args.surv_event_var:
                raise ValueError("--surv_event_var is required for Kaplan-Meier plots")

        if args.plot_type in ['cox']:
            if not args.important_features:
                raise ValueError("--important_features is required when plot_type is 'cox'")
            if not os.path.isfile(args.important_features):
                raise FileNotFoundError(f"Important features file not found: {args.important_features}")
            if not args.clinical_train:
                raise ValueError("--clinical_train is required when plot_type is 'cox'")
            if not os.path.isfile(args.clinical_train):
                raise FileNotFoundError(f"Training dataset file not found: {args.clinical_train}")
            if not args.clinical_test:

            if not args.surv_time_var:
                raise ValueError("--surv_time_var is required for Cox plots")
            if not args.surv_event_var:
                raise ValueError("--surv_event_var is required for Cox plots")
            if not args.clinical_variables:
                print("--clinical_variables is not set for Cox plots")
            if not isinstance(args.top_features, int) or args.top_features <= 0:
                raise ValueError("--top_features must be a positive integer")
            if not args.crossval:
                args.crossval = False
            if not isinstance(args.n_splits, int) or args.n_splits <= 0:
                raise ValueError("--n_splits must be a positive integer")
            if not isinstance(args.random_state, int):
                raise ValueError("--random_state must be an integer")
            if not args.layer:
                print("--layer is not specified, using all classes from labels")

        if args.plot_type in ['scatter']:
            if not args.labels:
                raise ValueError("--labels is required for scatter plots")
            if not args.target_value:

                output_name_base = f"{embeddings_name}_{args.method}"
            elif args.plot_type == 'kaplan_meier':
                survival_name = Path(args.survival_data).stem
                output_name_base = f"{survival_name}_km"
            elif args.plot_type == 'cox':
                model_name = Path(args.important_features).stem
                output_name_base = f"{model_name}_cox"
            elif args.plot_type == 'scatter':
                labels_name = Path(args.labels).stem
                output_name_base = f"{labels_name}_scatter"
            elif args.plot_type == 'concordance_heatmap':

        # Generate plots based on type
        if args.plot_type in ['dimred']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            labels = load_labels(args.labels)
            # Load embeddings data
            print(f"Loading embeddings from: {args.embeddings}")
            embeddings, sample_names = load_embeddings(args.embeddings)
            print(f"embeddings shape: {embeddings.shape}")

            # Match samples to embeddings
            matched_labels = match_samples_to_embeddings(sample_names, labels)
            print(f"Successfully matched {len(matched_labels)} samples for dimensionality reduction")
            print(f"Matched labels shape: {matched_labels.shape}")
            print(f"Columns in matched labels: {matched_labels.columns.tolist()}")
            generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base)

        elif args.plot_type in ['kaplan_meier']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            labels = load_labels(args.labels)
            # Load survival data
            print(f"Loading survival data from: {args.survival_data}")
            survival_data = load_labels(args.survival_data)
            print(f"Survival data shape: {survival_data.shape}")

            generate_km_plots(survival_data, labels, args, output_dir, output_name_base)

        elif args.plot_type in ['cox']:
            # Load important_features and datasets
            print(f"Loading important features from: {args.important_features}")
            important_features = load_labels(args.important_features)
            print(f"Loading training dataset from: {args.clinical_train}")
            clinical_train = load_omics(args.clinical_train)
            print(f"Loading test dataset from: {args.clinical_test}")
            clinical_test = load_omics(args.clinical_test)
            print(f"Loading training omics dataset from: {args.omics_train}")
            omics_train = load_omics(args.omics_train)
            print(f"Loading test omics dataset from: {args.omics_test}")
            omics_test = load_omics(args.omics_test)

            generate_cox_plots(important_features, clinical_train, clinical_test, omics_test, omics_train, args, output_dir, output_name_base)

        elif args.plot_type in ['scatter']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            labels = load_labels(args.labels)

            generate_plot_scatter(labels, args, output_dir, output_name_base)

        elif args.plot_type in ['concordance_heatmap']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            labels = load_labels(args.labels)

            generate_label_concordance_heatmap(labels, args, output_dir, output_name_base)

        elif args.plot_type in ['pr_curve']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            labels = load_labels(args.labels)

            generate_pr_curves(labels, args, output_dir, output_name_base)

        elif args.plot_type in ['roc_curve']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            labels = load_labels(args.labels)

            generate_roc_curves(labels, args, output_dir, output_name_base)

        elif args.plot_type in ['box_plot']:
            # Load labels
            print(f"Loading labels from: {args.labels}")
            labels = load_labels(args.labels)

            generate_box_plots(labels, args, output_dir, output_name_base)

        print("All plots generated successfully!")

    except (FileNotFoundError, ValueError, pd.errors.ParserError) as e:
        print(f"Error: {e}")