flexynesis: flexynesis_plot.py annotate

annotate flexynesis_plot.py @ 5:466b593fd87e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a

author	bgruening
date	Fri, 04 Jul 2025 14:57:40 +0000
parents	525c661a7fdc
children

rev	line source
3 525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1 #!/usr/bin/env python
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	2 """Generate plots using flexynesis
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	3 This script generates dimensionality reduction plots, Kaplan-Meier survival curves,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	4 and Cox proportional hazards models from data processed by flexynesis."""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	5
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	6 import argparse
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	7 import os
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	8 from pathlib import Path
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	9
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	10 import matplotlib.pyplot as plt
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	11 import numpy as np
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	12 import pandas as pd
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	13 import seaborn as sns
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	14 import torch
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	15 from flexynesis import (
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	16 build_cox_model,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	17 get_important_features,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	18 plot_dim_reduced,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	19 plot_hazard_ratios,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	20 plot_kaplan_meier_curves,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	21 plot_pr_curves,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	22 plot_roc_curves,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	23 plot_scatter
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	24 )
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	25 from scipy.stats import kruskal, mannwhitneyu
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	26
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	27
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	28 def load_embeddings(embeddings_path):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	29 """Load embeddings from a file"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	30 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	31 # Determine file extension
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	32 file_ext = Path(embeddings_path).suffix.lower()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	33
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	34 if file_ext == '.csv':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	35 df = pd.read_csv(embeddings_path, index_col=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	36 elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	37 df = pd.read_csv(embeddings_path, sep='\t', index_col=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	38 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	39 raise ValueError(f"Unsupported file extension: {file_ext}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	40
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	41 return df, df.index.tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	42
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	43 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	44 raise ValueError(f"Error loading embeddings from {embeddings_path}: {e}") from e
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	45
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	46
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	47 def load_labels(labels_input):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	48 """Load predicted labels from flexynesis"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	49 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	50 # Determine file extension
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	51 file_ext = Path(labels_input).suffix.lower()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	52
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	53 if file_ext == '.csv':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	54 df = pd.read_csv(labels_input)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	55 elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	56 df = pd.read_csv(labels_input, sep='\t')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	57
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	58 # Check if this is the specific format with sample_id, known_label, predicted_label
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	59 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	60 if all(col in df.columns for col in required_cols):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	61 return df
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	62 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	63 raise ValueError(f"Labels file {labels_input} does not contain required columns: {required_cols}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	64
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	65 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	66 raise ValueError(f"Error loading labels from {labels_input}: {e}") from e
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	67
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	68
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	69 def load_survival_data(survival_path):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	70 """Load survival data from a file. First column should be sample_id"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	71 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	72 # Determine file extension
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	73 file_ext = Path(survival_path).suffix.lower()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	74
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	75 if file_ext == '.csv':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	76 df = pd.read_csv(survival_path, index_col=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	77 elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	78 df = pd.read_csv(survival_path, sep='\t', index_col=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	79 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	80 raise ValueError(f"Unsupported file extension: {file_ext}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	81 return df
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	82
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	83 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	84 raise ValueError(f"Error loading survival data from {survival_path}: {e}") from e
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	85
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	86
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	87 def load_omics(omics_path):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	88 """Load omics data from a file. First column should be features"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	89 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	90 # Determine file extension
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	91 file_ext = Path(omics_path).suffix.lower()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	92
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	93 if file_ext == '.csv':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	94 df = pd.read_csv(omics_path, index_col=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	95 elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	96 df = pd.read_csv(omics_path, sep='\t', index_col=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	97 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	98 raise ValueError(f"Unsupported file extension: {file_ext}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	99 return df
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	100
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	101 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	102 raise ValueError(f"Error loading omics data from {omics_path}: {e}") from e
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	103
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	104
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	105 def load_model(model_path):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	106 """Load flexynesis model from pickle file"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	107 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	108 with open(model_path, 'rb') as f:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	109 model = torch.load(f, weights_only=False)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	110 return model
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	111 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	112 raise ValueError(f"Error loading model from {model_path}: {e}") from e
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	113
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	114
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	115 def match_samples_to_embeddings(sample_names, label_data):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	116 """Filter label data to match sample names in the embeddings"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	117 df_matched = label_data[label_data['sample_id'].isin(sample_names)]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	118 return df_matched
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	119
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	120
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	121 def detect_color_type(labels_series):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	122 """Auto-detect whether target variables should be treated as categorical or numerical"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	123 # Remove NaN
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	124 clean_labels = labels_series.dropna()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	125
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	126 if clean_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	127 return 'categorical' # default output if no labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	128
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	129 # Check if all values can be converted to numbers
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	130 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	131 numeric_labels = pd.to_numeric(clean_labels, errors='coerce')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	132
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	133 # If conversion failed -> categorical
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	134 if numeric_labels.isna().any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	135 return 'categorical'
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	136
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	137 # Check number of unique values
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	138 unique_count = len(clean_labels.unique())
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	139 total_count = len(clean_labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	140
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	141 # If few unique values relative to total -> categorical
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	142 # Threshold: if unique values < 10 OR unique/total < 0.1
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	143 if unique_count < 10 or (unique_count / total_count) < 0.1:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	144 return 'categorical'
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	145 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	146 return 'numerical'
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	147
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	148 except Exception:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	149 return 'categorical'
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	150
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	151
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	152 def plot_label_concordance_heatmap(labels1, labels2, figsize=(12, 10)):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	153 """
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	154 Plot a heatmap reflecting the concordance between two sets of labels using pandas crosstab.
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	155
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	156 Parameters:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	157 - labels1: The first set of labels.
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	158 - labels2: The second set of labels.
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	159 """
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	160 # Compute the cross-tabulation
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	161 ct = pd.crosstab(pd.Series(labels1, name='Labels Set 1'), pd.Series(labels2, name='Labels Set 2'))
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	162 # Normalize the cross-tabulation matrix column-wise
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	163 ct_normalized = ct.div(ct.sum(axis=1), axis=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	164
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	165 # Plot the heatmap
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	166 plt.figure(figsize=figsize)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	167 sns.heatmap(ct_normalized, annot=True, cmap='viridis', linewidths=.5) # col_cluster=False)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	168 plt.title('Concordance between label groups')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	169
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	170 return plt.gcf()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	171
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	172
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	173 def plot_boxplot(categorical_x, numerical_y, title_x='Categories', title_y='Values', figsize=(10, 6), jittersize=4):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	174 """
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	175 Create a boxplot with to visualize the distribution of predicted probabilities across different categories.
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	176 the x axis represents the true labels, and the y axis represents the predicted probabilities for specific categories.
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	177 """
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	178 df = pd.DataFrame({title_x: categorical_x, title_y: numerical_y})
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	179
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	180 # Compute p-value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	181 groups = df[title_x].unique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	182 if len(groups) == 2:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	183 group1 = df[df[title_x] == groups[0]][title_y]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	184 group2 = df[df[title_x] == groups[1]][title_y]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	185 stat, p = mannwhitneyu(group1, group2, alternative='two-sided')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	186 test_name = "Mann-Whitney U"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	187 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	188 group_data = [df[df[title_x] == group][title_y] for group in groups]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	189 stat, p = kruskal(*group_data)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	190 test_name = "Kruskal-Wallis"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	191
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	192 # Create a boxplot with jittered points
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	193 plt.figure(figsize=figsize)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	194 sns.boxplot(x=title_x, y=title_y, hue=title_x, data=df, palette='Set2', legend=False, fill=False)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	195 sns.stripplot(x=title_x, y=title_y, data=df, color='black', size=jittersize, jitter=True, dodge=True, alpha=0.4)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	196
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	197 # Labels and p-value annotation
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	198 plt.xlabel(title_x)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	199 plt.ylabel(title_y)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	200 plt.text(
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	201 x=-0.4,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	202 y=plt.ylim()[1],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	203 s=f'{test_name} p = {p:.3e}',
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	204 verticalalignment='top',
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	205 horizontalalignment='left',
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	206 fontsize=12,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	207 bbox=dict(boxstyle='round,pad=0.3', facecolor='white', edgecolor='gray')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	208 )
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	209
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	210 plt.tight_layout()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	211 return plt.gcf()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	212
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	213
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	214 def generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	215 """Generate dimensionality reduction plots"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	216
5 466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	217 # Parse target values from comma-separated string
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	218 if args.target_value:
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	219 target_values = [val.strip() for val in args.target_value.split(',')]
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	220 else:
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	221 # If no target values specified, use all unique variables
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	222 target_values = matched_labels['variable'].unique().tolist()
3 525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	223
5 466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	224 print(f"Generating {args.method.upper()} plots for {len(target_values)} target variable(s): {', '.join(target_values)}")
3 525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	225
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	226 # Check variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	227 available_vars = matched_labels['variable'].unique()
5 466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	228 missing_vars = [var for var in target_values if var not in available_vars]
3 525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	229
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	230 if missing_vars:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	231 print(f"Warning: The following target variables were not found in the data: {', '.join(missing_vars)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	232 print(f"Available variables: {', '.join(available_vars)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	233
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	234 # Filter to only process available variables
5 466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	235 valid_vars = [var for var in target_values if var in available_vars]
3 525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	236
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	237 if not valid_vars:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	238 raise ValueError(f"None of the specified target variables were found in the data. Available: {', '.join(available_vars)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	239
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	240 # Generate plots for each valid target variable
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	241 for var in valid_vars:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	242 print(f"\nPlotting variable: {var}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	243
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	244 # Filter matched labels for current variable
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	245 var_labels = matched_labels[matched_labels['variable'] == var].copy()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	246 var_labels = var_labels.drop_duplicates(subset='sample_id')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	247
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	248 if var_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	249 print(f"Warning: No data found for variable '{var}', skipping...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	250 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	251
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	252 # Auto-detect color type
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	253 known_color_type = detect_color_type(var_labels['known_label'])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	254 predicted_color_type = detect_color_type(var_labels['predicted_label'])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	255
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	256 print(f" Auto-detected color types - Known: {known_color_type}, Predicted: {predicted_color_type}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	257
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	258 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	259 # Plot 1: Known labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	260 print(f" Creating known labels plot for {var}...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	261 fig_known = plot_dim_reduced(
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	262 matrix=embeddings,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	263 labels=var_labels['known_label'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	264 method=args.method,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	265 color_type=known_color_type
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	266 )
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	267
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	268 output_path_known = output_dir / f"{output_name_base}_{var}_known.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	269 print(f" Saving known labels plot to: {output_path_known.name}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	270 fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	271
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	272 # Plot 2: Predicted labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	273 print(f" Creating predicted labels plot for {var}...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	274 fig_predicted = plot_dim_reduced(
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	275 matrix=embeddings,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	276 labels=var_labels['predicted_label'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	277 method=args.method,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	278 color_type=predicted_color_type
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	279 )
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	280
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	281 output_path_predicted = output_dir / f"{output_name_base}_{var}_predicted.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	282 print(f" Saving predicted labels plot to: {output_path_predicted.name}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	283 fig_predicted.save(output_path_predicted, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	284
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	285 print(f" ✓ Successfully created plots for variable '{var}'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	286
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	287 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	288 print(f" ✗ Error creating plots for variable '{var}': {e}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	289 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	290
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	291 print(f"\nDimensionality reduction plots completed for {len(valid_vars)} variable(s)!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	292
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	293
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	294 def generate_km_plots(survival_data, label_data, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	295 """Generate Kaplan-Meier plots"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	296 print("Generating Kaplan-Meier curves of risk subtypes...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	297
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	298 # Reset index and rename the index column to sample_id
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	299 survival_data = survival_data.reset_index()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	300 if survival_data.columns[0] != 'sample_id':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	301 survival_data = survival_data.rename(columns={survival_data.columns[0]: 'sample_id'})
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	302
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	303 # Convert survival event column to binary (0/1) based on event_value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	304 # Check if the event column exists
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	305 if args.surv_event_var not in survival_data.columns:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	306 raise ValueError(f"Column '{args.surv_event_var}' not found in survival data")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	307
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	308 # Convert to string for comparison to handle mixed types
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	309 survival_data[args.surv_event_var] = survival_data[args.surv_event_var].astype(str)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	310 event_value_str = str(args.event_value)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	311
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	312 # Create binary event column (1 if matches event_value, 0 otherwise)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	313 survival_data[f'{args.surv_event_var}_binary'] = (
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	314 survival_data[args.surv_event_var] == event_value_str
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	315 ).astype(int)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	316
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	317 # Filter for survival category and class_label == '1:DECEASED'
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	318 label_data['class_label'] = label_data['class_label'].astype(str)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	319
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	320 label_data = label_data[(label_data['variable'] == args.surv_event_var) & (label_data['class_label'] == event_value_str)]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	321
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	322 # check survival data
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	323 for col in [args.surv_time_var, args.surv_event_var]:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	324 if col not in survival_data.columns:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	325 raise ValueError(f"Column '{col}' not found in survival data")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	326
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	327 # Merge survival data with labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	328 df_deceased = pd.merge(survival_data, label_data, on='sample_id', how='inner')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	329
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	330 if df_deceased.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	331 raise ValueError("No matching samples found after merging survival and label data.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	332
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	333 # Get risk scores
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	334 risk_scores = df_deceased['probability'].values
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	335
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	336 # Compute groups (e.g., median split)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	337 quantiles = np.quantile(risk_scores, [0.5])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	338 groups = np.digitize(risk_scores, quantiles)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	339 group_labels = ['low_risk' if g == 0 else 'high_risk' for g in groups]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	340
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	341 fig_known = plot_kaplan_meier_curves(
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	342 durations=df_deceased[args.surv_time_var],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	343 events=df_deceased[f'{args.surv_event_var}_binary'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	344 categorical_variable=group_labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	345 )
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	346
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	347 output_path_known = output_dir / f"{output_name_base}_km_risk_subtypes.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	348 print(f"Saving Kaplan-Meier plot to: {output_path_known.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	349 fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	350
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	351 print("Kaplan-Meier plot saved successfully!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	352
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	353
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	354 def generate_cox_plots(model, clinical_train, clinical_test, omics_train, omics_test, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	355 """Generate Cox proportional hazards plots"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	356 print("Generating Cox proportional hazards analysis...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	357
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	358 # Parse clinical variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	359 clinical_vars = [var.strip() for var in args.clinical_variables.split(',')]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	360
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	361 # Validate that survival variables are included
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	362 required_vars = [args.surv_time_var, args.surv_event_var]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	363 for var in required_vars:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	364 if var not in clinical_vars:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	365 clinical_vars.append(var)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	366
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	367 print(f"Using clinical variables: {', '.join(clinical_vars)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	368
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	369 # filter datasets for clinical variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	370 if all(var in clinical_train.columns and var in clinical_test.columns for var in clinical_vars):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	371 df_clin_train = clinical_train[clinical_vars]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	372 df_clin_test = clinical_test[clinical_vars]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	373 # Drop rows with NaN in clinical variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	374 df_clin_train = df_clin_train.dropna(subset=clinical_vars)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	375 df_clin_test = df_clin_test.dropna(subset=clinical_vars)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	376 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	377 raise ValueError(f"Not all clinical variables found in datasets. Available in train dataset: {clinical_train.columns.tolist()}, Available in test dataset: {clinical_test.columns.tolist()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	378
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	379 # Combine
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	380 df_clin = pd.concat([df_clin_train, df_clin_test], axis=0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	381
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	382 # Get top survival markers
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	383 print(f"Extracting top {args.top_features} important features for {args.surv_event_var}...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	384 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	385 imp = get_important_features(model,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	386 var=args.surv_event_var,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	387 top=args.top_features
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	388 )['name'].unique().tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	389 print(f"Top features: {', '.join(imp)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	390 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	391 raise ValueError(f"Error getting important features: {e}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	392
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	393 # Extract feature data from omics datasets
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	394 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	395 omics_test = omics_test.loc[omics_test.index.isin(imp)]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	396 omics_train = omics_train.loc[omics_train.index.isin(imp)]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	397 # Drop rows with NaN in omics datasets
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	398 omics_test = omics_test.dropna(subset=omics_test.columns)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	399 omics_train = omics_train.dropna(subset=omics_train.columns)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	400
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	401 df_imp = pd.concat([omics_train, omics_test], axis=1)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	402 df_imp = df_imp.T # Transpose to have samples as rows
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	403
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	404 print(f"Feature data shape: {df_imp.shape}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	405 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	406 raise ValueError(f"Error extracting feature subset: {e}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	407
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	408 # Combine markers with clinical variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	409 df = pd.merge(df_imp, df_clin, left_index=True, right_index=True)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	410 print(f"Combined data shape: {df.shape}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	411
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	412 # Remove samples without survival endpoints
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	413 initial_samples = len(df)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	414 df = df[df[args.surv_event_var].notna()]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	415 final_samples = len(df)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	416 print(f"Removed {initial_samples - final_samples} samples without survival data")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	417
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	418 if df.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	419 raise ValueError("No samples remain after filtering for survival data")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	420
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	421 # Convert survival event column to binary (0/1) based on event_value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	422 # Convert to string for comparison to handle mixed types
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	423 df[args.surv_event_var] = df[args.surv_event_var].astype(str)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	424 event_value_str = str(args.event_value)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	425
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	426 df[f'{args.surv_event_var}'] = (
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	427 df[args.surv_event_var] == event_value_str
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	428 ).astype(int)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	429
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	430 # Build Cox model
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	431 print(f"Building Cox model with time variable: {args.surv_time_var}, event variable: {args.surv_event_var}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	432 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	433 coxm = build_cox_model(df,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	434 duration_col=args.surv_time_var,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	435 event_col=args.surv_event_var,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	436 crossval=args.crossval,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	437 n_splits=args.n_splits,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	438 random_state=args.random_state)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	439 print("Cox model built successfully")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	440 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	441 raise ValueError(f"Error building Cox model: {e}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	442
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	443 # Generate hazard ratios plot
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	444 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	445 print("Generating hazard ratios plot...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	446 fig = plot_hazard_ratios(coxm)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	447
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	448 output_path = output_dir / f"{output_name_base}_hazard_ratios.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	449 print(f"Saving hazard ratios plot to: {output_path.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	450 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	451
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	452 print("Cox proportional hazards analysis completed successfully!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	453
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	454 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	455 raise ValueError(f"Error generating hazard ratios plot: {e}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	456
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	457
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	458 def generate_plot_scatter(labels, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	459 """Generate scatter plot of known vs predicted labels"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	460 print("Generating scatter plots of known vs predicted labels...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	461
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	462 # Parse target values from comma-separated string
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	463 if args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	464 target_values = [val.strip() for val in args.target_value.split(',')]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	465 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	466 # If no target values specified, use all unique variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	467 target_values = labels['variable'].unique().tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	468
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	469 print(f"Processing target values: {target_values}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	470
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	471 successful_plots = 0
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	472 skipped_plots = 0
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	473
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	474 for target_value in target_values:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	475 print(f"\nProcessing target value: '{target_value}'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	476
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	477 # Filter labels for the current target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	478 target_labels = labels[labels['variable'] == target_value]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	479
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	480 if target_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	481 print(f" Warning: No data found for target value '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	482 skipped_plots += 1
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	483 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	484
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	485 # Check if labels are numeric and convert
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	486 true_values = pd.to_numeric(target_labels['known_label'], errors='coerce')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	487 predicted_values = pd.to_numeric(target_labels['predicted_label'], errors='coerce')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	488
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	489 if true_values.isna().all() or predicted_values.isna().all():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	490 print(f"No valid numeric values found for known or predicted labels in '{target_value}'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	491 skipped_plots += 1
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	492 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	493
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	494 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	495 print(f" Generating scatter plot for '{target_value}'...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	496 fig = plot_scatter(true_values, predicted_values)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	497
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	498 # Create output filename with target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	499 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	500 if len(target_values) > 1:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	501 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	502 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	503 output_filename = f"{output_name_base}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	504
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	505 output_path = output_dir / output_filename
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	506 print(f" Saving scatter plot to: {output_path.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	507 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	508
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	509 successful_plots += 1
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	510 print(f" Scatter plot for '{target_value}' generated successfully!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	511
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	512 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	513 print(f" Error generating plot for '{target_value}': {str(e)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	514 skipped_plots += 1
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	515
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	516 # Summary
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	517 print(" Summary:")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	518 print(f" Successfully generated: {successful_plots} plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	519 print(f" Skipped: {skipped_plots} plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	520
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	521 if successful_plots == 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	522 raise ValueError("No scatter plots could be generated. Check your data and target values.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	523
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	524 print("Scatter plot generation completed!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	525
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	526
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	527 def generate_label_concordance_heatmap(labels, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	528 """Generate label concordance heatmap"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	529 print("Generating label concordance heatmaps...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	530
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	531 # Parse target values from comma-separated string
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	532 if args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	533 target_values = [val.strip() for val in args.target_value.split(',')]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	534 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	535 # If no target values specified, use all unique variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	536 target_values = labels['variable'].unique().tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	537
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	538 print(f"Processing target values: {target_values}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	539
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	540 for target_value in target_values:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	541 print(f"\nProcessing target value: '{target_value}'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	542
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	543 # Filter labels for the current target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	544 target_labels = labels[labels['variable'] == target_value]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	545
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	546 if target_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	547 print(f" Warning: No data found for target value '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	548 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	549
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	550 true_values = target_labels['known_label'].tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	551 predicted_values = target_labels['predicted_label'].tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	552
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	553 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	554 print(f" Generating heatmap for '{target_value}'...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	555 fig = plot_label_concordance_heatmap(true_values, predicted_values)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	556 plt.close(fig)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	557
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	558 # Create output filename with target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	559 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	560 if len(target_values) > 1:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	561 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	562 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	563 output_filename = f"{output_name_base}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	564
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	565 output_path = output_dir / output_filename
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	566 print(f" Saving heatmap to: {output_path.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	567 fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	568
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	569 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	570 print(f" Error generating heatmap for '{target_value}': {str(e)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	571 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	572
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	573 print("Label concordance heatmap generated successfully!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	574
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	575
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	576 def generate_pr_curves(labels, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	577 """Generate precision-recall curves"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	578 print("Generating precision-recall curves...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	579
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	580 # Parse target values from comma-separated string
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	581 if args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	582 target_values = [val.strip() for val in args.target_value.split(',')]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	583 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	584 # If no target values specified, use all unique variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	585 target_values = labels['variable'].unique().tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	586
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	587 print(f"Processing target values: {target_values}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	588
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	589 for target_value in target_values:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	590 print(f"\nProcessing target value: '{target_value}'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	591
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	592 # Filter labels for the current target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	593 target_labels = labels[labels['variable'] == target_value]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	594
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	595 # Check if this is a regression problem (no class probabilities)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	596 prob_columns = target_labels['class_label'].unique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	597 non_na_probs = target_labels['probability'].notna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	598
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	599 print(f" Class labels found: {list(prob_columns)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	600 print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	601
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	602 # If most probabilities are NaN, this is likely a regression problem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	603 if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	604 print(" Detected regression problem - precision-recall curves not applicable")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	605 print(f" Skipping '{target_value}' (use regression evaluation metrics instead)")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	606 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	607
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	608 # Debug: Check data quality
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	609 total_rows = len(target_labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	610 missing_labels = target_labels['known_label'].isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	611 missing_probs = target_labels['probability'].isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	612 unique_samples = target_labels['sample_id'].nunique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	613 unique_classes = target_labels['class_label'].nunique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	614
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	615 print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	616 print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	617
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	618 if missing_labels > 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	619 print(f" Warning: Found {missing_labels} missing known_label values")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	620 missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	621 print(f" Sample IDs with missing known_label: {list(missing_samples)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	622
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	623 # Remove rows with missing known_label
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	624 target_labels = target_labels.dropna(subset=['known_label'])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	625 if target_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	626 print(f" Error: No valid known_label data remaining for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	627 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	628
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	629 # 1. Pivot to wide format
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	630 prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	631
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	632 print(f" After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	633 print(f" Class columns: {list(prob_df.columns)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	634
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	635 # Check for NaN values in probability data
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	636 nan_counts = prob_df.isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	637 if nan_counts.any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	638 print(f" NaN counts per class: {dict(nan_counts)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	639 print(f" Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	640
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	641 # Drop only rows where ALL probabilities are NaN
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	642 all_nan_rows = prob_df.isna().all(axis=1)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	643 if all_nan_rows.any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	644 print(f" Dropping {all_nan_rows.sum()} samples with all NaN probabilities")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	645 prob_df = prob_df[~all_nan_rows]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	646
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	647 remaining_nans = prob_df.isna().sum().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	648 if remaining_nans > 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	649 print(f" Warning: {remaining_nans} individual NaN values remain - filling with 0")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	650 prob_df = prob_df.fillna(0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	651
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	652 if prob_df.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	653 print(f" Error: No valid probability data remaining for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	654 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	655
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	656 # 2. Get true labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	657 true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	658
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	659 # 3. Align indices - only keep samples that exist in both datasets
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	660 common_indices = prob_df.index.intersection(true_labels_df.index)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	661 if len(common_indices) == 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	662 print(f" Error: No common sample_ids between probability and true label data for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	663 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	664
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	665 print(f" Found {len(common_indices)} samples with both probability and true label data")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	666
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	667 # Filter both datasets to common indices
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	668 prob_df_aligned = prob_df.loc[common_indices]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	669 y_true = true_labels_df.loc[common_indices]['known_label']
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	670
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	671 # 4. Final check for NaN values
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	672 if y_true.isna().any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	673 print(f" Error: True labels still contain NaN after alignment for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	674 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	675
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	676 if prob_df_aligned.isna().any().any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	677 print(f" Error: Probability data still contains NaN after alignment for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	678 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	679
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	680 # 5. Convert categorical labels to integer labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	681 # Create a mapping from class names to integers
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	682 class_names = list(prob_df_aligned.columns)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	683 class_to_int = {class_name: i for i, class_name in enumerate(class_names)}
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	684
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	685 print(f" Class mapping: {class_to_int}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	686
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	687 # Convert true labels to integers
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	688 y_true_np = y_true.map(class_to_int).to_numpy()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	689 y_probs_np = prob_df_aligned.to_numpy()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	690
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	691 print(f" Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	692 print(f" Unique true labels (integers): {set(y_true_np)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	693 print(f" Class labels (columns): {class_names}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	694 print(f" Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	695
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	696 # Check for any unmapped labels (will be NaN)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	697 if pd.isna(y_true_np).any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	698 print(" Error: Some true labels could not be mapped to class columns")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	699 unmapped_labels = set(y_true[y_true.map(class_to_int).isna()])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	700 print(f" Unmapped labels: {unmapped_labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	701 print(f" Available classes: {class_names}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	702 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	703
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	704 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	705 print(f" Generating precision-recall curve for '{target_value}'...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	706 fig = plot_pr_curves(y_true_np, y_probs_np)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	707
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	708 # Create output filename with target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	709 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	710 if len(target_values) > 1:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	711 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	712 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	713 output_filename = f"{output_name_base}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	714
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	715 output_path = output_dir / output_filename
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	716 print(f" Saving precision-recall curve to: {output_path.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	717 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	718
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	719 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	720 print(f" Error generating precision-recall curve for '{target_value}': {str(e)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	721 print(f" Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	722 print(f" Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	723 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	724
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	725 print("Precision-recall curves generated successfully!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	726
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	727
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	728 def generate_roc_curves(labels, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	729 """Generate ROC curves"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	730 print("Generating ROC curves...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	731
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	732 # Parse target values from comma-separated string
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	733 if args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	734 target_values = [val.strip() for val in args.target_value.split(',')]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	735 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	736 # If no target values specified, use all unique variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	737 target_values = labels['variable'].unique().tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	738
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	739 print(f"Processing target values: {target_values}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	740
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	741 for target_value in target_values:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	742 print(f"\nProcessing target value: '{target_value}'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	743
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	744 # Filter labels for the current target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	745 target_labels = labels[labels['variable'] == target_value]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	746
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	747 # Check if this is a regression problem (no class probabilities)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	748 prob_columns = target_labels['class_label'].unique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	749 non_na_probs = target_labels['probability'].notna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	750
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	751 print(f" Class labels found: {list(prob_columns)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	752 print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	753
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	754 # If most probabilities are NaN, this is likely a regression problem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	755 if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	756 print(" Detected regression problem - ROC curves not applicable")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	757 print(f" Skipping '{target_value}' (use regression evaluation metrics instead)")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	758 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	759
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	760 # Debug: Check data quality
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	761 total_rows = len(target_labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	762 missing_labels = target_labels['known_label'].isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	763 missing_probs = target_labels['probability'].isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	764 unique_samples = target_labels['sample_id'].nunique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	765 unique_classes = target_labels['class_label'].nunique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	766
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	767 print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	768 print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	769
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	770 if missing_labels > 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	771 print(f" Warning: Found {missing_labels} missing known_label values")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	772 missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	773 print(f" Sample IDs with missing known_label: {list(missing_samples)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	774
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	775 # Remove rows with missing known_label
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	776 target_labels = target_labels.dropna(subset=['known_label'])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	777 if target_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	778 print(f" Error: No valid known_label data remaining for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	779 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	780
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	781 # 1. Pivot to wide format
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	782 prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	783
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	784 print(f" After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	785 print(f" Class columns: {list(prob_df.columns)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	786
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	787 # Check for NaN values in probability data
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	788 nan_counts = prob_df.isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	789 if nan_counts.any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	790 print(f" NaN counts per class: {dict(nan_counts)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	791 print(f" Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	792
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	793 # Drop only rows where ALL probabilities are NaN
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	794 all_nan_rows = prob_df.isna().all(axis=1)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	795 if all_nan_rows.any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	796 print(f" Dropping {all_nan_rows.sum()} samples with all NaN probabilities")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	797 prob_df = prob_df[~all_nan_rows]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	798
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	799 remaining_nans = prob_df.isna().sum().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	800 if remaining_nans > 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	801 print(f" Warning: {remaining_nans} individual NaN values remain - filling with 0")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	802 prob_df = prob_df.fillna(0)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	803
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	804 if prob_df.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	805 print(f" Error: No valid probability data remaining for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	806 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	807
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	808 # 2. Get true labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	809 true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	810
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	811 # 3. Align indices - only keep samples that exist in both datasets
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	812 common_indices = prob_df.index.intersection(true_labels_df.index)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	813 if len(common_indices) == 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	814 print(f" Error: No common sample_ids between probability and true label data for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	815 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	816
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	817 print(f" Found {len(common_indices)} samples with both probability and true label data")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	818
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	819 # Filter both datasets to common indices
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	820 prob_df_aligned = prob_df.loc[common_indices]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	821 y_true = true_labels_df.loc[common_indices]['known_label']
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	822
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	823 # 4. Final check for NaN values
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	824 if y_true.isna().any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	825 print(f" Error: True labels still contain NaN after alignment for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	826 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	827
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	828 if prob_df_aligned.isna().any().any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	829 print(f" Error: Probability data still contains NaN after alignment for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	830 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	831
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	832 # 5. Convert categorical labels to integer labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	833 # Create a mapping from class names to integers
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	834 class_names = list(prob_df_aligned.columns)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	835 class_to_int = {class_name: i for i, class_name in enumerate(class_names)}
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	836
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	837 print(f" Class mapping: {class_to_int}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	838
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	839 # Convert true labels to integers
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	840 y_true_np = y_true.map(class_to_int).to_numpy()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	841 y_probs_np = prob_df_aligned.to_numpy()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	842
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	843 print(f" Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	844 print(f" Unique true labels (integers): {set(y_true_np)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	845 print(f" Class labels (columns): {class_names}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	846 print(f" Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	847
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	848 # Check for any unmapped labels (will be NaN)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	849 if pd.isna(y_true_np).any():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	850 print(" Error: Some true labels could not be mapped to class columns")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	851 unmapped_labels = set(y_true[y_true.map(class_to_int).isna()])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	852 print(f" Unmapped labels: {unmapped_labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	853 print(f" Available classes: {class_names}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	854 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	855
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	856 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	857 print(f" Generating ROC curve for '{target_value}'...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	858 fig = plot_roc_curves(y_true_np, y_probs_np)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	859
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	860 # Create output filename with target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	861 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	862 if len(target_values) > 1:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	863 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	864 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	865 output_filename = f"{output_name_base}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	866
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	867 output_path = output_dir / output_filename
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	868 print(f" Saving ROC curve to: {output_path.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	869 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	870
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	871 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	872 print(f" Error generating ROC curve for '{target_value}': {str(e)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	873 print(f" Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	874 print(f" Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	875 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	876
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	877 print("ROC curves generated successfully!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	878
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	879
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	880 def generate_box_plots(labels, args, output_dir, output_name_base):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	881 """Generate box plots for model predictions"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	882
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	883 print("Generating box plots...")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	884
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	885 # Parse target values from comma-separated string
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	886 if args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	887 target_values = [val.strip() for val in args.target_value.split(',')]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	888 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	889 # If no target values specified, use all unique variables
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	890 target_values = labels['variable'].unique().tolist()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	891
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	892 print(f"Processing target values: {target_values}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	893
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	894 for target_value in target_values:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	895 print(f"\nProcessing target value: '{target_value}'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	896
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	897 # Filter labels for the current target value
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	898 target_labels = labels[labels['variable'] == target_value]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	899
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	900 if target_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	901 print(f" Warning: No data found for target value '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	902 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	903
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	904 # Check if this is a classification problem (has probabilities)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	905 prob_columns = target_labels['class_label'].unique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	906 non_na_probs = target_labels['probability'].notna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	907
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	908 print(f" Class labels found: {list(prob_columns)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	909 print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	910
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	911 # If most probabilities are NaN, this is likely a regression problem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	912 if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	913 print(" Detected regression problem - precision-recall curves not applicable")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	914 print(f" Skipping '{target_value}' (use regression evaluation metrics instead)")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	915 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	916
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	917 # Debug: Check data quality
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	918 total_rows = len(target_labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	919 missing_labels = target_labels['known_label'].isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	920 missing_probs = target_labels['probability'].isna().sum()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	921 unique_samples = target_labels['sample_id'].nunique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	922 unique_classes = target_labels['class_label'].nunique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	923
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	924 print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	925 print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	926
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	927 if missing_labels > 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	928 print(f" Warning: Found {missing_labels} missing known_label values")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	929 missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	930 print(f" Sample IDs with missing known_label: {list(missing_samples)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	931
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	932 # Remove rows with missing known_label
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	933 target_labels = target_labels.dropna(subset=['known_label'])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	934 if target_labels.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	935 print(f" Error: No valid known_label data remaining for '{target_value}' - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	936 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	937
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	938 # Remove rows with missing data
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	939 clean_data = target_labels.dropna(subset=['known_label', 'probability'])
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	940
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	941 if clean_data.empty:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	942 print(" No valid data after cleaning - skipping")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	943 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	944
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	945 # Get unique classes
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	946 classes = clean_data['class_label'].unique()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	947
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	948 for class_label in classes:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	949 print(f" Generating box plot for class: {class_label}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	950
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	951 # Filter for current class
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	952 class_data = clean_data[clean_data['class_label'] == class_label]
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	953
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	954 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	955 # Create the box plot
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	956 fig = plot_boxplot(
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	957 categorical_x=class_data['known_label'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	958 numerical_y=class_data['probability'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	959 title_x='True Label',
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	960 title_y=f'Predicted Probability ({class_label})',
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	961 )
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	962
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	963 # Save the plot
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	964 safe_class_name = str(class_label).replace('/', '_').replace('\\', '_').replace(' ', '_').replace(':', '_')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	965 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	966 output_filename = f"{output_name_base}_{safe_target_name}_{safe_class_name}.{args.format}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	967 output_path = output_dir / output_filename
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	968
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	969 print(f" Saving box plot to: {output_path.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	970 fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	971 plt.close(fig)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	972
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	973 except Exception as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	974 print(f" Error generating box plot for class '{class_label}': {str(e)}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	975 continue
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	976
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	977
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	978 def main():
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	979 """Main function to parse arguments and generate plots"""
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	980 parser = argparse.ArgumentParser(description="Generate plots using flexynesis")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	981
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	982 # Required arguments
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	983 parser.add_argument("--labels", type=str, required=False,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	984 help="Path to labels file generated by flexynesis")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	985
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	986 # Plot type
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	987 parser.add_argument("--plot_type", type=str, required=True,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	988 choices=['dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	989 help="Type of plot to generate: 'dimred' for dimensionality reduction, 'kaplan_meier' for survival analysis, 'cox' for Cox proportional hazards analysis, 'scatter' for scatter plots, 'concordance_heatmap' for label concordance heatmaps, 'pr_curve' for precision-recall curves, 'roc_curve' for ROC curves, or 'box_plot' for box plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	990
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	991 # Arguments for dimensionality reduction
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	992 parser.add_argument("--embeddings", type=str,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	993 help="Path to input data embeddings file (CSV or tabular format). Required for dimred plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	994 parser.add_argument("--method", type=str, default='pca', choices=['pca', 'umap'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	995 help="Transformation method ('pca' or 'umap'). Default is 'pca'. Used for dimred plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	996
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	997 # Arguments for Kaplan-Meier
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	998 parser.add_argument("--survival_data", type=str,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	999 help="Path to survival data file with columns: duration and event. Required for kaplan_meier plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1000 parser.add_argument("--surv_time_var", type=str, required=False,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1001 help="Column name for survival time")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1002 parser.add_argument("--surv_event_var", type=str, required=False,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1003 help="Column name for survival event")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1004 parser.add_argument("--event_value", type=str, required=False,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1005 help="Value in event column that represents an event (e.g., 'DECEASED')")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1006
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1007 # Arguments for Cox analysis
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1008 parser.add_argument("--model", type=str,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1009 help="Path to trained flexynesis model (pickle file). Required for cox plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1010 parser.add_argument("--clinical_train", type=str,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1011 help="Path to training dataset (pickle file). Required for cox plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1012 parser.add_argument("--clinical_test", type=str,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1013 help="Path to test dataset (pickle file). Required for cox plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1014 parser.add_argument("--omics_train", type=str, default=None,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1015 help="Path to training omics dataset. Optional for cox plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1016 parser.add_argument("--omics_test", type=str, default=None,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1017 help="Path to test omics dataset. Optional for cox plots.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1018 parser.add_argument("--clinical_variables", type=str,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1019 help="Comma-separated list of clinical variables to include in Cox model (e.g., 'AGE,SEX,HISTOLOGICAL_DIAGNOSIS,STUDY')")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1020 parser.add_argument("--top_features", type=int, default=20,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1021 help="Number of top important features to include in Cox model. Default is 5")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1022 parser.add_argument("--crossval", action='store_true',
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1023 help="If True, performs K-fold cross-validation and returns average C-index. Default is False")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1024 parser.add_argument("--n_splits", type=int, default=5,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1025 help="Number of folds for cross-validation. Default is 5")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1026 parser.add_argument("--random_state", type=int, default=42,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1027 help="Random seed for reproducibility. Default is 42")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1028
5 466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 3 diff changeset	1029 # Arguments for dimred, scatter plot, heatmap, PR curves, ROC curves, and box plots
3 525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1030 parser.add_argument("--target_value", type=str, default=None,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1031 help="Target value for scatter plot.")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1032
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1033 # Common arguments
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1034 parser.add_argument("--output_dir", type=str, default='output',
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1035 help="Output directory. Default is 'output'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1036 parser.add_argument("--output_name", type=str, default=None,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1037 help="Output filename base")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1038 parser.add_argument("--format", type=str, default='jpg', choices=['png', 'pdf', 'svg', 'jpg'],
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1039 help="Output format for the plot. Default is 'jpg'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1040 parser.add_argument("--dpi", type=int, default=300,
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1041 help="DPI for the output image. Default is 300")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1042
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1043 args = parser.parse_args()
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1044
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1045 try:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1046 # validate plot type
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1047 if not args.plot_type:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1048 raise ValueError("Please specify a plot type using --plot_type")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1049 if args.plot_type not in ['dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1050 raise ValueError(f"Invalid plot type: {args.plot_type}. Must be one of: 'dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1051
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1052 # Validate plot type requirements
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1053 if args.plot_type in ['dimred']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1054 if not args.embeddings:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1055 raise ValueError("--embeddings is required when plot_type is 'dimred'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1056 if not os.path.isfile(args.embeddings):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1057 raise FileNotFoundError(f"embeddings file not found: {args.embeddings}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1058 if not args.labels:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1059 raise ValueError("--labels is required for dimensionality reduction plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1060 if not args.method:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1061 raise ValueError("--method is required for dimensionality reduction plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1062
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1063 if args.plot_type in ['kaplan_meier']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1064 if not args.survival_data:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1065 raise ValueError("--survival_data is required when plot_type is 'kaplan_meier'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1066 if not os.path.isfile(args.survival_data):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1067 raise FileNotFoundError(f"Survival data file not found: {args.survival_data}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1068 if not args.labels:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1069 raise ValueError("--labels is required for dimensionality reduction plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1070 if not args.method:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1071 raise ValueError("--method is required for dimensionality reduction plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1072 if not args.surv_time_var:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1073 raise ValueError("--surv_time_var is required for Kaplan-Meier plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1074 if not args.surv_event_var:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1075 raise ValueError("--surv_event_var is required for Kaplan-Meier plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1076 if not args.event_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1077 raise ValueError("--event_value is required for Kaplan-Meier plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1078
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1079 if args.plot_type in ['cox']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1080 if not args.model:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1081 raise ValueError("--model is required when plot_type is 'cox'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1082 if not os.path.isfile(args.model):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1083 raise FileNotFoundError(f"Model file not found: {args.model}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1084 if not args.clinical_train:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1085 raise ValueError("--clinical_train is required when plot_type is 'cox'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1086 if not os.path.isfile(args.clinical_train):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1087 raise FileNotFoundError(f"Training dataset file not found: {args.clinical_train}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1088 if not args.clinical_test:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1089 raise ValueError("--clinical_test is required when plot_type is 'cox'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1090 if not os.path.isfile(args.clinical_test):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1091 raise FileNotFoundError(f"Test dataset file not found: {args.clinical_test}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1092 if not args.omics_train:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1093 raise ValueError("--omics_train is required when plot_type is 'cox'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1094 if not os.path.isfile(args.omics_train):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1095 raise FileNotFoundError(f"Training omics dataset file not found: {args.omics_train}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1096 if not args.omics_test:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1097 raise ValueError("--omics_test is required when plot_type is 'cox'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1098 if not os.path.isfile(args.omics_test):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1099 raise FileNotFoundError(f"Test omics dataset file not found: {args.omics_test}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1100 if not args.surv_time_var:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1101 raise ValueError("--surv_time_var is required for Cox plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1102 if not args.surv_event_var:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1103 raise ValueError("--surv_event_var is required for Cox plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1104 if not args.clinical_variables:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1105 raise ValueError("--clinical_variables is required for Cox plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1106 if not isinstance(args.top_features, int) or args.top_features <= 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1107 raise ValueError("--top_features must be a positive integer")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1108 if not args.event_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1109 raise ValueError("--event_value is required for Kaplan-Meier plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1110 if not args.crossval:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1111 args.crossval = False
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1112 if not isinstance(args.n_splits, int) or args.n_splits <= 0:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1113 raise ValueError("--n_splits must be a positive integer")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1114 if not isinstance(args.random_state, int):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1115 raise ValueError("--random_state must be an integer")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1116
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1117 if args.plot_type in ['scatter']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1118 if not args.labels:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1119 raise ValueError("--labels is required for scatter plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1120 if not args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1121 print("--target_value is not specified, using all unique variables from labels")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1122 if not os.path.isfile(args.labels):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1123 raise FileNotFoundError(f"Labels file not found: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1124
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1125 if args.plot_type in ['concordance_heatmap']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1126 if not args.labels:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1127 raise ValueError("--labels is required for concordance heatmap")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1128 if not args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1129 print("--target_value is not specified, using all unique variables from labels")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1130 if not os.path.isfile(args.labels):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1131 raise FileNotFoundError(f"Labels file not found: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1132
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1133 if args.plot_type in ['pr_curve']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1134 if not args.labels:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1135 raise ValueError("--labels is required for precision-recall curves")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1136 if not args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1137 print("--target_value is not specified, using all unique variables from labels")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1138 if not os.path.isfile(args.labels):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1139 raise FileNotFoundError(f"Labels file not found: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1140
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1141 if args.plot_type in ['roc_curve']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1142 if not args.labels:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1143 raise ValueError("--labels is required for ROC curves")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1144 if not args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1145 print("--target_value is not specified, using all unique variables from labels")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1146 if not os.path.isfile(args.labels):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1147 raise FileNotFoundError(f"Labels file not found: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1148
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1149 if args.plot_type in ['box_plot']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1150 if not args.labels:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1151 raise ValueError("--labels is required for box plots")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1152 if not args.target_value:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1153 print("--target_value is not specified, using all unique variables from labels")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1154 if not os.path.isfile(args.labels):
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1155 raise FileNotFoundError(f"Labels file not found: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1156
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1157 # Validate other arguments
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1158 if args.method not in ['pca', 'umap']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1159 raise ValueError("Method must be 'pca' or 'umap'")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1160
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1161 # Create output directory
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1162 output_dir = Path(args.output_dir)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1163 output_dir.mkdir(parents=True, exist_ok=True)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1164 print(f"Output directory: {output_dir.absolute()}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1165
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1166 # Generate output filename base
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1167 if args.output_name:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1168 output_name_base = args.output_name
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1169 else:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1170 if args.plot_type == 'dimred':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1171 embeddings_name = Path(args.embeddings).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1172 output_name_base = f"{embeddings_name}_{args.method}"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1173 elif args.plot_type == 'kaplan_meier':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1174 survival_name = Path(args.survival_data).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1175 output_name_base = f"{survival_name}_km"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1176 elif args.plot_type == 'cox':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1177 model_name = Path(args.model).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1178 output_name_base = f"{model_name}_cox"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1179 elif args.plot_type == 'scatter':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1180 labels_name = Path(args.labels).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1181 output_name_base = f"{labels_name}_scatter"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1182 elif args.plot_type == 'concordance_heatmap':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1183 labels_name = Path(args.labels).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1184 output_name_base = f"{labels_name}_concordance"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1185 elif args.plot_type == 'pr_curve':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1186 labels_name = Path(args.labels).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1187 output_name_base = f"{labels_name}_pr_curves"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1188 elif args.plot_type == 'roc_curve':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1189 labels_name = Path(args.labels).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1190 output_name_base = f"{labels_name}_roc_curves"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1191 elif args.plot_type == 'box_plot':
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1192 labels_name = Path(args.labels).stem
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1193 output_name_base = f"{labels_name}_box_plot"
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1194
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1195 # Generate plots based on type
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1196 if args.plot_type in ['dimred']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1197 # Load labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1198 print(f"Loading labels from: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1199 label_data = load_labels(args.labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1200 # Load embeddings data
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1201 print(f"Loading embeddings from: {args.embeddings}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1202 embeddings, sample_names = load_embeddings(args.embeddings)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1203 print(f"embeddings shape: {embeddings.shape}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1204
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1205 # Match samples to embeddings
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1206 matched_labels = match_samples_to_embeddings(sample_names, label_data)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1207 print(f"Successfully matched {len(matched_labels)} samples for dimensionality reduction")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1208
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1209 generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1210
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1211 elif args.plot_type in ['kaplan_meier']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1212 # Load labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1213 print(f"Loading labels from: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1214 label_data = load_labels(args.labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1215 # Load survival data
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1216 print(f"Loading survival data from: {args.survival_data}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1217 survival_data = load_survival_data(args.survival_data)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1218 print(f"Survival data shape: {survival_data.shape}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1219
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1220 generate_km_plots(survival_data, label_data, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1221
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1222 elif args.plot_type in ['cox']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1223 # Load model and datasets
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1224 print(f"Loading model from: {args.model}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1225 model = load_model(args.model)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1226 print(f"Loading training dataset from: {args.clinical_train}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1227 clinical_train = load_omics(args.clinical_train)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1228 print(f"Loading test dataset from: {args.clinical_test}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1229 clinical_test = load_omics(args.clinical_test)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1230 print(f"Loading training omics dataset from: {args.omics_train}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1231 omics_train = load_omics(args.omics_train)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1232 print(f"Loading test omics dataset from: {args.omics_test}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1233 omics_test = load_omics(args.omics_test)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1234
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1235 generate_cox_plots(model, clinical_train, clinical_test, omics_test, omics_train, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1236
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1237 elif args.plot_type in ['scatter']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1238 # Load labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1239 print(f"Loading labels from: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1240 label_data = load_labels(args.labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1241
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1242 generate_plot_scatter(label_data, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1243
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1244 elif args.plot_type in ['concordance_heatmap']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1245 # Load labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1246 print(f"Loading labels from: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1247 label_data = load_labels(args.labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1248
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1249 generate_label_concordance_heatmap(label_data, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1250
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1251 elif args.plot_type in ['pr_curve']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1252 # Load labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1253 print(f"Loading labels from: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1254 label_data = load_labels(args.labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1255
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1256 generate_pr_curves(label_data, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1257
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1258 elif args.plot_type in ['roc_curve']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1259 # Load labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1260 print(f"Loading labels from: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1261 label_data = load_labels(args.labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1262
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1263 generate_roc_curves(label_data, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1264
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1265 elif args.plot_type in ['box_plot']:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1266 # Load labels
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1267 print(f"Loading labels from: {args.labels}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1268 label_data = load_labels(args.labels)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1269
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1270 generate_box_plots(label_data, args, output_dir, output_name_base)
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1271
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1272 print("All plots generated successfully!")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1273
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1274 except (FileNotFoundError, ValueError, pd.errors.ParserError) as e:
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1275 print(f"Error: {e}")
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1276 return 1
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1277
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1278 return 0
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1279
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1280
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1281 if __name__ == "__main__":
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1282 exit(main())

Mercurial > repos > bgruening > flexynesis

annotate flexynesis_plot.py @ 5:466b593fd87e draft default tip