Mercurial > repos > bgruening > flexynesis_cbioportal_import

annotate flexynesis_plot.py @ 8:461b8e2d79d5 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit bcee55468e70cd025cc5359bef5e9991e893eca9
author bgruening
date Thu, 16 Oct 2025 20:15:31 +0000
parents 693011647a67
children
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1 #!/usr/bin/env python
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2 """Generate plots using flexynesis
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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3 This script generates dimensionality reduction plots, Kaplan-Meier survival curves,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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4 and Cox proportional hazards models from data processed by flexynesis."""
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6 import argparse
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7 import os
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8 from pathlib import Path
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9
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10 import matplotlib.pyplot as plt
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11 import numpy as np
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12 import pandas as pd
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13 import seaborn as sns
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14 from flexynesis.utils import (
2
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15 build_cox_model,
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16 plot_dim_reduced,
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17 plot_hazard_ratios,
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18 plot_kaplan_meier_curves,
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19 plot_pr_curves,
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20 plot_roc_curves,
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21 plot_scatter
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22 )
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23 from scipy.stats import kruskal, mannwhitneyu
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26 def load_embeddings(embeddings_path):
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27 """Load embeddings from a file"""
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28 try:
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29 # Determine file extension
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30 file_ext = Path(embeddings_path).suffix.lower()
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32 if file_ext == '.csv':
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33 df = pd.read_csv(embeddings_path, index_col=0)
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34 elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
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35 df = pd.read_csv(embeddings_path, sep='\t', index_col=0)
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36 else:
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37 raise ValueError(f"Unsupported file extension: {file_ext}")
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39 return df, df.index.tolist()
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41 except Exception as e:
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42 raise ValueError(f"Error loading embeddings from {embeddings_path}: {e}") from e
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45 def load_labels(labels_input):
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46 """Load predicted labels from flexynesis"""
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47 try:
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48 # Determine file extension
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49 file_ext = Path(labels_input).suffix.lower()
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51 if file_ext == '.csv':
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52 df = pd.read_csv(labels_input)
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53 elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
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54 df = pd.read_csv(labels_input, sep='\t')
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56 print(f"available columns: {df.columns.tolist()}")
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57 return df
2
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59 except Exception as e:
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60 raise ValueError(f"Error loading labels from {labels_input}: {e}") from e
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63 def load_omics(omics_path):
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64 """Load omics data from a file. First column should be features"""
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65 try:
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66 # Determine file extension
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67 file_ext = Path(omics_path).suffix.lower()
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69 if file_ext == '.csv':
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70 df = pd.read_csv(omics_path, index_col=0)
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71 elif file_ext in ['.tsv', '.txt', '.tab', '.tabular']:
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72 df = pd.read_csv(omics_path, sep='\t', index_col=0)
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73 else:
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74 raise ValueError(f"Unsupported file extension: {file_ext}")
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75 return df
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77 except Exception as e:
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78 raise ValueError(f"Error loading omics data from {omics_path}: {e}") from e
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80
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81 def match_samples_to_embeddings(sample_names, labels):
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82 """Filter label data to match sample names in the embeddings"""
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83 # Create a DataFrame from sample_names to preserve order
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84 sample_df = pd.DataFrame({'sample_names': sample_names})
2
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85
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86 # left_join
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87 first_column = labels.columns[0]
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88 df_matched = sample_df.merge(labels, left_on='sample_names', right_on=first_column, how='left')
2
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89
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90 # remove sample_names to keep the initial structure
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91 df_matched = df_matched.drop('sample_names', axis=1)
2
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92 return df_matched
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93
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94
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95 def detect_color_type(labels_series):
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96 """Auto-detect whether target variables should be treated as categorical or numerical"""
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97 # Remove NaN
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98 clean_labels = labels_series.dropna()
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99
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100 if clean_labels.empty:
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101 return 'categorical' # default output if no labels
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102
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103 # Check if all values can be converted to numbers
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104 try:
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105 numeric_labels = pd.to_numeric(clean_labels, errors='coerce')
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106
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107 # If conversion failed -> categorical
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108 if numeric_labels.isna().any():
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109 return 'categorical'
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110
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111 # Check number of unique values
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112 unique_count = len(clean_labels.unique())
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113 total_count = len(clean_labels)
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114
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115 # If few unique values relative to total -> categorical
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116 # Threshold: if unique values < 10 OR unique/total < 0.1
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117 if unique_count < 10 or (unique_count / total_count) < 0.1:
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118 return 'categorical'
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119 else:
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120 return 'numerical'
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121
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122 except Exception:
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123 return 'categorical'
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124
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125
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126 def plot_label_concordance_heatmap(labels1, labels2, figsize=(12, 10)):
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127 """
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128 Plot a heatmap reflecting the concordance between two sets of labels using pandas crosstab.
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129
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130 Parameters:
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131 - labels1: The first set of labels.
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132 - labels2: The second set of labels.
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133 """
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134 # Compute the cross-tabulation
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135 ct = pd.crosstab(pd.Series(labels1, name='Labels Set 1'), pd.Series(labels2, name='Labels Set 2'))
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136 # Normalize the cross-tabulation matrix column-wise
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137 ct_normalized = ct.div(ct.sum(axis=1), axis=0)
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138
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139 # Plot the heatmap
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140 plt.figure(figsize=figsize)
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141 sns.heatmap(ct_normalized, annot=True, cmap='viridis', linewidths=.5) # col_cluster=False)
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142 plt.title('Concordance between label groups')
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143
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144 return plt.gcf()
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145
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146
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147 def plot_boxplot(categorical_x, numerical_y, title_x='Categories', title_y='Values', figsize=(10, 6), jittersize=4):
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148 """
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149 Create a boxplot with to visualize the distribution of predicted probabilities across different categories.
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150 the x axis represents the true labels, and the y axis represents the predicted probabilities for specific categories.
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151 """
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152 df = pd.DataFrame({title_x: categorical_x, title_y: numerical_y})
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153
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154 # Compute p-value
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155 groups = df[title_x].unique()
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156 if len(groups) == 2:
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157 group1 = df[df[title_x] == groups[0]][title_y]
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158 group2 = df[df[title_x] == groups[1]][title_y]
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159 stat, p = mannwhitneyu(group1, group2, alternative='two-sided')
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160 test_name = "Mann-Whitney U"
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161 else:
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162 group_data = [df[df[title_x] == group][title_y] for group in groups]
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163 stat, p = kruskal(*group_data)
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164 test_name = "Kruskal-Wallis"
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165
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166 # Create a boxplot with jittered points
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167 plt.figure(figsize=figsize)
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168 sns.boxplot(x=title_x, y=title_y, hue=title_x, data=df, palette='Set2', legend=False, fill=False)
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169 sns.stripplot(x=title_x, y=title_y, data=df, color='black', size=jittersize, jitter=True, dodge=True, alpha=0.4)
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170
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171 # Labels and p-value annotation
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172 plt.xlabel(title_x)
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173 plt.ylabel(title_y)
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174 plt.text(
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175 x=-0.4,
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176 y=plt.ylim()[1],
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177 s=f'{test_name} p = {p:.3e}',
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178 verticalalignment='top',
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179 horizontalalignment='left',
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180 fontsize=12,
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181 bbox=dict(boxstyle='round,pad=0.3', facecolor='white', edgecolor='gray')
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182 )
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183
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184 plt.tight_layout()
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185 return plt.gcf()
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186
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187
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188 def generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base):
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189 """Generate dimensionality reduction plots"""
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190
7
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191 # Check if this is the specific format with sample_id, known_label, predicted_label
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192 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
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193 is_flexynesis_format = all(col in matched_labels.columns for col in required_cols)
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194
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195 if not args.color:
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196 if is_flexynesis_format:
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197 print("Detected flexynesis labels format")
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198 print(f"Generating {args.method.upper()} plots for known and predicted labels...")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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199 else:
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200 print("Labels are not in flexynesis format (Custom labels), please specify a color variable with --color")
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201
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202 # Parse target values from comma-separated string
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203 if args.target_value:
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204 target_values = [val.strip() for val in args.target_value.split(',')]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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205 else:
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206 # If no target values specified, use all unique variables
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207 target_values = matched_labels['variable'].unique().tolist()
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208
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209 print(f"Generating {args.method.upper()} plots for {len(target_values)} target variable(s): {', '.join(target_values)}")
2
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210
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211 # Check variables
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212 available_vars = matched_labels['variable'].unique()
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213 missing_vars = [var for var in target_values if var not in available_vars]
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214
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215 if missing_vars:
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216 print(f"Warning: The following target variables were not found in the data: {', '.join(missing_vars)}")
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217 print(f"Available variables: {', '.join(available_vars)}")
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218
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219 # Filter to only process available variables
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220 valid_vars = [var for var in target_values if var in available_vars]
2
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221
7
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222 if not valid_vars:
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223 raise ValueError(f"None of the specified target variables were found in the data. Available: {', '.join(available_vars)}")
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224
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225 # Generate plots for each valid target variable
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226 for var in valid_vars:
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227 print(f"\nPlotting variable: {var}")
2
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228
7
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229 # Filter matched labels for current variable
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230 var_labels = matched_labels[matched_labels['variable'] == var].copy()
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231 var_labels = var_labels.drop_duplicates(subset='sample_id')
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232
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233 if var_labels.empty:
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234 print(f"Warning: No data found for variable '{var}', skipping...")
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235 continue
2
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236
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237 # Auto-detect color type
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238 known_color_type = detect_color_type(var_labels['known_label'])
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239 predicted_color_type = detect_color_type(var_labels['predicted_label'])
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240
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241 print(f" Auto-detected color types - Known: {known_color_type}, Predicted: {predicted_color_type}")
2
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242
7
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243 try:
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244 # Plot 1: Known labels
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245 print(f" Creating known labels plot for {var}...")
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246 fig_known = plot_dim_reduced(
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247 matrix=embeddings,
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248 labels=var_labels['known_label'],
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249 method=args.method,
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250 color_type=known_color_type
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251 )
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252
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253 output_path_known = output_dir / f"{output_name_base}_{var}_known.{args.format}"
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254 print(f" Saving known labels plot to: {output_path_known.name}")
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255 fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')
2
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256
7
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257 # Plot 2: Predicted labels
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258 print(f" Creating predicted labels plot for {var}...")
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259 fig_predicted = plot_dim_reduced(
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260 matrix=embeddings,
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261 labels=var_labels['predicted_label'],
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262 method=args.method,
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263 color_type=predicted_color_type
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264 )
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265
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266 output_path_predicted = output_dir / f"{output_name_base}_{var}_predicted.{args.format}"
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267 print(f" Saving predicted labels plot to: {output_path_predicted.name}")
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268 fig_predicted.save(output_path_predicted, dpi=args.dpi, bbox_inches='tight')
2
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269
7
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270 print(f" ✓ Successfully created plots for variable '{var}'")
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271
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272 except Exception as e:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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273 print(f" ✗ Error creating plots for variable '{var}': {e}")
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274 continue
2
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275
7
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276 print(f"\nDimensionality reduction plots completed for {len(valid_vars)} variable(s)!")
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277
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278 else:
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279 # check if the color variable exists in matched_labels
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280 if args.color not in matched_labels.columns:
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281 raise ValueError(f"Color variable '{args.color}' not found in matched labels. Available columns: {matched_labels.columns.tolist()}")
2
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282
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283 # Auto-detect color type
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284 color_type = detect_color_type(matched_labels[args.color])
2
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285
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286 print(f" Auto-detected color type: {color_type}")
2
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287
7
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288 # Plot: Specified color column
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289 print(f" Creating plot for {args.color}...")
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290 fig = plot_dim_reduced(
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291 matrix=embeddings,
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292 labels=matched_labels[args.color],
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293 method=args.method,
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294 color_type=color_type
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295 )
2
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296
7
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297 output_path = output_dir / f"{output_name_base}_{args.color}.{args.format}"
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298 print(f" Saving plot to: {output_path.name}")
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299 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
2
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300
7
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301 print(f" ✓ Successfully created plot for variable '{args.color}'")
2
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302
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303
7
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304 def generate_km_plots(survival_data, labels, args, output_dir, output_name_base):
2
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305 """Generate Kaplan-Meier plots"""
7
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306
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307 # Check if this is the specific format with sample_id, known_label, predicted_label
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308 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
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309 is_flexynesis_format = all(col in labels.columns for col in required_cols)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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310
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311 if not is_flexynesis_format:
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312 raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")
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313
2
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314 print("Generating Kaplan-Meier curves of risk subtypes...")
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315
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316 if survival_data.columns[0] != 'sample_id':
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317 survival_data = survival_data.rename(columns={survival_data.columns[0]: 'sample_id'})
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318
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319 # Check if the event column exists
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320 if args.surv_event_var not in survival_data.columns:
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321 raise ValueError(f"Column '{args.surv_event_var}' not found in survival data")
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322
7
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323 labels = labels[(labels['variable'] == args.surv_event_var)]
2
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324
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325 # Merge survival data with labels
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326 df_deceased = pd.merge(survival_data, labels, on='sample_id', how='inner')
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327 df_deceased = df_deceased.dropna(subset=[args.surv_time_var, args.surv_event_var])
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328
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329 if df_deceased.empty:
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330 raise ValueError("No matching samples found after merging survival and label data.")
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331
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332 # Get risk scores
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333 risk_scores = df_deceased['predicted_label'].values
2
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334
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335 # Compute groups (e.g., median split)
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336 quantiles = np.quantile(risk_scores, [0.5])
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337 groups = np.digitize(risk_scores, quantiles)
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338 group_labels = ['low_risk' if g == 0 else 'high_risk' for g in groups]
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339
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340 fig_known = plot_kaplan_meier_curves(
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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341 durations=df_deceased[args.surv_time_var],
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342 events=df_deceased[args.surv_event_var],
2
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343 categorical_variable=group_labels
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344 )
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345
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346 output_path_known = output_dir / f"{output_name_base}_km_risk_subtypes.{args.format}"
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347 print(f"Saving Kaplan-Meier plot to: {output_path_known.absolute()}")
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348 fig_known.save(output_path_known, dpi=args.dpi, bbox_inches='tight')
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349
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350 print("Kaplan-Meier plot saved successfully!")
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351
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352
7
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diff changeset
353 def generate_cox_plots(important_features, clinical_train, clinical_test, omics_train, omics_test, args, output_dir, output_name_base):
2
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354 """Generate Cox proportional hazards plots"""
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355 print("Generating Cox proportional hazards analysis...")
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diff changeset
356
7
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diff changeset
357 # Check if this is the specific format with target_variable, importance
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diff changeset
358 required_cols = ['target_variable', 'layer', 'importance']
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diff changeset
359 is_flexynesis_format = all(col in important_features.columns for col in required_cols)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 6
diff changeset
360
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diff changeset
361 if not is_flexynesis_format:
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diff changeset
362 raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid important_features file with the required columns, {required_cols}.")
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diff changeset
363
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
364 # Parse clinical variables
7
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diff changeset
365 clinical_vars = []
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
366 if args.clinical_variables:
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367 clinical_vars = [var.strip() for var in args.clinical_variables.split(',')]
2
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diff changeset
368
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369 # Validate that survival variables are included
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bgruening
parents:
diff changeset
370 required_vars = [args.surv_time_var, args.surv_event_var]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
371 for var in required_vars:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
372 if var not in clinical_vars:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
373 clinical_vars.append(var)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
374
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
375 print(f"Using clinical variables: {', '.join(clinical_vars)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
376
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
377 # filter datasets for clinical variables
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
378 if all(var in clinical_train.columns and var in clinical_test.columns for var in clinical_vars):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
379 df_clin_train = clinical_train[clinical_vars]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
380 df_clin_test = clinical_test[clinical_vars]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
381 # Drop rows with NaN in clinical variables
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
382 df_clin_train = df_clin_train.dropna(subset=clinical_vars)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
383 df_clin_test = df_clin_test.dropna(subset=clinical_vars)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
384 else:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
385 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()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
386
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
387 # Combine
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
388 df_clin = pd.concat([df_clin_train, df_clin_test], axis=0)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
389
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
390 # Get top survival markers
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
391 print(f"Extracting top {args.top_features} important features for {args.surv_event_var}...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
392 try:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
393 print(f"Loading {args.top_features} important features from: {args.important_features}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
394 imp_features = load_labels(args.important_features)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
395 imp_features = imp_features[imp_features['target_variable'] == args.surv_event_var]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
396 if args.layer not in imp_features['layer'].unique():
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
397 print(f"Available class labels: {imp_features['layer'].unique()}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
398 raise ValueError(f"Class label '{args.layer}' not found in important features data: {args.important_features}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
399 imp_features = imp_features[imp_features['layer'] == args.layer]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
400 if imp_features.empty:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
401 raise ValueError(f"No important features found for target variable '{args.surv_event_var}' in {args.important_features}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
402 imp_features = imp_features.sort_values(by='importance', ascending=False)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
403
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
404 if len(imp_features) < args.top_features:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
405 raise ValueError(f"Requested top {args.top_features} features, but only {len(imp_features)} available in {args.important_features}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
406
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
407 imp = imp_features['name'].unique().tolist()[0:args.top_features]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
408
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
409 print(f"Top features: {', '.join(imp)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
410 except Exception as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
411 raise ValueError(f"Error getting important features: {e}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
412
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
413 # Extract feature data from omics datasets
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
414 try:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
415 omics_test = omics_test.loc[omics_test.index.isin(imp)]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
416 omics_train = omics_train.loc[omics_train.index.isin(imp)]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
417 # Drop rows with NaN in omics datasets
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
418 omics_test = omics_test.dropna(subset=omics_test.columns)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
419 omics_train = omics_train.dropna(subset=omics_train.columns)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
420
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
421 df_imp = pd.concat([omics_train, omics_test], axis=1)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
422 df_imp = df_imp.T # Transpose to have samples as rows
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
423
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
424 print(f"Feature data shape: {df_imp.shape}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
425 except Exception as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
426 raise ValueError(f"Error extracting feature subset: {e}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
427
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
428 # Combine markers with clinical variables
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
429 df = pd.merge(df_imp, df_clin, left_index=True, right_index=True)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
430 print(f"Combined data shape: {df.shape}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
431
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
432 # Remove samples without survival endpoints
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
433 initial_samples = len(df)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
434 df = df[df[args.surv_event_var].notna()]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
435 final_samples = len(df)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
436 print(f"Removed {initial_samples - final_samples} samples without survival data")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
437
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
438 if df.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
439 raise ValueError("No samples remain after filtering for survival data")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
440
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
441 # Build Cox model
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
442 print(f"Building Cox model with time variable: {args.surv_time_var}, event variable: {args.surv_event_var}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
443 try:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
444 coxm = build_cox_model(df,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
445 duration_col=args.surv_time_var,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
446 event_col=args.surv_event_var,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
447 crossval=args.crossval,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
448 n_splits=args.n_splits,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
449 random_state=args.random_state)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
450 print("Cox model built successfully")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
451 except Exception as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
452 raise ValueError(f"Error building Cox model: {e}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
453
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
454 # Generate hazard ratios plot
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
455 try:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
456 print("Generating hazard ratios plot...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
457 fig = plot_hazard_ratios(coxm)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
458
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
459 output_path = output_dir / f"{output_name_base}_hazard_ratios.{args.format}"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
460 print(f"Saving hazard ratios plot to: {output_path.absolute()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
461 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
462
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
463 print("Cox proportional hazards analysis completed successfully!")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
464
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
465 except Exception as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
466 raise ValueError(f"Error generating hazard ratios plot: {e}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
467
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
468
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
469 def generate_plot_scatter(labels, args, output_dir, output_name_base):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
470 """Generate scatter plot of known vs predicted labels"""
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
471 print("Generating scatter plots of known vs predicted labels...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
472
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
473 # Check if this is the specific format with sample_id, known_label, predicted_label
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
474 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
475 is_flexynesis_format = all(col in labels.columns for col in required_cols)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
476
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
477 if is_flexynesis_format:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
478 # Parse target values from comma-separated string
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
479 if args.target_value:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
480 target_values = [val.strip() for val in args.target_value.split(',')]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
481 else:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
482 # If no target values specified, use all unique variables
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
483 target_values = labels['variable'].unique().tolist()
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
484
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
485 print(f"Processing target values: {target_values}")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
486
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
487 successful_plots = 0
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
488 skipped_plots = 0
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
489
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
490 for target_value in target_values:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
491 print(f"\nProcessing target value: '{target_value}'")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
492
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
493 # Filter labels for the current target value
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
494 target_labels = labels[labels['variable'] == target_value]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
495
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
496 if target_labels.empty:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
497 print(f" Warning: No data found for target value '{target_value}' - skipping")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
498 skipped_plots += 1
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
499 continue
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
500
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
501 # Check if labels are numeric and convert
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
502 true_values = pd.to_numeric(target_labels['known_label'], errors='coerce')
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
503 predicted_values = pd.to_numeric(target_labels['predicted_label'], errors='coerce')
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
504
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
505 if true_values.isna().all() or predicted_values.isna().all():
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
506 print(f"No valid numeric values found for known or predicted labels in '{target_value}'")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
507 skipped_plots += 1
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
508 continue
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
509
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
510 try:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
511 print(f" Generating scatter plot for '{target_value}'...")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
512 fig = plot_scatter(true_values, predicted_values)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
513
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
514 # Create output filename with target value
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
515 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
516 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
517
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
518 output_path = output_dir / output_filename
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
519 print(f" Saving scatter plot to: {output_path.absolute()}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
520 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
521
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
522 successful_plots += 1
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
523 print(f" Scatter plot for '{target_value}' generated successfully!")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
524
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
525 except Exception as e:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
526 print(f" Error generating plot for '{target_value}': {str(e)}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
527 skipped_plots += 1
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
528
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
529 # Summary
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
530 print(" Summary:")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
531 print(f" Successfully generated: {successful_plots} plots")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
532 print(f" Skipped: {skipped_plots} plots")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
533
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
534 if successful_plots == 0:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
535 raise ValueError("No scatter plots could be generated. Check your data and target values.")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
536
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
537 print("Scatter plot generation completed!")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
538
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
539 if not is_flexynesis_format:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
540 print("Labels are not in flexynesis format (Custom labels)")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
541
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
542 if not args.true_label or not args.predicted_label:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
543 raise ValueError("For custom labels, please specify --true_label and --predicted_label arguments.")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
544
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
545 # Check if labels are numeric and convert
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
546 true_values = pd.to_numeric(labels[args.true_label], errors='coerce')
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
547 predicted_values = pd.to_numeric(labels[args.predicted_label], errors='coerce')
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
548
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
549 if true_values.isna().all() or predicted_values.isna().all():
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
550 print("No valid numeric values found for known or predicted labels")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
551
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
552 try:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
553 print(" Generating scatter plot...")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
554 fig = plot_scatter(true_values, predicted_values)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
555
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
556 # Create output filename with target value
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
557 output_filename = f"{output_name_base}.{args.format}"
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
558
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
559 output_path = output_dir / output_filename
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
560 print(f" Saving scatter plot to: {output_path.absolute()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
561 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
562
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
563 except Exception as e:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
564 print(f" Error generating plot: {str(e)}")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
565
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
566 print("Scatter plot generation completed!")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
567
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
568
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
569 def generate_label_concordance_heatmap(labels, args, output_dir, output_name_base):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
570 """Generate label concordance heatmap"""
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
571 print("Generating label concordance heatmaps...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
572
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
573 # Check if this is the specific format with sample_id, known_label, predicted_label
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
574 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
575 is_flexynesis_format = all(col in labels.columns for col in required_cols)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
576
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
577 if is_flexynesis_format:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
578 # Parse target values from comma-separated string
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
579 if args.target_value:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
580 target_values = [val.strip() for val in args.target_value.split(',')]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
581 else:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
582 # If no target values specified, use all unique variables
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
583 target_values = labels['variable'].unique().tolist()
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
584
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
585 print(f"Processing target values: {target_values}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
586
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
587 for target_value in target_values:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
588 print(f"\nProcessing target value: '{target_value}'")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
589
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
590 # Filter labels for the current target value
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
591 target_labels = labels[labels['variable'] == target_value]
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
592
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
593 if target_labels.empty:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
594 print(f" Warning: No data found for target value '{target_value}' - skipping")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
595 continue
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
596
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
597 true_values = target_labels['known_label'].tolist()
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
598 predicted_values = target_labels['predicted_label'].tolist()
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
599
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
600 try:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
601 print(f" Generating heatmap for '{target_value}'...")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
602 fig = plot_label_concordance_heatmap(true_values, predicted_values)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
603 plt.close(fig)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
604
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
605 # Create output filename with target value
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
606 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
607 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
608
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
609 output_path = output_dir / output_filename
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
610 print(f" Saving heatmap to: {output_path.absolute()}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
611 fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
612
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
613 except Exception as e:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
614 print(f" Error generating heatmap for '{target_value}': {str(e)}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
615 continue
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
616
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
617 print("Label concordance heatmap generated successfully!")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
618
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
619 if not is_flexynesis_format:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
620 print("Labels are not in flexynesis format (Custom labels)")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
621
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
622 if not args.true_label or not args.predicted_label:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
623 raise ValueError("For custom labels, please specify --true_label and --predicted_label arguments.")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
624
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
625 true_values = labels[args.true_label].tolist()
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
626 predicted_values = labels[args.predicted_label].tolist()
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
627
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
628 try:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
629 print(" Generating heatmap for...")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
630 fig = plot_label_concordance_heatmap(true_values, predicted_values)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
631 plt.close(fig)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
632
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
633 # Create output filename with target value
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
634 output_filename = f"{output_name_base}.{args.format}"
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
635
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
636 output_path = output_dir / output_filename
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
637 print(f" Saving heatmap to: {output_path.absolute()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
638 fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
639
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
640 except Exception as e:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
641 print(f" Error generating heatmap': {str(e)}")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
642
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
643 print("Label concordance heatmap generated successfully!")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
644
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
645
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
646 def generate_pr_curves(labels, args, output_dir, output_name_base):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
647 """Generate precision-recall curves"""
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
648 print("Generating precision-recall curves...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
649
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
650 # Check if this is the specific format with sample_id, known_label, predicted_label
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
651 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
652 is_flexynesis_format = all(col in labels.columns for col in required_cols)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
653
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
654 if not is_flexynesis_format:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
655 raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
656
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
657 # Parse target values from comma-separated string
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
658 if args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
659 target_values = [val.strip() for val in args.target_value.split(',')]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
660 else:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
661 # If no target values specified, use all unique variables
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
662 target_values = labels['variable'].unique().tolist()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
663
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
664 print(f"Processing target values: {target_values}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
665
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
666 for target_value in target_values:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
667 print(f"\nProcessing target value: '{target_value}'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
668
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
669 # Filter labels for the current target value
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
670 target_labels = labels[labels['variable'] == target_value]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
671
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
672 # Check if this is a regression problem (no class probabilities)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
673 prob_columns = target_labels['class_label'].unique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
674 non_na_probs = target_labels['probability'].notna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
675
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
676 print(f" Class labels found: {list(prob_columns)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
677 print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
678
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
679 # If most probabilities are NaN, this is likely a regression problem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
680 if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
681 print(" Detected regression problem - precision-recall curves not applicable")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
682 print(f" Skipping '{target_value}' (use regression evaluation metrics instead)")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
683 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
684
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
685 # Debug: Check data quality
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
686 total_rows = len(target_labels)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
687 missing_labels = target_labels['known_label'].isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
688 missing_probs = target_labels['probability'].isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
689 unique_samples = target_labels['sample_id'].nunique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
690 unique_classes = target_labels['class_label'].nunique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
691
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
692 print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
693 print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
694
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
695 if missing_labels > 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
696 print(f" Warning: Found {missing_labels} missing known_label values")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
697 missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
698 print(f" Sample IDs with missing known_label: {list(missing_samples)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
699
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
700 # Remove rows with missing known_label
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
701 target_labels = target_labels.dropna(subset=['known_label'])
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
702 if target_labels.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
703 print(f" Error: No valid known_label data remaining for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
704 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
705
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
706 # 1. Pivot to wide format
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
707 prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
708
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
709 print(f" After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
710 print(f" Class columns: {list(prob_df.columns)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
711
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
712 # Check for NaN values in probability data
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
713 nan_counts = prob_df.isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
714 if nan_counts.any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
715 print(f" NaN counts per class: {dict(nan_counts)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
716 print(f" Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
717
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
718 # Drop only rows where ALL probabilities are NaN
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
719 all_nan_rows = prob_df.isna().all(axis=1)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
720 if all_nan_rows.any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
721 print(f" Dropping {all_nan_rows.sum()} samples with all NaN probabilities")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
722 prob_df = prob_df[~all_nan_rows]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
723
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
724 remaining_nans = prob_df.isna().sum().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
725 if remaining_nans > 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
726 print(f" Warning: {remaining_nans} individual NaN values remain - filling with 0")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
727 prob_df = prob_df.fillna(0)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
728
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
729 if prob_df.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
730 print(f" Error: No valid probability data remaining for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
731 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
732
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
733 # 2. Get true labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
734 true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
735
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
736 # 3. Align indices - only keep samples that exist in both datasets
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
737 common_indices = prob_df.index.intersection(true_labels_df.index)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
738 if len(common_indices) == 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
739 print(f" Error: No common sample_ids between probability and true label data for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
740 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
741
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
742 print(f" Found {len(common_indices)} samples with both probability and true label data")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
743
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
744 # Filter both datasets to common indices
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
745 prob_df_aligned = prob_df.loc[common_indices]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
746 y_true = true_labels_df.loc[common_indices]['known_label']
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
747
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
748 # 4. Final check for NaN values
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
749 if y_true.isna().any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
750 print(f" Error: True labels still contain NaN after alignment for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
751 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
752
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
753 if prob_df_aligned.isna().any().any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
754 print(f" Error: Probability data still contains NaN after alignment for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
755 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
756
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
757 # 5. Convert categorical labels to integer labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
758 # Create a mapping from class names to integers
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
759 class_names = list(prob_df_aligned.columns)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
760 class_to_int = {class_name: i for i, class_name in enumerate(class_names)}
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
761
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
762 print(f" Class mapping: {class_to_int}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
763
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
764 # Convert true labels to integers
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
765 y_true_np = y_true.map(class_to_int).to_numpy()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
766 y_probs_np = prob_df_aligned.to_numpy()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
767
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
768 print(f" Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
769 print(f" Unique true labels (integers): {set(y_true_np)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
770 print(f" Class labels (columns): {class_names}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
771 print(f" Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
772
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
773 # Check for any unmapped labels (will be NaN)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
774 if pd.isna(y_true_np).any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
775 print(" Error: Some true labels could not be mapped to class columns")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
776 unmapped_labels = set(y_true[y_true.map(class_to_int).isna()])
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
777 print(f" Unmapped labels: {unmapped_labels}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
778 print(f" Available classes: {class_names}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
779 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
780
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
781 try:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
782 print(f" Generating precision-recall curve for '{target_value}'...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
783 fig = plot_pr_curves(y_true_np, y_probs_np)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
784
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
785 # Create output filename with target value
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
786 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
787 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
788
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
789 output_path = output_dir / output_filename
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
790 print(f" Saving precision-recall curve to: {output_path.absolute()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
791 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
792
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
793 except Exception as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
794 print(f" Error generating precision-recall curve for '{target_value}': {str(e)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
795 print(f" Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
796 print(f" Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
797 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
798
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
799 print("Precision-recall curves generated successfully!")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
800
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
801
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
802 def generate_roc_curves(labels, args, output_dir, output_name_base):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
803 """Generate ROC curves"""
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
804 print("Generating ROC curves...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
805
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
806 # Check if this is the specific format with sample_id, known_label, predicted_label
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
807 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
808 is_flexynesis_format = all(col in labels.columns for col in required_cols)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
809
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
810 if not is_flexynesis_format:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
811 raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
812
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
813 # Parse target values from comma-separated string
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
814 if args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
815 target_values = [val.strip() for val in args.target_value.split(',')]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
816 else:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
817 # If no target values specified, use all unique variables
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
818 target_values = labels['variable'].unique().tolist()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
819
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
820 print(f"Processing target values: {target_values}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
821
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
822 for target_value in target_values:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
823 print(f"\nProcessing target value: '{target_value}'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
824
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
825 # Filter labels for the current target value
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
826 target_labels = labels[labels['variable'] == target_value]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
827
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
828 # Check if this is a regression problem (no class probabilities)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
829 prob_columns = target_labels['class_label'].unique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
830 non_na_probs = target_labels['probability'].notna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
831
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
832 print(f" Class labels found: {list(prob_columns)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
833 print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
834
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
835 # If most probabilities are NaN, this is likely a regression problem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
836 if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
837 print(" Detected regression problem - ROC curves not applicable")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
838 print(f" Skipping '{target_value}' (use regression evaluation metrics instead)")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
839 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
840
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
841 # Debug: Check data quality
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
842 total_rows = len(target_labels)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
843 missing_labels = target_labels['known_label'].isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
844 missing_probs = target_labels['probability'].isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
845 unique_samples = target_labels['sample_id'].nunique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
846 unique_classes = target_labels['class_label'].nunique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
847
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
848 print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
849 print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
850
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
851 if missing_labels > 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
852 print(f" Warning: Found {missing_labels} missing known_label values")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
853 missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
854 print(f" Sample IDs with missing known_label: {list(missing_samples)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
855
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
856 # Remove rows with missing known_label
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
857 target_labels = target_labels.dropna(subset=['known_label'])
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
858 if target_labels.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
859 print(f" Error: No valid known_label data remaining for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
860 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
861
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
862 # 1. Pivot to wide format
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
863 prob_df = target_labels.pivot(index='sample_id', columns='class_label', values='probability')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
864
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
865 print(f" After pivot: {prob_df.shape[0]} samples x {prob_df.shape[1]} classes")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
866 print(f" Class columns: {list(prob_df.columns)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
867
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
868 # Check for NaN values in probability data
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
869 nan_counts = prob_df.isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
870 if nan_counts.any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
871 print(f" NaN counts per class: {dict(nan_counts)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
872 print(f" Samples with any NaN: {prob_df.isna().any(axis=1).sum()}/{len(prob_df)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
873
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
874 # Drop only rows where ALL probabilities are NaN
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
875 all_nan_rows = prob_df.isna().all(axis=1)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
876 if all_nan_rows.any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
877 print(f" Dropping {all_nan_rows.sum()} samples with all NaN probabilities")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
878 prob_df = prob_df[~all_nan_rows]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
879
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
880 remaining_nans = prob_df.isna().sum().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
881 if remaining_nans > 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
882 print(f" Warning: {remaining_nans} individual NaN values remain - filling with 0")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
883 prob_df = prob_df.fillna(0)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
884
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
885 if prob_df.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
886 print(f" Error: No valid probability data remaining for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
887 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
888
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
889 # 2. Get true labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
890 true_labels_df = target_labels.drop_duplicates('sample_id')[['sample_id', 'known_label']].set_index('sample_id')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
891
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
892 # 3. Align indices - only keep samples that exist in both datasets
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
893 common_indices = prob_df.index.intersection(true_labels_df.index)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
894 if len(common_indices) == 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
895 print(f" Error: No common sample_ids between probability and true label data for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
896 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
897
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
898 print(f" Found {len(common_indices)} samples with both probability and true label data")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
899
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
900 # Filter both datasets to common indices
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
901 prob_df_aligned = prob_df.loc[common_indices]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
902 y_true = true_labels_df.loc[common_indices]['known_label']
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
903
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
904 # 4. Final check for NaN values
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
905 if y_true.isna().any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
906 print(f" Error: True labels still contain NaN after alignment for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
907 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
908
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
909 if prob_df_aligned.isna().any().any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
910 print(f" Error: Probability data still contains NaN after alignment for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
911 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
912
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
913 # 5. Convert categorical labels to integer labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
914 # Create a mapping from class names to integers
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
915 class_names = list(prob_df_aligned.columns)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
916 class_to_int = {class_name: i for i, class_name in enumerate(class_names)}
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
917
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
918 print(f" Class mapping: {class_to_int}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
919
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
920 # Convert true labels to integers
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
921 y_true_np = y_true.map(class_to_int).to_numpy()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
922 y_probs_np = prob_df_aligned.to_numpy()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
923
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
924 print(f" Data shape: y_true={y_true_np.shape}, y_probs={y_probs_np.shape}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
925 print(f" Unique true labels (integers): {set(y_true_np)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
926 print(f" Class labels (columns): {class_names}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
927 print(f" Label distribution: {dict(zip(*np.unique(y_true_np, return_counts=True)))}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
928
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
929 # Check for any unmapped labels (will be NaN)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
930 if pd.isna(y_true_np).any():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
931 print(" Error: Some true labels could not be mapped to class columns")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
932 unmapped_labels = set(y_true[y_true.map(class_to_int).isna()])
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
933 print(f" Unmapped labels: {unmapped_labels}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
934 print(f" Available classes: {class_names}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
935 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
936
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
937 try:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
938 print(f" Generating ROC curve for '{target_value}'...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
939 fig = plot_roc_curves(y_true_np, y_probs_np)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
940
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
941 # Create output filename with target value
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
942 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
943 output_filename = f"{output_name_base}_{safe_target_name}.{args.format}"
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
944
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
945 output_path = output_dir / output_filename
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
946 print(f" Saving ROC curve to: {output_path.absolute()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
947 fig.save(output_path, dpi=args.dpi, bbox_inches='tight')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
948
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
949 except Exception as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
950 print(f" Error generating ROC curve for '{target_value}': {str(e)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
951 print(f" Debug info - y_true type: {type(y_true_np)}, contains NaN: {pd.isna(y_true_np).any()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
952 print(f" Debug info - y_probs type: {type(y_probs_np)}, contains NaN: {pd.isna(y_probs_np).any()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
953 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
954
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
955 print("ROC curves generated successfully!")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
956
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
957
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
958 def generate_box_plots(labels, args, output_dir, output_name_base):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
959 """Generate box plots for model predictions"""
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
960
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
961 # Check if this is the specific format with sample_id, known_label, predicted_label
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
962 required_cols = ['sample_id', 'variable', 'class_label', 'probability', 'known_label', 'predicted_label']
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
963 is_flexynesis_format = all(col in labels.columns for col in required_cols)
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
964
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
965 if not is_flexynesis_format:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
966 raise ValueError(f"Labels are not in flexynesis format (Custom labels). Please provide a valid label file with the required columns, {required_cols}.")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
967
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
968 print("Generating box plots...")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
969
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
970 # Parse target values from comma-separated string
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
971 if args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
972 target_values = [val.strip() for val in args.target_value.split(',')]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
973 else:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
974 # If no target values specified, use all unique variables
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
975 target_values = labels['variable'].unique().tolist()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
976
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
977 print(f"Processing target values: {target_values}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
978
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
979 for target_value in target_values:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
980 print(f"\nProcessing target value: '{target_value}'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
981
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
982 # Filter labels for the current target value
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
983 target_labels = labels[labels['variable'] == target_value]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
984
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
985 if target_labels.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
986 print(f" Warning: No data found for target value '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
987 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
988
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
989 # Check if this is a classification problem (has probabilities)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
990 prob_columns = target_labels['class_label'].unique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
991 non_na_probs = target_labels['probability'].notna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
992
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
993 print(f" Class labels found: {list(prob_columns)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
994 print(f" Non-NaN probabilities: {non_na_probs}/{len(target_labels)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
995
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
996 # If most probabilities are NaN, this is likely a regression problem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
997 if non_na_probs < len(target_labels) * 0.1: # Less than 10% valid probabilities
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
998 print(" Detected regression problem - precision-recall curves not applicable")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
999 print(f" Skipping '{target_value}' (use regression evaluation metrics instead)")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1000 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1001
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1002 # Debug: Check data quality
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1003 total_rows = len(target_labels)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1004 missing_labels = target_labels['known_label'].isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1005 missing_probs = target_labels['probability'].isna().sum()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1006 unique_samples = target_labels['sample_id'].nunique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1007 unique_classes = target_labels['class_label'].nunique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1008
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1009 print(f" Data summary: {total_rows} total rows, {unique_samples} unique samples, {unique_classes} unique classes")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1010 print(f" Missing data: {missing_labels} missing known_label, {missing_probs} missing probability")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1011
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1012 if missing_labels > 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1013 print(f" Warning: Found {missing_labels} missing known_label values")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1014 missing_samples = target_labels[target_labels['known_label'].isna()]['sample_id'].unique()[:5]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1015 print(f" Sample IDs with missing known_label: {list(missing_samples)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1016
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1017 # Remove rows with missing known_label
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1018 target_labels = target_labels.dropna(subset=['known_label'])
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1019 if target_labels.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1020 print(f" Error: No valid known_label data remaining for '{target_value}' - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1021 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1022
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1023 # Remove rows with missing data
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1024 clean_data = target_labels.dropna(subset=['known_label', 'probability'])
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1025
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1026 if clean_data.empty:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1027 print(" No valid data after cleaning - skipping")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1028 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1029
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1030 # Get unique classes
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1031 classes = clean_data['class_label'].unique()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1032
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1033 for class_label in classes:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1034 print(f" Generating box plot for class: {class_label}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1035
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1036 # Filter for current class
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1037 class_data = clean_data[clean_data['class_label'] == class_label]
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1038
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1039 try:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1040 # Create the box plot
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1041 fig = plot_boxplot(
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1042 categorical_x=class_data['known_label'],
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1043 numerical_y=class_data['probability'],
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1044 title_x='True Label',
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1045 title_y=f'Predicted Probability ({class_label})',
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1046 )
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1047
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1048 # Save the plot
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1049 safe_class_name = str(class_label).replace('/', '_').replace('\\', '_').replace(' ', '_').replace(':', '_')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1050 safe_target_name = target_value.replace('/', '_').replace('\\', '_').replace(' ', '_')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1051 output_filename = f"{output_name_base}_{safe_target_name}_{safe_class_name}.{args.format}"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1052 output_path = output_dir / output_filename
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1053
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1054 print(f" Saving box plot to: {output_path.absolute()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1055 fig.savefig(output_path, dpi=args.dpi, bbox_inches='tight')
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1056 plt.close(fig)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1057
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1058 except Exception as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1059 print(f" Error generating box plot for class '{class_label}': {str(e)}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1060 continue
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1061
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1062
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1063 def main():
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1064 """Main function to parse arguments and generate plots"""
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1065 parser = argparse.ArgumentParser(description="Generate plots using flexynesis")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1066
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1067 # Required arguments
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1068 parser.add_argument("--labels", type=str, required=False,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1069 help="Path to labels file generated by flexynesis")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1070
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1071 # Plot type
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1072 parser.add_argument("--plot_type", type=str, required=True,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1073 choices=['dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot'],
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1074 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.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1075
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1076 # Arguments for dimensionality reduction
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1077 parser.add_argument("--embeddings", type=str,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1078 help="Path to input data embeddings file (CSV or tabular format). Required for dimred plots.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1079 parser.add_argument("--method", type=str, default='pca', choices=['pca', 'umap'],
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1080 help="Transformation method ('pca' or 'umap'). Default is 'pca'. Used for dimred plots.")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1081 parser.add_argument("--color", type=str, default=None,
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1082 help="User-defined color for the plot.")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1083
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1084 # Arguments for Kaplan-Meier
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1085 parser.add_argument("--survival_data", type=str,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1086 help="Path to survival data file with columns: duration and event. Required for kaplan_meier plots.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1087 parser.add_argument("--surv_time_var", type=str, required=False,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1088 help="Column name for survival time")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1089 parser.add_argument("--surv_event_var", type=str, required=False,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1090 help="Column name for survival event")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1091
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1092 # Arguments for Cox analysis
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1093 parser.add_argument("--important_features", type=str,
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1094 help="Path to calculated feature importance file. Required for cox plots.")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1095 parser.add_argument("--clinical_train", type=str,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1096 help="Path to training dataset (pickle file). Required for cox plots.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1097 parser.add_argument("--clinical_test", type=str,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1098 help="Path to test dataset (pickle file). Required for cox plots.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1099 parser.add_argument("--omics_train", type=str, default=None,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1100 help="Path to training omics dataset. Optional for cox plots.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1101 parser.add_argument("--omics_test", type=str, default=None,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1102 help="Path to test omics dataset. Optional for cox plots.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1103 parser.add_argument("--clinical_variables", type=str,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1104 help="Comma-separated list of clinical variables to include in Cox model (e.g., 'AGE,SEX,HISTOLOGICAL_DIAGNOSIS,STUDY')")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1105 parser.add_argument("--top_features", type=int, default=20,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1106 help="Number of top important features to include in Cox model. Default is 5")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1107 parser.add_argument("--crossval", action='store_true',
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1108 help="If True, performs K-fold cross-validation and returns average C-index. Default is False")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1109 parser.add_argument("--n_splits", type=int, default=5,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1110 help="Number of folds for cross-validation. Default is 5")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1111 parser.add_argument("--random_state", type=int, default=42,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1112 help="Random seed for reproducibility. Default is 42")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1113 parser.add_argument("--layer", type=str, default=None,
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1114 help="Class label for filtering important features.")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1115
6
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 2
diff changeset
1116 # Arguments for dimred, scatter plot, heatmap, PR curves, ROC curves, and box plots
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1117 parser.add_argument("--target_value", type=str, default=None,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1118 help="Target value for scatter plot.")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1119
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1120 # Arguments for scatter plots and concordance heatmaps
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1121 parser.add_argument("--true_label", type=str, default=None,
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1122 help="Column name for true labels in scatter plots and concordance heatmaps.")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1123 parser.add_argument("--predicted_label", type=str, default=None,
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1124 help="Column name for predicted labels in scatter plots and concordance heatmaps.")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1125 # Common arguments
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1126 parser.add_argument("--output_dir", type=str, default='output',
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1127 help="Output directory. Default is 'output'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1128 parser.add_argument("--output_name", type=str, default=None,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1129 help="Output filename base")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1130 parser.add_argument("--format", type=str, default='jpg', choices=['png', 'pdf', 'svg', 'jpg'],
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1131 help="Output format for the plot. Default is 'jpg'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1132 parser.add_argument("--dpi", type=int, default=300,
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1133 help="DPI for the output image. Default is 300")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1134
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1135 args = parser.parse_args()
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1136
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1137 try:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1138 # validate plot type
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1139 if not args.plot_type:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1140 raise ValueError("Please specify a plot type using --plot_type")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1141 if args.plot_type not in ['dimred', 'kaplan_meier', 'cox', 'scatter', 'concordance_heatmap', 'pr_curve', 'roc_curve', 'box_plot']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1142 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'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1143
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1144 # Validate plot type requirements
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1145 if args.plot_type in ['dimred']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1146 if not args.embeddings:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1147 raise ValueError("--embeddings is required when plot_type is 'dimred'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1148 if not os.path.isfile(args.embeddings):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1149 raise FileNotFoundError(f"embeddings file not found: {args.embeddings}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1150 if not args.labels:
ee7e61ab554d 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 dimensionality reduction plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1152 if not args.method:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1153 raise ValueError("--method is required for dimensionality reduction plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1154
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1155 if args.plot_type in ['kaplan_meier']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1156 if not args.survival_data:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1157 raise ValueError("--survival_data is required when plot_type is 'kaplan_meier'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1158 if not os.path.isfile(args.survival_data):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1159 raise FileNotFoundError(f"Survival data file not found: {args.survival_data}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1160 if not args.labels:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1161 raise ValueError("--labels is required for dimensionality reduction plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1162 if not args.method:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1163 raise ValueError("--method is required for dimensionality reduction plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1164 if not args.surv_time_var:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1165 raise ValueError("--surv_time_var is required for Kaplan-Meier plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1166 if not args.surv_event_var:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1167 raise ValueError("--surv_event_var is required for Kaplan-Meier plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1168
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1169 if args.plot_type in ['cox']:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1170 if not args.important_features:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1171 raise ValueError("--important_features is required when plot_type is 'cox'")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1172 if not os.path.isfile(args.important_features):
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1173 raise FileNotFoundError(f"Important features file not found: {args.important_features}")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1174 if not args.clinical_train:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1175 raise ValueError("--clinical_train is required when plot_type is 'cox'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1176 if not os.path.isfile(args.clinical_train):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1177 raise FileNotFoundError(f"Training dataset file not found: {args.clinical_train}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1178 if not args.clinical_test:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1179 raise ValueError("--clinical_test is required when plot_type is 'cox'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1180 if not os.path.isfile(args.clinical_test):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1181 raise FileNotFoundError(f"Test dataset file not found: {args.clinical_test}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1182 if not args.omics_train:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1183 raise ValueError("--omics_train is required when plot_type is 'cox'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1184 if not os.path.isfile(args.omics_train):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1185 raise FileNotFoundError(f"Training omics dataset file not found: {args.omics_train}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1186 if not args.omics_test:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1187 raise ValueError("--omics_test is required when plot_type is 'cox'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1188 if not os.path.isfile(args.omics_test):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1189 raise FileNotFoundError(f"Test omics dataset file not found: {args.omics_test}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1190 if not args.surv_time_var:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1191 raise ValueError("--surv_time_var is required for Cox plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1192 if not args.surv_event_var:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1193 raise ValueError("--surv_event_var is required for Cox plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1194 if not args.clinical_variables:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1195 print("--clinical_variables is not set for Cox plots")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1196 if not isinstance(args.top_features, int) or args.top_features <= 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1197 raise ValueError("--top_features must be a positive integer")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1198 if not args.crossval:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1199 args.crossval = False
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1200 if not isinstance(args.n_splits, int) or args.n_splits <= 0:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1201 raise ValueError("--n_splits must be a positive integer")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1202 if not isinstance(args.random_state, int):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1203 raise ValueError("--random_state must be an integer")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1204 if not args.layer:
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1205 print("--layer is not specified, using all classes from labels")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1206
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1207 if args.plot_type in ['scatter']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1208 if not args.labels:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1209 raise ValueError("--labels is required for scatter plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1210 if not args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1211 print("--target_value is not specified, using all unique variables from labels")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1212 if not os.path.isfile(args.labels):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1213 raise FileNotFoundError(f"Labels file not found: {args.labels}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1214
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1215 if args.plot_type in ['concordance_heatmap']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1216 if not args.labels:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1217 raise ValueError("--labels is required for concordance heatmap")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1218 if not args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1219 print("--target_value is not specified, using all unique variables from labels")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1220 if not os.path.isfile(args.labels):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1221 raise FileNotFoundError(f"Labels file not found: {args.labels}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1222
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1223 if args.plot_type in ['pr_curve']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1224 if not args.labels:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1225 raise ValueError("--labels is required for precision-recall curves")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1226 if not args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1227 print("--target_value is not specified, using all unique variables from labels")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1228 if not os.path.isfile(args.labels):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1229 raise FileNotFoundError(f"Labels file not found: {args.labels}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1230
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1231 if args.plot_type in ['roc_curve']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1232 if not args.labels:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1233 raise ValueError("--labels is required for ROC curves")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1234 if not args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1235 print("--target_value is not specified, using all unique variables from labels")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1236 if not os.path.isfile(args.labels):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1237 raise FileNotFoundError(f"Labels file not found: {args.labels}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1238
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1239 if args.plot_type in ['box_plot']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1240 if not args.labels:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1241 raise ValueError("--labels is required for box plots")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1242 if not args.target_value:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1243 print("--target_value is not specified, using all unique variables from labels")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1244 if not os.path.isfile(args.labels):
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1245 raise FileNotFoundError(f"Labels file not found: {args.labels}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1246
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1247 # Validate other arguments
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1248 if args.method not in ['pca', 'umap']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1249 raise ValueError("Method must be 'pca' or 'umap'")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1250
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1251 # Create output directory
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1252 output_dir = Path(args.output_dir)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1253 output_dir.mkdir(parents=True, exist_ok=True)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1254 print(f"Output directory: {output_dir.absolute()}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1255
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1256 # Generate output filename base
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1257 if args.output_name:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1258 output_name_base = args.output_name
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1259 else:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1260 if args.plot_type == 'dimred':
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1261 embeddings_name = Path(args.embeddings).stem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1262 output_name_base = f"{embeddings_name}_{args.method}"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1263 elif args.plot_type == 'kaplan_meier':
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1264 survival_name = Path(args.survival_data).stem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1265 output_name_base = f"{survival_name}_km"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1266 elif args.plot_type == 'cox':
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1267 model_name = Path(args.important_features).stem
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1268 output_name_base = f"{model_name}_cox"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1269 elif args.plot_type == 'scatter':
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1270 labels_name = Path(args.labels).stem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1271 output_name_base = f"{labels_name}_scatter"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1272 elif args.plot_type == 'concordance_heatmap':
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1273 labels_name = Path(args.labels).stem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1274 output_name_base = f"{labels_name}_concordance"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1275 elif args.plot_type == 'pr_curve':
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1276 labels_name = Path(args.labels).stem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1277 output_name_base = f"{labels_name}_pr_curves"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1278 elif args.plot_type == 'roc_curve':
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1279 labels_name = Path(args.labels).stem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1280 output_name_base = f"{labels_name}_roc_curves"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1281 elif args.plot_type == 'box_plot':
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1282 labels_name = Path(args.labels).stem
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1283 output_name_base = f"{labels_name}_box_plot"
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1284
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1285 # Generate plots based on type
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1286 if args.plot_type in ['dimred']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1287 # Load labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1288 print(f"Loading labels from: {args.labels}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1289 labels = load_labels(args.labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1290 # Load embeddings data
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1291 print(f"Loading embeddings from: {args.embeddings}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1292 embeddings, sample_names = load_embeddings(args.embeddings)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1293 print(f"embeddings shape: {embeddings.shape}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1294
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1295 # Match samples to embeddings
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1296 matched_labels = match_samples_to_embeddings(sample_names, labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1297 print(f"Successfully matched {len(matched_labels)} samples for dimensionality reduction")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1298 print(f"Matched labels shape: {matched_labels.shape}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1299 print(f"Columns in matched labels: {matched_labels.columns.tolist()}")
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1300 generate_dimred_plots(embeddings, matched_labels, args, output_dir, output_name_base)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1301
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1302 elif args.plot_type in ['kaplan_meier']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1303 # Load labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1304 print(f"Loading labels from: {args.labels}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1305 labels = load_labels(args.labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1306 # Load survival data
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1307 print(f"Loading survival data from: {args.survival_data}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1308 survival_data = load_labels(args.survival_data)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1309 print(f"Survival data shape: {survival_data.shape}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1310
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1311 generate_km_plots(survival_data, labels, args, output_dir, output_name_base)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1312
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1313 elif args.plot_type in ['cox']:
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1314 # Load important_features and datasets
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1315 print(f"Loading important features from: {args.important_features}")
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1316 important_features = load_labels(args.important_features)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1317 print(f"Loading training dataset from: {args.clinical_train}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1318 clinical_train = load_omics(args.clinical_train)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1319 print(f"Loading test dataset from: {args.clinical_test}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1320 clinical_test = load_omics(args.clinical_test)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1321 print(f"Loading training omics dataset from: {args.omics_train}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1322 omics_train = load_omics(args.omics_train)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1323 print(f"Loading test omics dataset from: {args.omics_test}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1324 omics_test = load_omics(args.omics_test)
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1325
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1326 generate_cox_plots(important_features, clinical_train, clinical_test, omics_test, omics_train, args, output_dir, output_name_base)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1327
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1328 elif args.plot_type in ['scatter']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1329 # Load labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1330 print(f"Loading labels from: {args.labels}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1331 labels = load_labels(args.labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1332
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1333 generate_plot_scatter(labels, args, output_dir, output_name_base)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1334
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1335 elif args.plot_type in ['concordance_heatmap']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1336 # Load labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1337 print(f"Loading labels from: {args.labels}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1338 labels = load_labels(args.labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1339
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1340 generate_label_concordance_heatmap(labels, args, output_dir, output_name_base)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1341
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1342 elif args.plot_type in ['pr_curve']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1343 # Load labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1344 print(f"Loading labels from: {args.labels}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1345 labels = load_labels(args.labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1346
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1347 generate_pr_curves(labels, args, output_dir, output_name_base)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1348
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1349 elif args.plot_type in ['roc_curve']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1350 # Load labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1351 print(f"Loading labels from: {args.labels}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1352 labels = load_labels(args.labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1353
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1354 generate_roc_curves(labels, args, output_dir, output_name_base)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1355
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1356 elif args.plot_type in ['box_plot']:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1357 # Load labels
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1358 print(f"Loading labels from: {args.labels}")
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1359 labels = load_labels(args.labels)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1360
7
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
diff changeset
1361 generate_box_plots(labels, args, output_dir, output_name_base)
2
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1362
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1363 print("All plots generated successfully!")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1364
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1365 except (FileNotFoundError, ValueError, pd.errors.ParserError) as e:
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1366 print(f"Error: {e}")
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1367 return 1
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1368
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1369 return 0
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1370
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1371
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1372 if __name__ == "__main__":
ee7e61ab554d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
1373 exit(main())