annotate feature_importance.py @ 8:1aed7d47c5ec draft default tip

planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
author goeckslab
date Fri, 25 Jul 2025 19:02:32 +0000
parents f4cb41f458fd
children
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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1 import base64
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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2 import logging
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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3 import os
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4
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5 import matplotlib.pyplot as plt
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6 import pandas as pd
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7 import shap
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8 from pycaret.classification import ClassificationExperiment
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9 from pycaret.regression import RegressionExperiment
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11 logging.basicConfig(level=logging.DEBUG)
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12 LOG = logging.getLogger(__name__)
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15 class FeatureImportanceAnalyzer:
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16 def __init__(
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17 self,
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18 task_type,
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19 output_dir,
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20 data_path=None,
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21 data=None,
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22 target_col=None,
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23 exp=None,
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24 best_model=None,
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25 ):
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26
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27 self.task_type = task_type
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28 self.output_dir = output_dir
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29 self.exp = exp
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30 self.best_model = best_model
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32 if exp is not None:
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33 # Assume all configs (data, target) are in exp
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34 self.data = exp.dataset.copy()
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35 self.target = exp.target_param
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36 LOG.info("Using provided experiment object")
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37 else:
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38 if data is not None:
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39 self.data = data
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40 LOG.info("Data loaded from memory")
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41 else:
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42 self.target_col = target_col
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43 self.data = pd.read_csv(data_path, sep=None, engine='python')
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44 self.data.columns = self.data.columns.str.replace('.', '_')
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45 self.data = self.data.fillna(self.data.median(numeric_only=True))
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46 self.target = self.data.columns[int(target_col) - 1]
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47 self.exp = (
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48 ClassificationExperiment()
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49 if task_type == "classification"
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50 else RegressionExperiment()
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51 )
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52
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53 self.plots = {}
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54
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55 def setup_pycaret(self):
6
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56 if self.exp is not None and hasattr(self.exp, 'is_setup') and self.exp.is_setup:
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57 LOG.info("Experiment already set up. Skipping PyCaret setup.")
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58 return
0
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59 LOG.info("Initializing PyCaret")
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60 setup_params = {
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61 'target': self.target,
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62 'session_id': 123,
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63 'html': True,
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64 'log_experiment': False,
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65 'system_log': False,
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66 }
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67 self.exp.setup(self.data, **setup_params)
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68
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69 def save_tree_importance(self):
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70 model = self.best_model or self.exp.get_config('best_model')
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71 processed_features = self.exp.get_config('X_transformed').columns
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72
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73 # Try feature_importances_ or coef_ if available
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74 importances = None
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75 model_type = model.__class__.__name__
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76 self.tree_model_name = model_type # Store the model name for reporting
0
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77
8
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78 if hasattr(model, 'feature_importances_'):
6
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79 importances = model.feature_importances_
8
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80 elif hasattr(model, 'coef_'):
6
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81 # For linear models, flatten coef_ and take abs (importance as magnitude)
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82 importances = abs(model.coef_).flatten()
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83 else:
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84 # Neither attribute exists; skip the plot
8
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85 LOG.warning(
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86 f"Model {model_type} does not have feature_importances_ or coef_ attribute. Skipping feature importance plot."
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87 )
6
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88 self.tree_model_name = None # No plot generated
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89 return
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90
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91 # Defensive: handle mismatch in number of features
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92 if len(importances) != len(processed_features):
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93 LOG.warning(
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94 f"Number of importances ({len(importances)}) does not match number of features ({len(processed_features)}). Skipping plot."
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95 )
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96 self.tree_model_name = None
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97 return
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98
8
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99 feature_importances = pd.DataFrame(
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100 {'Feature': processed_features, 'Importance': importances}
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101 ).sort_values(by='Importance', ascending=False)
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102 plt.figure(figsize=(10, 6))
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103 plt.barh(feature_importances['Feature'], feature_importances['Importance'])
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104 plt.xlabel('Importance')
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105 plt.title(f'Feature Importance ({model_type})')
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106 plot_path = os.path.join(self.output_dir, 'tree_importance.png')
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107 plt.savefig(plot_path)
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108 plt.close()
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109 self.plots['tree_importance'] = plot_path
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110
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111 def save_shap_values(self):
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112
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113 model = self.best_model or self.exp.get_config("best_model")
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114
8
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115 X_data = None
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116 for key in ("X_test_transformed", "X_train_transformed"):
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117 try:
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118 X_data = self.exp.get_config(key)
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119 break
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120 except KeyError:
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121 continue
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122 if X_data is None:
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123 raise RuntimeError(
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124 "Could not find 'X_test_transformed' or 'X_train_transformed' in the experiment. "
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125 "Make sure PyCaret setup/compare_models was run with feature_selection=True."
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126 )
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127
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128 try:
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129 used_features = model.booster_.feature_name()
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130 except Exception:
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131 used_features = getattr(model, "feature_names_in_", X_data.columns.tolist())
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132 X_data = X_data[used_features]
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133
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134 max_bg = min(len(X_data), 100)
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135 bg = X_data.sample(max_bg, random_state=42)
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136
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137 predict_fn = model.predict_proba if hasattr(model, "predict_proba") else model.predict
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138
8
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139 explainer = shap.Explainer(predict_fn, bg)
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140 self.shap_model_name = explainer.__class__.__name__
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141
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142 shap_values = explainer(X_data)
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143
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144 output_names = getattr(shap_values, "output_names", None)
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145 if output_names is None and hasattr(model, "classes_"):
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146 output_names = list(model.classes_)
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147 if output_names is None:
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148 n_out = shap_values.values.shape[-1]
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149 output_names = list(map(str, range(n_out)))
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150
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diff changeset
151 values = shap_values.values
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152 if values.ndim == 3:
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153 for j, name in enumerate(output_names):
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154 safe = name.replace(" ", "_").replace("/", "_")
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155 out_path = os.path.join(self.output_dir, f"shap_summary_{safe}.png")
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diff changeset
156 plt.figure()
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157 shap.plots.beeswarm(shap_values[..., j], show=False)
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158 plt.title(f"SHAP for {model.__class__.__name__} ⇒ {name}")
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159 plt.savefig(out_path)
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160 plt.close()
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161 self.plots[f"shap_summary_{safe}"] = out_path
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162 else:
8
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diff changeset
163 plt.figure()
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164 shap.plots.beeswarm(shap_values, show=False)
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165 plt.title(f"SHAP Summary for {model.__class__.__name__}")
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166 out_path = os.path.join(self.output_dir, "shap_summary.png")
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167 plt.savefig(out_path)
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168 plt.close()
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169 self.plots["shap_summary"] = out_path
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170
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171 def generate_html_report(self):
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172 LOG.info("Generating HTML report")
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173
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174 plots_html = ""
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175 for plot_name, plot_path in self.plots.items():
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176 # Special handling for tree importance: skip if no model name (not generated)
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177 if plot_name == 'tree_importance' and not getattr(
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178 self, 'tree_model_name', None
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179 ):
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180 continue
0
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181 encoded_image = self.encode_image_to_base64(plot_path)
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182 if plot_name == 'tree_importance' and getattr(
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183 self, 'tree_model_name', None
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184 ):
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185 section_title = (
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186 f"Feature importance analysis from a trained {self.tree_model_name}"
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187 )
6
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188 elif plot_name == 'shap_summary':
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189 section_title = f"SHAP Summary from a trained {getattr(self, 'shap_model_name', 'model')}"
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190 else:
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191 section_title = plot_name
0
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192 plots_html += f"""
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193 <div class="plot" id="{plot_name}">
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194 <h2>{section_title}</h2>
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195 <img src="data:image/png;base64,{encoded_image}" alt="{plot_name}">
0
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196 </div>
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197 """
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198
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199 html_content = f"""
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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200 {plots_html}
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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201 """
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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202
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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203 return html_content
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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204
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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205 def encode_image_to_base64(self, img_path):
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206 with open(img_path, 'rb') as img_file:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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207 return base64.b64encode(img_file.read()).decode('utf-8')
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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208
6
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209 def run(self):
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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210 if (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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211 self.exp is None
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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212 or not hasattr(self.exp, 'is_setup')
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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213 or not self.exp.is_setup
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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214 ):
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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215 self.setup_pycaret()
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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216 self.save_tree_importance()
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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217 self.save_shap_values()
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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218 html_content = self.generate_html_report()
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219 return html_content