Mercurial > repos > goeckslab > pycaret_predict

annotate base_model_trainer.py @ 7:f4cb41f458fd draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam commit b430f8b466655878c3bf63b053655fdbf039ddb0
author goeckslab
date Wed, 09 Jul 2025 01:13:01 +0000
parents a32ff7201629
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
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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4 import tempfile
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5
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6 import h5py
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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7 import joblib
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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8 import numpy as np
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9 import pandas as pd
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10 from feature_help_modal import get_feature_metrics_help_modal
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11 from feature_importance import FeatureImportanceAnalyzer
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12 from sklearn.metrics import average_precision_score
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13 from utils import get_html_closing, get_html_template
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15 logging.basicConfig(level=logging.DEBUG)
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16 LOG = logging.getLogger(__name__)
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19 class BaseModelTrainer:
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20 def __init__(
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21 self,
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22 input_file,
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23 target_col,
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24 output_dir,
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25 task_type,
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26 random_seed,
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27 test_file=None,
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28 **kwargs,
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29 ):
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30 self.exp = None # This will be set in the subclass
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31 self.input_file = input_file
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32 self.target_col = target_col
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33 self.output_dir = output_dir
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34 self.task_type = task_type
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35 self.random_seed = random_seed
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36 self.data = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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37 self.target = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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38 self.best_model = None
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39 self.results = None
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40 self.features_name = None
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41 self.plots = {}
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42 self.expaliner = None
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43 self.plots_explainer_html = None
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44 self.trees = []
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45 for key, value in kwargs.items():
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46 setattr(self, key, value)
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47 self.setup_params = {}
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48 self.test_file = test_file
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49 self.test_data = None
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50
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51 if not self.output_dir:
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52 raise ValueError("output_dir must be specified and not None")
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53
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54 LOG.info(f"Model kwargs: {self.__dict__}")
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55
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56 def load_data(self):
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57 LOG.info(f"Loading data from {self.input_file}")
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58 self.data = pd.read_csv(self.input_file, sep=None, engine="python")
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59 self.data.columns = self.data.columns.str.replace(".", "_")
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60
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61 # Remove prediction_label if present
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62 if "prediction_label" in self.data.columns:
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63 self.data = self.data.drop(columns=["prediction_label"])
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64
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65 numeric_cols = self.data.select_dtypes(include=["number"]).columns
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66 non_numeric_cols = self.data.select_dtypes(exclude=["number"]).columns
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67
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68 self.data[numeric_cols] = self.data[numeric_cols].apply(
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69 pd.to_numeric, errors="coerce"
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70 )
0
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71
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72 if len(non_numeric_cols) > 0:
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73 LOG.info(f"Non-numeric columns found: {non_numeric_cols.tolist()}")
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74
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75 names = self.data.columns.to_list()
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76 target_index = int(self.target_col) - 1
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77 self.target = names[target_index]
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78 self.features_name = [name for i, name in enumerate(names) if i != target_index]
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79 if hasattr(self, "missing_value_strategy"):
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80 if self.missing_value_strategy == "mean":
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81 self.data = self.data.fillna(self.data.mean(numeric_only=True))
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82 elif self.missing_value_strategy == "median":
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83 self.data = self.data.fillna(self.data.median(numeric_only=True))
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84 elif self.missing_value_strategy == "drop":
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85 self.data = self.data.dropna()
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86 else:
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87 # Default strategy if not specified
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88 self.data = self.data.fillna(self.data.median(numeric_only=True))
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89
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90 if self.test_file:
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91 LOG.info(f"Loading test data from {self.test_file}")
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92 self.test_data = pd.read_csv(self.test_file, sep=None, engine="python")
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93 self.test_data = self.test_data[numeric_cols].apply(
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94 pd.to_numeric, errors="coerce"
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95 )
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96 self.test_data.columns = self.test_data.columns.str.replace(".", "_")
0
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97
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98 def setup_pycaret(self):
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99 LOG.info("Initializing PyCaret")
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100 self.setup_params = {
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101 "target": self.target,
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102 "session_id": self.random_seed,
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103 "html": True,
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104 "log_experiment": False,
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105 "system_log": False,
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106 "index": False,
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107 }
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108
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109 if self.test_data is not None:
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110 self.setup_params["test_data"] = self.test_data
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111
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112 if (
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113 hasattr(self, "train_size")
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114 and self.train_size is not None
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115 and self.test_data is None
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116 ):
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117 self.setup_params["train_size"] = self.train_size
0
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118
6
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119 if hasattr(self, "normalize") and self.normalize is not None:
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120 self.setup_params["normalize"] = self.normalize
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121
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122 if hasattr(self, "feature_selection") and self.feature_selection is not None:
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123 self.setup_params["feature_selection"] = self.feature_selection
0
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124
6
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125 if (
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126 hasattr(self, "cross_validation")
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127 and self.cross_validation is not None
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128 and self.cross_validation is False
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129 ):
7
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130 logging.info(
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131 "cross_validation is set to False. This will disable cross-validation."
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132 )
0
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133
7
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134 if hasattr(self, "cross_validation") and self.cross_validation:
6
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135 if hasattr(self, "cross_validation_folds"):
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136 self.setup_params["fold"] = self.cross_validation_folds
0
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137
6
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138 if hasattr(self, "remove_outliers") and self.remove_outliers is not None:
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139 self.setup_params["remove_outliers"] = self.remove_outliers
0
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140
6
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141 if (
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142 hasattr(self, "remove_multicollinearity")
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143 and self.remove_multicollinearity is not None
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144 ):
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145 self.setup_params["remove_multicollinearity"] = (
0
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146 self.remove_multicollinearity
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147 )
0
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148
6
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149 if (
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150 hasattr(self, "polynomial_features")
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151 and self.polynomial_features is not None
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152 ):
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153 self.setup_params["polynomial_features"] = self.polynomial_features
0
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154
6
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155 if hasattr(self, "fix_imbalance") and self.fix_imbalance is not None:
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156 self.setup_params["fix_imbalance"] = self.fix_imbalance
0
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157
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158 LOG.info(self.setup_params)
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159
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160 # Solution: instantiate the correct PyCaret experiment based on task_type
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161 if self.task_type == "classification":
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162 from pycaret.classification import ClassificationExperiment
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163
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164 self.exp = ClassificationExperiment()
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165 elif self.task_type == "regression":
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166 from pycaret.regression import RegressionExperiment
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167
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168 self.exp = RegressionExperiment()
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169 else:
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170 raise ValueError("task_type must be 'classification' or 'regression'")
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171
0
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172 self.exp.setup(self.data, **self.setup_params)
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173
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174 def train_model(self):
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175 LOG.info("Training and selecting the best model")
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176 if self.task_type == "classification":
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177 average_displayed = "Weighted"
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178 self.exp.add_metric(
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179 id=f"PR-AUC-{average_displayed}",
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180 name=f"PR-AUC-{average_displayed}",
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181 target="pred_proba",
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182 score_func=average_precision_score,
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183 average="weighted",
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184 )
0
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185
6
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186 if hasattr(self, "models") and self.models is not None:
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187 self.best_model = self.exp.compare_models(include=self.models, cross_validation=self.cross_validation)
0
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188 else:
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diff changeset
189 self.best_model = self.exp.compare_models(cross_validation=self.cross_validation)
0
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190 self.results = self.exp.pull()
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diff changeset
191
0
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192 if self.task_type == "classification":
6
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diff changeset
193 self.results.rename(columns={"AUC": "ROC-AUC"}, inplace=True)
0
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194
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195 _ = self.exp.predict_model(self.best_model)
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196 self.test_result_df = self.exp.pull()
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197 if self.task_type == "classification":
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198 self.test_result_df.rename(columns={"AUC": "ROC-AUC"}, inplace=True)
0
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199
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200 def save_model(self):
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201 hdf5_model_path = "pycaret_model.h5"
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diff changeset
202 with h5py.File(hdf5_model_path, "w") as f:
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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203 with tempfile.NamedTemporaryFile(delete=False) as temp_file:
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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204 joblib.dump(self.best_model, temp_file.name)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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205 temp_file.seek(0)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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206 model_bytes = temp_file.read()
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diff changeset
207 f.create_dataset("model", data=np.void(model_bytes))
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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208
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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209 def generate_plots(self):
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210 raise NotImplementedError("Subclasses should implement this method")
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211
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diff changeset
212 def encode_image_to_base64(self, img_path):
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213 with open(img_path, "rb") as img_file:
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214 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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215
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diff changeset
216 def save_html_report(self):
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217 LOG.info("Saving HTML report")
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218
6
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219 if not self.output_dir:
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220 raise ValueError("output_dir must be specified and not None")
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diff changeset
221
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
222 model_name = type(self.best_model).__name__
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diff changeset
223 excluded_params = ["html", "log_experiment", "system_log", "test_data"]
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
224 filtered_setup_params = {
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
225 k: v for k, v in self.setup_params.items() if k not in excluded_params
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
226 }
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
227 setup_params_table = pd.DataFrame(
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
228 list(filtered_setup_params.items()), columns=["Parameter", "Value"]
3
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goeckslab
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diff changeset
229 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
230
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
231 best_model_params = pd.DataFrame(
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
232 self.best_model.get_params().items(), columns=["Parameter", "Value"]
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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diff changeset
233 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
234 best_model_params.to_csv(
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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diff changeset
235 os.path.join(self.output_dir, "best_model.csv"), index=False
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
goeckslab
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diff changeset
236 )
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
237 self.results.to_csv(os.path.join(self.output_dir, "comparison_results.csv"))
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
238 self.test_result_df.to_csv(os.path.join(self.output_dir, "test_results.csv"))
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
239
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
240 plots_html = ""
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
241 length = len(self.plots)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
242 for i, (plot_name, plot_path) in enumerate(self.plots.items()):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
243 encoded_image = self.encode_image_to_base64(plot_path)
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a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
244 plots_html += (
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
245 f'<div class="plot">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
246 f"<h3>{plot_name.capitalize()}</h3>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
247 f'<img src="data:image/png;base64,{encoded_image}" alt="{plot_name}">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
248 f"</div>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
249 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
250 if i < length - 1:
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
251 plots_html += "<hr>"
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
252
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
253 tree_plots = ""
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
254 for i, tree in enumerate(self.trees):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
255 if tree:
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
256 tree_plots += (
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
257 f'<div class="plot">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
258 f"<h3>Tree {i + 1}</h3>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
259 f'<img src="data:image/png;base64,{tree}" alt="tree {i + 1}">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
260 f"</div>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
261 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
262
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
263 analyzer = FeatureImportanceAnalyzer(
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
264 data=self.data,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
265 target_col=self.target_col,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
266 task_type=self.task_type,
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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diff changeset
267 output_dir=self.output_dir,
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
268 exp=self.exp,
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
269 best_model=self.best_model,
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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diff changeset
270 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
271 feature_importance_html = analyzer.run()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
272
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
273 # --- Feature Metrics Help Button ---
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
274 feature_metrics_button_html = (
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
275 '<button class="help-modal-btn" id="openFeatureMetricsHelp" style="margin-bottom:12px;">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
276 "Help: Metrics Guide"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
277 "</button>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
278 "<style>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
279 ".help-modal-btn {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
280 "background-color: #17623b;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
281 "color: #fff;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
282 "border: none;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
283 "border-radius: 24px;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
284 "padding: 10px 28px;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
285 "font-size: 1.1rem;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
286 "font-weight: bold;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
287 "letter-spacing: 0.03em;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
288 "cursor: pointer;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
289 "transition: background 0.2s, box-shadow 0.2s;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
290 "box-shadow: 0 2px 8px rgba(23,98,59,0.07);"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
291 "}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
292 ".help-modal-btn:hover, .help-modal-btn:focus {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
293 "background-color: #21895e;"
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294 "outline: none;"
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295 "box-shadow: 0 4px 16px rgba(23,98,59,0.14);"
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296 "}"
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297 "</style>"
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298 )
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299
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300 html_content = (
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301 f"{get_html_template()}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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302 "<h1>Tabular Learner Model Report</h1>"
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303 f"{feature_metrics_button_html}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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304 '<div class="tabs">'
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305 '<div class="tab" onclick="openTab(event, \'summary\')">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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306 "Validation Result Summary & Config</div>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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307 '<div class="tab" onclick="openTab(event, \'plots\')">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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308 "Test Results</div>"
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309 '<div class="tab" onclick="openTab(event, \'feature\')">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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310 "Feature Importance</div>"
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diff changeset
311 )
2
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312 if self.plots_explainer_html:
6
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313 html_content += (
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
314 '<div class="tab" onclick="openTab(event, \'explainer\')">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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315 "Explainer Plots</div>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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316 )
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
317 html_content += (
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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318 "</div>"
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diff changeset
319 '<div id="summary" class="tab-content">'
7
f4cb41f458fd planemo upload for repository https://github.com/goeckslab/gleam commit b430f8b466655878c3bf63b053655fdbf039ddb0
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320 f"<h2>Model Metrics from {'Cross-Validation Set' if self.cross_validation else 'Validation set'}</h2>"
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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321 f"<h2>Best Model: {model_name}</h2>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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322 "<h5>The best model is selected by: Accuracy (Classification)"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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323 " or R2 (Regression).</h5>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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324 f"{self.results.to_html(index=False, classes='table sortable')}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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325 "<h2>Best Model's Hyperparameters</h2>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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326 f"{best_model_params.to_html(index=False, header=True, classes='table sortable')}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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327 "<h2>Setup Parameters</h2>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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328 f"{setup_params_table.to_html(index=False, header=True, classes='table sortable')}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
329 "<h5>If you want to know all the experiment setup parameters,"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
330 " please check the PyCaret documentation for"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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331 " the classification/regression <code>exp</code> function.</h5>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
332 "</div>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
333 '<div id="plots" class="tab-content">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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334 f"<h2>Best Model: {model_name}</h2>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
335 "<h5>The best model is selected by: Accuracy (Classification)"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
336 " or R2 (Regression).</h5>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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337 "<h2>Test Metrics</h2>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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338 f"{self.test_result_df.to_html(index=False)}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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339 "<h2>Test Results</h2>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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340 f"{plots_html}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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341 "</div>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
342 '<div id="feature" class="tab-content">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
343 f"{feature_importance_html}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
344 "</div>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
345 )
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
346 if self.plots_explainer_html:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
347 html_content += (
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
348 '<div id="explainer" class="tab-content">'
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
349 f"{self.plots_explainer_html}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
350 f"{tree_plots}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
351 "</div>"
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diff changeset
352 )
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
353 html_content += (
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
354 "<script>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
355 "document.addEventListener(\"DOMContentLoaded\", function() {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
356 "var tables = document.querySelectorAll(\"table.sortable\");"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
357 "tables.forEach(function(table) {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
358 "var headers = table.querySelectorAll(\"th\");"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
359 "headers.forEach(function(header, index) {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
360 "header.style.cursor = \"pointer\";"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
361 "// Add initial arrow (up) to indicate sortability, use Unicode ↑ (U+2191)"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
362 "header.innerHTML += '<span class=\"sort-arrow\"> ↑</span>';"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
363 "header.addEventListener(\"click\", function() {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents: 3
diff changeset
364 "var direction = this.getAttribute("
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
365 "\"data-sort-direction\""
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
366 ") || \"asc\";"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
367 "// Reset arrows in all headers of this table"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
368 "headers.forEach(function(h) {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
369 "var arrow = h.querySelector(\".sort-arrow\");"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
370 "if (arrow) arrow.textContent = \" ↑\";"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
371 "});"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
372 "// Set arrow for clicked header"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
373 "var arrow = this.querySelector(\".sort-arrow\");"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
374 "arrow.textContent = direction === \"asc\" ? \" ↓\" : \" ↑\";"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
375 "sortTable(table, index, direction);"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
376 "this.setAttribute(\"data-sort-direction\","
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
377 "direction === \"asc\" ? \"desc\" : \"asc\");"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
378 "});"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
379 "});"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents: 3
diff changeset
380 "});"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
381 "});"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents: 3
diff changeset
382 "function sortTable(table, colNum, direction) {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
383 "var tb = table.tBodies[0];"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
384 "var tr = Array.prototype.slice.call(tb.rows, 0);"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
385 "var multiplier = direction === \"asc\" ? 1 : -1;"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
386 "tr = tr.sort(function(a, b) {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
387 "var aText = a.cells[colNum].textContent.trim();"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
388 "var bText = b.cells[colNum].textContent.trim();"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
389 "// Remove arrow from text comparison"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
390 "aText = aText.replace(/[↑↓]/g, '').trim();"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
391 "bText = bText.replace(/[↑↓]/g, '').trim();"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents: 3
diff changeset
392 "if (!isNaN(aText) && !isNaN(bText)) {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
393 "return multiplier * ("
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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394 "parseFloat(aText) - parseFloat(bText)"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
395 ");"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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396 "} else {"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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397 "return multiplier * aText.localeCompare(bText);"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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398 "}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
399 "});"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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400 "for (var i = 0; i < tr.length; ++i) tb.appendChild(tr[i]);"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
401 "}"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
402 "</script>"
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
403 )
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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404 # --- Add the Feature Metrics Help Modal ---
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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405 html_content += get_feature_metrics_help_modal()
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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406 html_content += f"{get_html_closing()}"
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
goeckslab
parents: 2
diff changeset
407 with open(
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
goeckslab
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408 os.path.join(self.output_dir, "comparison_result.html"),
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
409 "w",
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
410 encoding="utf-8",
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
goeckslab
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diff changeset
411 ) as file:
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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412 file.write(html_content)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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413
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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414 def save_dashboard(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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415 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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416
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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417 def generate_plots_explainer(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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418 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
419
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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420 def generate_tree_plots(self):
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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421 from sklearn.ensemble import RandomForestClassifier, RandomForestRegressor
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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422 from xgboost import XGBClassifier, XGBRegressor
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
423 from explainerdashboard.explainers import RandomForestExplainer
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
424
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
425 LOG.info("Generating tree plots")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
426 X_test = self.exp.X_test_transformed.copy()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
427 y_test = self.exp.y_test_transformed
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
428
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
429 is_rf = isinstance(
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents: 3
diff changeset
430 self.best_model, (RandomForestClassifier, RandomForestRegressor)
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
431 )
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
432 is_xgb = isinstance(self.best_model, (XGBClassifier, XGBRegressor))
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
433
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
434 num_trees = None
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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435 if is_rf:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
436 num_trees = self.best_model.n_estimators
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
437 elif is_xgb:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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438 num_trees = len(self.best_model.get_booster().get_dump())
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
439 else:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
440 LOG.warning("Tree plots not supported for this model type.")
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
441 return
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
442
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
443 try:
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
444 explainer = RandomForestExplainer(self.best_model, X_test, y_test)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
445 for i in range(num_trees):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
446 fig = explainer.decisiontree_encoded(tree_idx=i, index=0)
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
447 LOG.info(f"Tree {i + 1}")
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
448 LOG.info(fig)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
449 self.trees.append(fig)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
450 except Exception as e:
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
451 LOG.error(f"Error generating tree plots: {e}")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
452
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
453 def run(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
454 self.load_data()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
455 self.setup_pycaret()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
456 self.train_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
457 self.save_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
458 self.generate_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
459 self.generate_plots_explainer()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
460 self.generate_tree_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
461 self.save_html_report()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
462 # self.save_dashboard()