Mercurial > repos > goeckslab > pycaret_predict

annotate base_model_trainer.py @ 9:c6c1f8777aae draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam commit 4a11e8a4c4e9daa884bddedfa47090476c517667
author goeckslab
date Thu, 31 Jul 2025 15:41:24 +0000
parents 1aed7d47c5ec
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 tempfile
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4 from pathlib import Path
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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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
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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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 (
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14 add_hr_to_html,
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15 add_plot_to_html,
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16 build_tabbed_html,
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17 encode_image_to_base64,
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18 get_html_closing,
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19 get_html_template,
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20 )
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22 logging.basicConfig(level=logging.DEBUG)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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23 LOG = logging.getLogger(__name__)
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26 class BaseModelTrainer:
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27 def __init__(
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28 self,
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29 input_file,
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30 target_col,
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31 output_dir,
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32 task_type,
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33 random_seed,
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34 test_file=None,
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35 **kwargs,
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36 ):
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37 self.exp = None
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38 self.input_file = input_file
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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39 self.target_col = target_col
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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40 self.output_dir = output_dir
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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41 self.task_type = task_type
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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42 self.random_seed = random_seed
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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43 self.data = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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44 self.target = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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45 self.best_model = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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46 self.results = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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47 self.features_name = None
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48 self.plots = {}
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49 self.explainer_plots = {}
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50 self.plots_explainer_html = None
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51 self.trees = []
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52 self.user_kwargs = kwargs.copy()
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53 for key, value in self.user_kwargs.items():
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54 setattr(self, key, value)
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55 self.setup_params = {}
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56 self.test_file = test_file
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57 self.test_data = None
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58
6
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59 if not self.output_dir:
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60 raise ValueError("output_dir must be specified and not None")
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61
0
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62 LOG.info(f"Model kwargs: {self.__dict__}")
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63
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64 def load_data(self):
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65 LOG.info(f"Loading data from {self.input_file}")
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66 self.data = pd.read_csv(self.input_file, sep=None, engine="python")
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67 self.data.columns = self.data.columns.str.replace(".", "_")
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68 if "prediction_label" in self.data.columns:
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69 self.data = self.data.drop(columns=["prediction_label"])
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70
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71 numeric_cols = self.data.select_dtypes(include=["number"]).columns
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72 non_numeric_cols = self.data.select_dtypes(exclude=["number"]).columns
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73 self.data[numeric_cols] = self.data[numeric_cols].apply(
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74 pd.to_numeric, errors="coerce"
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75 )
0
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76 if len(non_numeric_cols) > 0:
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77 LOG.info(f"Non-numeric columns found: {non_numeric_cols.tolist()}")
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78
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79 names = self.data.columns.to_list()
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80 target_index = int(self.target_col) - 1
0
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81 self.target = names[target_index]
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82 self.features_name = [n for i, n in enumerate(names) if i != target_index]
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83
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84 if getattr(self, "missing_value_strategy", None):
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85 strat = self.missing_value_strategy
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86 if strat == "mean":
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87 self.data = self.data.fillna(self.data.mean(numeric_only=True))
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88 elif strat == "median":
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89 self.data = self.data.fillna(self.data.median(numeric_only=True))
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90 elif strat == "drop":
0
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91 self.data = self.data.dropna()
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92 else:
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93 self.data = self.data.fillna(self.data.median(numeric_only=True))
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94
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95 if self.test_file:
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96 LOG.info(f"Loading test data from {self.test_file}")
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97 df_test = pd.read_csv(self.test_file, sep=None, engine="python")
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98 df_test.columns = df_test.columns.str.replace(".", "_")
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99 self.test_data = df_test
0
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100
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101 def setup_pycaret(self):
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102 LOG.info("Initializing PyCaret")
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103 self.setup_params = {
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104 "target": self.target,
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105 "session_id": self.random_seed,
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106 "html": True,
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107 "log_experiment": False,
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108 "system_log": False,
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109 "index": False,
0
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110 }
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111 if self.test_data is not None:
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112 self.setup_params["test_data"] = self.test_data
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113 for attr in [
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114 "train_size",
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115 "normalize",
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116 "feature_selection",
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117 "remove_outliers",
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118 "remove_multicollinearity",
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119 "polynomial_features",
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120 "feature_interaction",
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121 "feature_ratio",
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122 "fix_imbalance",
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123 ]:
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124 val = getattr(self, attr, None)
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125 if val is not None:
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126 self.setup_params[attr] = val
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127 if getattr(self, "cross_validation_folds", None) is not None:
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128 self.setup_params["fold"] = self.cross_validation_folds
0
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129 LOG.info(self.setup_params)
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130
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131 if self.task_type == "classification":
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132 from pycaret.classification import ClassificationExperiment
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133
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diff changeset
134 self.exp = ClassificationExperiment()
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135 elif self.task_type == "regression":
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136 from pycaret.regression import RegressionExperiment
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137
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138 self.exp = RegressionExperiment()
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139 else:
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140 raise ValueError("task_type must be 'classification' or 'regression'")
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141
0
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142 self.exp.setup(self.data, **self.setup_params)
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diff changeset
143 self.setup_params.update(self.user_kwargs)
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144
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145 def train_model(self):
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146 LOG.info("Training and selecting the best model")
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147 if self.task_type == "classification":
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diff changeset
148 self.exp.add_metric(
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diff changeset
149 id="PR-AUC-Weighted",
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150 name="PR-AUC-Weighted",
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diff changeset
151 target="pred_proba",
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152 score_func=average_precision_score,
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153 average="weighted",
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154 )
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diff changeset
155 # Build arguments for compare_models()
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156 compare_kwargs = {}
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157 if getattr(self, "models", None):
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diff changeset
158 compare_kwargs["include"] = self.models
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159
8
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160 # Respect explicit cross-validation flag
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161 if getattr(self, "cross_validation", None) is not None:
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162 compare_kwargs["cross_validation"] = self.cross_validation
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diff changeset
163
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diff changeset
164 # Respect explicit fold count
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165 if getattr(self, "cross_validation_folds", None) is not None:
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diff changeset
166 compare_kwargs["fold"] = self.cross_validation_folds
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diff changeset
167
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168 LOG.info(f"compare_models kwargs: {compare_kwargs}")
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diff changeset
169 self.best_model = self.exp.compare_models(**compare_kwargs)
0
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diff changeset
170 self.results = self.exp.pull()
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diff changeset
171 if getattr(self, "tune_model", False):
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diff changeset
172 LOG.info("Tuning hyperparameters of the best model")
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diff changeset
173 self.best_model = self.exp.tune_model(self.best_model)
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diff changeset
174 self.results = self.exp.pull()
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175
0
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176 if self.task_type == "classification":
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177 self.results.rename(columns={"AUC": "ROC-AUC"}, inplace=True)
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178
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diff changeset
179 prob_thresh = getattr(self, "probability_threshold", None)
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180 if self.task_type == "classification" and prob_thresh is not None:
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181 _ = self.exp.predict_model(self.best_model, probability_threshold=prob_thresh)
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182 else:
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183 _ = self.exp.predict_model(self.best_model)
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184
0
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diff changeset
185 self.test_result_df = self.exp.pull()
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186 if self.task_type == "classification":
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187 self.test_result_df.rename(columns={"AUC": "ROC-AUC"}, inplace=True)
0
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188
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189 def save_model(self):
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diff changeset
190 hdf5_path = Path(self.output_dir) / "pycaret_model.h5"
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191 with h5py.File(hdf5_path, "w") as f:
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192 with tempfile.NamedTemporaryFile(delete=False) as tmp:
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193 joblib.dump(self.best_model, tmp.name)
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diff changeset
194 tmp.seek(0)
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diff changeset
195 model_bytes = tmp.read()
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196 f.create_dataset("model", data=np.void(model_bytes))
0
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197
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198 def generate_plots(self):
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199 LOG.info("Generating PyCaret diagnostic pltos")
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200
8
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201 # choose the right plots based on task
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202 if self.task_type == "classification":
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203 plot_names = [
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204 "learning",
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205 "vc",
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206 "calibration",
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207 "dimension",
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208 "manifold",
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209 "rfe",
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210 "threshold",
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211 "percentage_above_below",
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212 "class_report",
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213 "pr_auc",
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214 "roc_auc",
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215 ]
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216 else:
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217 plot_names = ["residuals", "vc", "parameter", "error", "learning"]
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218 for name in plot_names:
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219 try:
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220 ax = self.exp.plot_model(self.best_model, plot=name, save=False)
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221 out_path = Path(self.output_dir) / f"plot_{name}.png"
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222 fig = ax.get_figure()
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223 fig.savefig(out_path, bbox_inches="tight")
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224 self.plots[name] = str(out_path)
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225 except Exception as e:
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226 LOG.warning(f"Could not generate {name} plot: {e}")
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227
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228 def encode_image_to_base64(self, img_path: str) -> str:
6
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229 with open(img_path, "rb") as img_file:
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230 return base64.b64encode(img_file.read()).decode("utf-8")
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231
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232 def save_html_report(self):
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233 LOG.info("Saving HTML report")
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234
8
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235 # 1) Determine best model name
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236 try:
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237 best_model_name = str(self.results.iloc[0]["Model"])
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238 except Exception:
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239 best_model_name = type(self.best_model).__name__
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240 LOG.info(f"Best model determined as: {best_model_name}")
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241
9
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242 # 2) Compute training sample count
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243 try:
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244 n_train = self.exp.X_train.shape[0]
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245 except Exception:
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246 n_train = getattr(self.exp, "X_train_transformed", pd.DataFrame()).shape[0]
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247 total_rows = self.data.shape[0]
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248
8
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249 # 3) Build setup parameters table
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250 all_params = self.setup_params.copy()
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251 if self.task_type == "classification" and hasattr(self, "probability_threshold"):
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252 all_params["probability_threshold"] = self.probability_threshold
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253
8
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254 display_keys = [
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255 "Target",
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256 "Session ID",
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257 "Train Size",
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258 "Normalize",
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259 "Feature Selection",
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260 "Cross Validation",
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261 "Cross Validation Folds",
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262 "Remove Outliers",
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263 "Remove Multicollinearity",
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264 "Polynomial Features",
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265 "Fix Imbalance",
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266 "Models",
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267 "Probability Threshold",
8
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268 ]
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diff changeset
269 setup_rows = []
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270 for key in display_keys:
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271 pk = key.lower().replace(" ", "_")
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272 v = all_params.get(pk)
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273 if key == "Train Size":
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274 frac = (
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275 float(v)
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diff changeset
276 if v is not None
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277 else (n_train / total_rows if total_rows else 0)
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278 )
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diff changeset
279 dv = f"{frac:.2f} ({n_train} rows)"
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280 elif key in {
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281 "Normalize",
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282 "Feature Selection",
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283 "Cross Validation",
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284 "Remove Outliers",
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285 "Remove Multicollinearity",
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286 "Polynomial Features",
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diff changeset
287 "Fix Imbalance",
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288 }:
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289 dv = bool(v)
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290 elif key == "Cross Validation Folds":
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291 dv = v if v is not None else "None"
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292 elif key == "Models":
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293 dv = ", ".join(map(str, v)) if isinstance(v, (list, tuple)) else "None"
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294 elif key == "Probability Threshold":
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295 dv = v if v is not None else "None"
8
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296 else:
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297 dv = v if v is not None else "None"
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298 setup_rows.append([key, dv])
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299 if hasattr(self.exp, "_fold_metric"):
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300 setup_rows.append(["best_model_metric", self.exp._fold_metric])
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301
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302 df_setup = pd.DataFrame(setup_rows, columns=["Parameter", "Value"])
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303 df_setup.to_csv(Path(self.output_dir) / "setup_params.csv", index=False)
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304
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305 # 4) Persist CSVs
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306 self.results.to_csv(
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307 Path(self.output_dir) / "comparison_results.csv", index=False
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308 )
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309 self.test_result_df.to_csv(
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310 Path(self.output_dir) / "test_results.csv", index=False
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311 )
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312 pd.DataFrame(
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313 self.best_model.get_params().items(), columns=["Parameter", "Value"]
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314 ).to_csv(Path(self.output_dir) / "best_model.csv", index=False)
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315
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316 # 5) Header
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317 header = f"<h2>Best Model: {best_model_name}</h2>"
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318
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319 # — Validation Summary & Configuration —
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320 val_df = self.results.copy()
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321 # mapping raw plot keys to user-friendly titles
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322 plot_title_map = {
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323 "learning": "Learning Curve",
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324 "vc": "Validation Curve",
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325 "calibration": "Calibration Curve",
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326 "dimension": "Dimensionality Reduction",
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327 "manifold": "Manifold Learning",
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328 "rfe": "Recursive Feature Elimination",
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329 "threshold": "Threshold Plot",
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330 "percentage_above_below": "Percentage Above vs. Below Cutoff",
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331 "class_report": "Classification Report",
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332 "pr_auc": "Precision-Recall AUC",
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333 "roc_auc": "Receiver Operating Characteristic AUC",
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334 "residuals": "Residuals Distribution",
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335 "error": "Prediction Error Distribution",
0
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336 }
8
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337 val_df.drop(columns=["TT (Ec)", "TT (Sec)"], errors="ignore", inplace=True)
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338 summary_html = (
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339 header
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340 + "<h2>Train & Validation Summary</h2>"
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341 + '<div class="table-wrapper">'
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342 + val_df.to_html(index=False, classes="table sortable")
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343 + "</div>"
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344 + "<h2>Setup Parameters</h2>"
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345 + '<div class="table-wrapper">'
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346 + df_setup.to_html(index=False, classes="table sortable")
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347 + "</div>"
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348 # — Hyperparameters
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349 + "<h2>Best Model Hyperparameters</h2>"
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350 + '<div class="table-wrapper">'
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351 + pd.DataFrame(
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352 self.best_model.get_params().items(), columns=["Parameter", "Value"]
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353 ).to_html(index=False, classes="table sortable")
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354 + "</div>"
3
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355 )
0
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356
8
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357 # choose summary plots based on task type
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358 if self.task_type == "classification":
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359 summary_plots = [
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360 "learning",
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diff changeset
361 "vc",
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362 "calibration",
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363 "dimension",
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364 "manifold",
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365 "rfe",
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366 "threshold",
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diff changeset
367 "percentage_above_below",
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368 ]
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369 else:
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370 summary_plots = ["learning", "vc", "parameter", "residuals"]
0
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371
8
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diff changeset
372 for name in summary_plots:
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373 if name in self.plots:
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374 summary_html += "<hr>"
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375 b64 = encode_image_to_base64(self.plots[name])
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376 title = plot_title_map.get(name, name.replace("_", " ").title())
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377 summary_html += (
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378 '<div class="plot">'
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379 f"<h2>{title}</h2>"
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380 f'<img src="data:image/png;base64,{b64}" '
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381 'style="max-width:90%;max-height:600px;border:1px solid #ddd;"/>'
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382 "</div>"
6
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383 )
0
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384
8
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diff changeset
385 # — Test Summary —
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386 test_html = (
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387 header
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388 + '<div class="table-wrapper">'
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389 + self.test_result_df.to_html(index=False, classes="table sortable")
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390 + "</div>"
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diff changeset
391 )
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diff changeset
392 if self.task_type == "regression":
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diff changeset
393 try:
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diff changeset
394 y_true = (
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diff changeset
395 pd.Series(self.exp.y_test_transformed)
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diff changeset
396 .reset_index(drop=True)
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397 .rename("True")
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diff changeset
398 )
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diff changeset
399 y_pred = pd.Series(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
400 self.best_model.predict(self.exp.X_test_transformed)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
401 ).rename("Predicted")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
402 df_tp = pd.concat([y_true, y_pred], axis=1)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
403 test_html += "<h2>True vs Predicted Values</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
404 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
405 '<div class="table-wrapper" style="max-height:400px; overflow-y:auto;">'
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
406 + df_tp.head(50).to_html(index=False, classes="table sortable")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
407 + "</div>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
408 + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
409 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
410 except Exception as e:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
411 LOG.warning(f"Could not generate True vs Predicted table: {e}")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
412
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
413 # 5a) Explainer-substituted plots in order
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
414 if self.task_type == "regression":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
415 test_order = ["residuals"]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
416 else:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
417 test_order = [
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
418 "confusion_matrix",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
419 "roc_auc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
420 "pr_auc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
421 "lift_curve",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
422 "threshold",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
423 "cumulative_precision",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
424 ]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
425 for key in test_order:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
426 fig_or_fn = self.explainer_plots.pop(key, None)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
427 if fig_or_fn is not None:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
428 fig = fig_or_fn() if callable(fig_or_fn) else fig_or_fn
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
429 title = plot_title_map.get(key, key.replace("_", " ").title())
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
430 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
431 f"<h2>{title}</h2>" + add_plot_to_html(fig) + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
432 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
433 # 5b) Remaining PyCaret test plots
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
434 for name, path in self.plots.items():
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
435 # classification: include only the small extras, before skipping anything
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
436 if self.task_type == "classification" and name in {
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
437 "threshold",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
438 "pr_auc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
439 "class_report",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
440 }:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
441 title = plot_title_map.get(name, name.replace("_", " ").title())
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
442 b64 = encode_image_to_base64(path)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
443 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
444 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
445 "<div class='plot'>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
446 f"<img src='data:image/png;base64,{b64}' "
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
447 "style='max-width:90%;max-height:600px;border:1px solid #ddd;'/>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
448 "</div>" + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
449 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
450 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
451
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
452 # regression: explicitly include the 'error' plot, before skipping
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
453 if self.task_type == "regression" and name == "error":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
454 title = plot_title_map.get("error", "Prediction Error Distribution")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
455 b64 = encode_image_to_base64(path)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
456 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
457 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
458 "<div class='plot'>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
459 f"<img src='data:image/png;base64,{b64}' "
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
460 "style='max-width:90%;max-height:600px;border:1px solid #ddd;'/>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
461 "</div>" + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
462 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
463 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
464
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
465 # now skip any plots already rendered via test_order
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
466 if name in test_order:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
467 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
468
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
469 # — Feature Importance —
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
470 feature_html = header
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
471
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
472 # 6a) PyCaret’s default feature importances
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
473 feature_html += FeatureImportanceAnalyzer(
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
474 data=self.data,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
475 target_col=self.target_col,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
476 task_type=self.task_type,
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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parents: 2
diff changeset
477 output_dir=self.output_dir,
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
478 exp=self.exp,
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
479 best_model=self.best_model,
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
480 ).run()
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
481
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
482 # 6b) Explainer SHAP importances
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
483 for key in ["shap_mean", "shap_perm"]:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
484 fig_or_fn = self.explainer_plots.pop(key, None)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
485 if fig_or_fn is not None:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
486 fig = fig_or_fn() if callable(fig_or_fn) else fig_or_fn
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
487 # give SHAP plots explicit titles
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
488 title = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
489 "Mean Absolute SHAP Value Impact"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
490 if key == "shap_mean"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
491 else "Permutation Feature Importance"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
492 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
493 feature_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
494 f"<h2>{title}</h2>" + add_plot_to_html(fig) + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
495 )
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
496
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
497 # 6c) PDPs last
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
498 pdp_keys = sorted(k for k in self.explainer_plots if k.startswith("pdp__"))
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
499 for k in pdp_keys:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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500 fig_or_fn = self.explainer_plots[k]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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501 fig = fig_or_fn() if callable(fig_or_fn) else fig_or_fn
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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502 # extract feature name
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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503 feature = k.split("__", 1)[1]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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504 title = f"Partial Dependence for {feature}"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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505 feature_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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506 f"<h2>{title}</h2>" + add_plot_to_html(fig) + add_hr_to_html()
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a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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507 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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508 # 7) Assemble final HTML (three tabs)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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509 html = get_html_template()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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510 html += "<h1>Tabular Learner Model Report</h1>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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511 html += build_tabbed_html(summary_html, test_html, feature_html)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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512 html += get_feature_metrics_help_modal()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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513 html += get_html_closing()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
514
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
515 # 8) Write out
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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516 (Path(self.output_dir) / "comparison_result.html").write_text(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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517 html, encoding="utf-8"
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a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
518 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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519 LOG.info(f"HTML report generated at: {self.output_dir}/comparison_result.html")
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
520
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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521 def save_dashboard(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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522 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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523
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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524 def generate_plots_explainer(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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525 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
526
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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527 def generate_tree_plots(self):
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528 from sklearn.ensemble import RandomForestClassifier, RandomForestRegressor
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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529 from xgboost import XGBClassifier, XGBRegressor
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
530 from explainerdashboard.explainers import RandomForestExplainer
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
531
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
532 LOG.info("Generating tree plots")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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533 X_test = self.exp.X_test_transformed.copy()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
534 y_test = self.exp.y_test_transformed
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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535
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
536 if isinstance(self.best_model, (RandomForestClassifier, RandomForestRegressor)):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
537 n_trees = self.best_model.n_estimators
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
538 elif isinstance(self.best_model, (XGBClassifier, XGBRegressor)):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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539 n_trees = len(self.best_model.get_booster().get_dump())
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a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff changeset
540 else:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
541 LOG.warning("Tree plots not supported for this model type.")
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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542 return
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
543
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
544 explainer = RandomForestExplainer(self.best_model, X_test, y_test)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
545 for i in range(n_trees):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
546 fig = explainer.decisiontree_encoded(tree_idx=i, index=0)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
547 self.trees.append(fig)
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
548
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
549 def run(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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550 self.load_data()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
551 self.setup_pycaret()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
552 self.train_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
553 self.save_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
554 self.generate_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
555 self.generate_plots_explainer()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
556 self.generate_tree_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
557 self.save_html_report()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
558 # self.save_dashboard()