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annotate plotly_plots.py @ 17:db9be962dc13 draft

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
author goeckslab
date Wed, 10 Dec 2025 00:24:13 +0000
parents d17e3a1b8659
children
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85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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1 import json
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2 from pathlib import Path
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85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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3 from typing import Dict, List, Optional
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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4
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5 import numpy as np
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6 import pandas as pd
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85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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7 import plotly.graph_objects as go
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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8 import plotly.io as pio
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9 from constants import LABEL_COLUMN_NAME, SPLIT_COLUMN_NAME
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10 from sklearn.metrics import (
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11 accuracy_score,
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12 auc,
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13 average_precision_score,
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14 f1_score,
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15 precision_recall_curve,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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16 precision_score,
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17 recall_score,
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18 roc_curve,
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19 )
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20 from sklearn.preprocessing import label_binarize
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23 def _style_fig(fig: go.Figure, font_size: int = 12) -> go.Figure:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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24 """Apply consistent styling across Plotly figures."""
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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25 fig.update_layout(
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26 font=dict(size=font_size),
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27 plot_bgcolor="#ffffff",
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28 paper_bgcolor="#ffffff",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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29 )
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30 fig.update_xaxes(gridcolor="#e8e8e8")
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31 fig.update_yaxes(gridcolor="#e8e8e8")
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32 return fig
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34
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35 def _fig_to_html(
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36 fig: go.Figure, *, include_js: bool = False, config: Optional[dict] = None
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37 ) -> str:
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38 """Render a Plotly figure to a lightweight HTML fragment."""
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39 include_plotlyjs = "cdn" if include_js else False
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40 return pio.to_html(
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41 fig,
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42 full_html=False,
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43 include_plotlyjs=include_plotlyjs,
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44 config=config,
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45 )
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47
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48 def _wrap_plot(
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49 title: str,
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50 fig: go.Figure,
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51 *,
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52 include_js: bool = False,
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53 config: Optional[dict] = None,
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54 ) -> Dict[str, str]:
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55 """Package a figure with its title for downstream HTML rendering."""
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56 return {"title": title, "html": _fig_to_html(fig, include_js=include_js, config=config)}
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57
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58
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59 def _line_chart(
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60 traces: List[tuple],
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61 *,
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62 title: str,
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63 yaxis_title: str,
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64 ) -> go.Figure:
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65 """Build a basic epoch-indexed line chart for train/val/test curves."""
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66 fig = go.Figure()
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67 for name, series in traces:
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68 if not series:
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69 continue
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70 epochs = list(range(1, len(series) + 1))
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71 fig.add_trace(
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72 go.Scatter(
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73 x=epochs,
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74 y=series,
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75 mode="lines+markers",
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76 name=name,
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77 line=dict(width=4),
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78 )
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79 )
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80
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81 fig.update_layout(
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82 title=dict(text=title, x=0.5),
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83 xaxis_title="Epoch",
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84 yaxis_title=yaxis_title,
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85 width=760,
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86 height=520,
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87 hovermode="x unified",
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88 )
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89 _style_fig(fig)
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90 return fig
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91
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92
15
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93 def _labels_from_metadata_dict(meta_dict: dict) -> List[str]:
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94 """Extract ordered label names from Ludwig train_set_metadata."""
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95 if not isinstance(meta_dict, dict):
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96 return []
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97
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98 for key in ("idx2str", "idx2label", "vocab"):
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99 seq = meta_dict.get(key)
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100 if isinstance(seq, list) and seq:
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101 return [str(v) for v in seq]
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102
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103 str2idx = meta_dict.get("str2idx")
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104 if isinstance(str2idx, dict) and str2idx:
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105 int_indices = [v for v in str2idx.values() if isinstance(v, int)]
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106 if int_indices:
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107 max_idx = max(int_indices)
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108 ordered = [None] * (max_idx + 1)
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109 for name, idx in str2idx.items():
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110 if isinstance(idx, int) and 0 <= idx < len(ordered):
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111 ordered[idx] = name
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112 return [str(v) for v in ordered if v is not None]
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113
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114 return []
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115
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116
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117 def _resolve_confusion_labels(
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118 label_stats: dict,
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119 n_classes: int,
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120 metadata_csv_path: Optional[str],
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121 train_set_metadata_path: Optional[str],
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122 ) -> List[str]:
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123 """Prefer original labels from metadata; fall back to stats if unavailable."""
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124 if train_set_metadata_path:
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125 try:
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126 meta_path = Path(train_set_metadata_path)
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127 if meta_path.exists():
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128 with open(meta_path, "r") as f:
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129 meta_json = json.load(f)
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130 label_meta = meta_json.get(LABEL_COLUMN_NAME)
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131 if not isinstance(label_meta, dict):
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132 label_meta = next(
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133 (
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134 v
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135 for v in meta_json.values()
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136 if isinstance(v, dict)
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137 and any(k in v for k in ("idx2str", "str2idx", "idx2label", "vocab"))
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138 ),
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139 None,
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140 )
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141 labels_from_meta = _labels_from_metadata_dict(label_meta) if label_meta else []
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142 if labels_from_meta and len(labels_from_meta) >= n_classes:
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143 return [str(label) for label in labels_from_meta[:n_classes]]
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144 except Exception as exc:
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145 print(f"Warning: Unable to read labels from train_set_metadata: {exc}")
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146
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147 if metadata_csv_path:
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148 try:
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149 csv_path = Path(metadata_csv_path)
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150 if csv_path.exists():
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151 df_meta = pd.read_csv(csv_path)
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152 if LABEL_COLUMN_NAME in df_meta.columns:
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153 uniques = df_meta[LABEL_COLUMN_NAME].dropna().unique().tolist()
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154 if uniques and len(uniques) >= n_classes:
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155 return [str(u) for u in uniques[:n_classes]]
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156 except Exception as exc:
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157 print(f"Warning: Unable to read labels from metadata CSV: {exc}")
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158
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159 pcs = label_stats.get("per_class_stats", {})
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160 if pcs:
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161 pcs_labels = [str(k) for k in pcs.keys()]
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162 if len(pcs_labels) >= n_classes:
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163 return pcs_labels[:n_classes]
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164
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165 labels = label_stats.get("labels")
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166 if not labels:
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167 labels = [str(i) for i in range(n_classes)]
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168 if len(labels) < n_classes:
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169 labels = labels + [str(i) for i in range(len(labels), n_classes)]
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170 return [str(label) for label in labels[:n_classes]]
8
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171
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172
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173 def build_classification_plots(
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174 test_stats_path: str,
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175 training_stats_path: Optional[str] = None,
15
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176 metadata_csv_path: Optional[str] = None,
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177 train_set_metadata_path: Optional[str] = None,
17
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178 threshold: Optional[float] = None,
8
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179 ) -> List[Dict[str, str]]:
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180 """
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181 Read Ludwig’s test_statistics.json and build three interactive Plotly panels:
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182 - Confusion Matrix
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183 - ROC-AUC
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184 - Classification Report Heatmap
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185
15
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186 If metadata paths are provided, the confusion matrix axes will use the original
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187 label values from the training metadata rather than integer-encoded labels.
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188
8
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189 Returns a list of dicts, each with:
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190 {
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191 "title": <plot title>,
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192 "html": <HTML fragment for embedding>
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193 }
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194 """
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195 # --- Load test stats ---
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196 with open(test_stats_path, "r") as f:
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197 test_stats = json.load(f)
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198 label_stats = test_stats["label"]
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199
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200 # common sizing
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201 cell = 40
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202 n_classes = len(label_stats["confusion_matrix"])
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203 side_px = max(cell * n_classes + 200, 600)
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204 common_cfg = {"displayModeBar": True, "scrollZoom": True}
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205
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206 plots: List[Dict[str, str]] = []
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207
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208 # 0) Confusion Matrix
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209 cm = np.array(label_stats["confusion_matrix"], dtype=int)
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210 labels = _resolve_confusion_labels(
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211 label_stats,
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212 n_classes,
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213 metadata_csv_path=metadata_csv_path,
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214 train_set_metadata_path=train_set_metadata_path,
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215 )
8
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216 total = cm.sum()
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217
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218 fig_cm = go.Figure(
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219 go.Heatmap(
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220 z=cm,
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221 x=labels,
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222 y=labels,
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223 colorscale="Blues",
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224 showscale=True,
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225 colorbar=dict(title="Count"),
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226 )
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227 )
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228 fig_cm.update_traces(xgap=2, ygap=2)
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229 cm_title = "Confusion Matrix"
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230 if threshold is not None:
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231 cm_title = f"Confusion Matrix (Threshold: {threshold})"
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232 fig_cm.update_layout(
17
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233 title=dict(text=cm_title, x=0.5),
8
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234 xaxis_title="Predicted",
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235 yaxis_title="Observed",
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236 yaxis_autorange="reversed",
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237 width=side_px,
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238 height=side_px,
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239 margin=dict(t=100, l=80, r=80, b=80),
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240 )
15
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241 _style_fig(fig_cm)
8
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242
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243 # annotate counts and percentages
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244 mval = cm.max() if cm.size else 0
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245 thresh = mval / 2
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246 for i in range(cm.shape[0]):
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247 for j in range(cm.shape[1]):
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248 v = cm[i, j]
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249 pct = (v / total * 100) if total > 0 else 0
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250 color = "white" if v > thresh else "black"
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251 fig_cm.add_annotation(
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252 x=labels[j],
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253 y=labels[i],
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254 text=f"<b>{v}</b>",
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255 showarrow=False,
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256 font=dict(color=color, size=14),
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257 xanchor="center",
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258 yanchor="bottom",
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259 yshift=2,
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260 )
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261 fig_cm.add_annotation(
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262 x=labels[j],
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263 y=labels[i],
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264 text=f"{pct:.1f}%",
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265 showarrow=False,
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266 font=dict(color=color, size=13),
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267 xanchor="center",
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268 yanchor="top",
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269 yshift=-2,
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270 )
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271
17
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272 plots.append(
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273 _wrap_plot("Confusion Matrix", fig_cm, include_js=True, config=common_cfg)
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274 )
8
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275
17
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276 # 1) ROC / PR curves only for binary tasks
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277 if n_classes == 2:
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278 roc_plot = _build_static_roc_plot(label_stats, common_cfg, friendly_labels=labels)
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279 if roc_plot:
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280 plots.append(roc_plot)
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281
17
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282 pr_plot = _build_precision_recall_plot(label_stats, common_cfg)
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283 if pr_plot:
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284 plots.append(pr_plot)
15
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285
8
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286 # 2) Classification Report Heatmap
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287 pcs = label_stats.get("per_class_stats", {})
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288 if pcs:
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289 classes = list(pcs.keys())
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290 metrics = [
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291 "precision",
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292 "recall",
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293 "f1_score",
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294 "accuracy",
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295 "matthews_correlation_coefficient",
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296 "specificity",
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297 ]
8
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298 z, txt = [], []
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299 for c in classes:
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300 row, trow = [], []
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301 for m in metrics:
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302 val = pcs[c].get(m, 0)
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303 row.append(val)
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304 trow.append(f"{val:.2f}")
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305 z.append(row)
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306 txt.append(trow)
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307
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308 fig_cr = go.Figure(
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309 go.Heatmap(
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310 z=z,
15
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311 x=[m.replace("_", " ") for m in metrics],
8
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312 y=[str(c) for c in classes],
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313 text=txt,
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314 texttemplate="%{text}",
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315 colorscale="Reds",
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316 showscale=True,
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317 colorbar=dict(title="Value"),
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318 )
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319 )
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320 fig_cr.update_layout(
15
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321 title="Per-Class metrics",
8
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322 xaxis_title="",
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323 yaxis_title="Class",
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324 width=side_px,
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325 height=side_px,
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326 margin=dict(t=80, l=80, r=80, b=80),
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327 )
15
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328 _style_fig(fig_cr)
17
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329 plots.append(
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330 _wrap_plot("Per-Class metrics", fig_cr, config=common_cfg)
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331 )
8
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332
15
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333 # 3) Prediction Diagnostics (from predictions.csv)
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334 # Note: appended separately in generate_html_report, not returned here.
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335
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336 return plots
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337
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338
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339 def build_train_validation_plots(train_stats_path: str) -> List[Dict[str, str]]:
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340 """Generate Train/Validation learning curve plots from training_statistics.json."""
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341 if not train_stats_path or not Path(train_stats_path).exists():
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342 return []
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343 try:
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344 with open(train_stats_path, "r") as f:
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345 train_stats = json.load(f)
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346 except Exception as exc:
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347 print(f"Warning: Unable to read training statistics: {exc}")
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348 return []
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349
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350 label_train = (train_stats.get("training") or {}).get("label", {})
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351 label_val = (train_stats.get("validation") or {}).get("label", {})
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352 if not label_train and not label_val:
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353 return []
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354 plots: List[Dict[str, str]] = []
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355 include_js = True # Load Plotly.js once for this group
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356
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357 def _get_series(stats: dict, metric: str) -> List[float]:
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358 vals = stats.get(metric, [])
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359 if isinstance(vals, list):
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360 return [float(v) for v in vals]
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361 try:
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362 return [float(vals)]
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363 except Exception:
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364 return []
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365
17
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366 metric_specs = [
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367 ("loss", "Loss across epochs", "Loss"),
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368 ("accuracy", "Accuracy across epochs", "Accuracy"),
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369 ("roc_auc", "ROC-AUC across epochs", "ROC-AUC"),
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370 ("precision", "Precision across epochs", "Precision"),
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371 ("recall", "Recall/Sensitivity across epochs", "Recall"),
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372 ("specificity", "Specificity across epochs", "Specificity"),
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373 ]
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diff changeset
374
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375 for key, title, yaxis in metric_specs:
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376 train_series = _get_series(label_train, key)
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377 val_series = _get_series(label_val, key)
15
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378 if not train_series and not val_series:
17
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diff changeset
379 continue
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380 fig = _line_chart(
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381 [("Train", train_series), ("Validation", val_series)],
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382 title=title,
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383 yaxis_title=yaxis,
15
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diff changeset
384 )
17
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385 plots.append(_wrap_plot(title, fig, include_js=include_js))
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diff changeset
386 include_js = False
15
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387
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388 # Precision vs Recall evolution (validation)
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389 val_prec = _get_series(label_val, "precision")
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390 val_rec = _get_series(label_val, "recall")
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391 if val_prec and val_rec:
17
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392 max_len = min(len(val_prec), len(val_rec))
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393 fig_pr = _line_chart(
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394 [
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395 ("Precision", val_prec[:max_len]),
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396 ("Recall", val_rec[:max_len]),
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397 ],
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398 title="Validation Precision and Recall by Epoch",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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399 yaxis_title="Value",
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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400 )
17
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401 plots.append(_wrap_plot("Precision vs Recall Evolution", fig_pr, include_js=include_js))
15
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402 include_js = False
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403
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404 def _compute_f1(p: List[float], r: List[float]) -> List[float]:
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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405 return [
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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406 0.0 if (prec + rec) == 0 else 2 * prec * rec / (prec + rec)
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407 for prec, rec in zip(p, r)
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408 ]
15
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409
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410 f1_train = _compute_f1(_get_series(label_train, "precision"), _get_series(label_train, "recall"))
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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411 f1_val = _compute_f1(val_prec, val_rec)
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412 if f1_train or f1_val:
17
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413 fig_f1 = _line_chart(
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414 [("Train", f1_train), ("Validation", f1_val)],
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415 title="F1-Score across epochs (derived)",
15
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416 yaxis_title="F1-Score",
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417 )
17
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418 plots.append(_wrap_plot("F1-Score across epochs (derived)", fig_f1, include_js=include_js))
15
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419 include_js = False
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420
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421 # Overfitting Gap: Train vs Val ROC-AUC (gap)
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422 roc_train = _get_series(label_train, "roc_auc")
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423 roc_val = _get_series(label_val, "roc_auc")
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424 if roc_train and roc_val:
17
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425 max_len = min(len(roc_train), len(roc_val))
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426 gaps = [t - v for t, v in zip(roc_train[:max_len], roc_val[:max_len])]
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427 fig_gap = _line_chart(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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428 [("Train - Val ROC-AUC", gaps)],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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429 title="Overfitting gap: ROC-AUC across epochs",
15
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430 yaxis_title="Gap",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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431 )
17
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432 plots.append(_wrap_plot("Overfitting gap: ROC-AUC across epochs", fig_gap, include_js=include_js))
15
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433 include_js = False
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434
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435 # Best Epoch Dashboard (based on max val ROC-AUC)
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436 if roc_val:
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437 best_idx = int(np.argmax(roc_val))
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438 best_epoch = best_idx + 1
17
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439 metrics_at_best: Dict[str, Optional[float]] = {
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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440 "ROC-AUC": roc_val[best_idx] if best_idx < len(roc_val) else None
15
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441 }
17
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diff changeset
442
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443 for metric_key, label in [
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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444 ("accuracy", "Accuracy"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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445 ("balanced_accuracy", "Balanced Accuracy"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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446 ("precision", "Precision"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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447 ("recall", "Recall"),
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448 ("specificity", "Specificity"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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449 ("loss", "Loss"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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450 ]:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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451 series = _get_series(label_val, metric_key)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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452 if series and best_idx < len(series):
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453 metrics_at_best[label] = series[best_idx]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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454
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455 if f1_val and best_idx < len(f1_val):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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456 metrics_at_best["F1-Score (derived)"] = f1_val[best_idx]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
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457
15
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458 fig_best = go.Figure()
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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459 for name, value in metrics_at_best.items():
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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460 if value is not None:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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461 fig_best.add_trace(go.Bar(name=name, x=[name], y=[value]))
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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462 fig_best.update_layout(
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463 title=dict(text=f"Best Epoch Dashboard (Val ROC-AUC @ epoch {best_epoch})", x=0.5),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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464 xaxis_title="Metric",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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465 yaxis_title="Value",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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466 width=760,
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467 height=520,
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468 showlegend=False,
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diff changeset
469 )
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470 _style_fig(fig_best)
17
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471 plots.append(_wrap_plot("Best Validation Epoch Snapshot (Metrics)", fig_best, include_js=include_js))
15
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diff changeset
472
8
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473 return plots
11
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474
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475
15
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476 def _get_regression_series(split_stats: dict, metric: str) -> List[float]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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477 if metric not in split_stats:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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478 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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479 vals = split_stats.get(metric, [])
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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480 if isinstance(vals, list):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
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diff changeset
481 return [float(v) for v in vals]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
482 try:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
483 return [float(vals)]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
484 except Exception:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
485 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
486
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
487
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
488 def _regression_line_plot(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
489 train_split: dict,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
490 val_split: dict,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
491 metric_key: str,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
492 title: str,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
493 yaxis_title: str,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
494 include_js: bool,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
495 ) -> Optional[Dict[str, str]]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
496 train_series = _get_regression_series(train_split, metric_key)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
497 val_series = _get_regression_series(val_split, metric_key)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
498 if not train_series and not val_series:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
499 return None
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
500
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
501 fig = _line_chart(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
502 [("Train", train_series), ("Validation", val_series)],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
503 title=title,
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
504 yaxis_title=yaxis_title,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
505 )
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
506 return _wrap_plot(title, fig, include_js=include_js)
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
507
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
508
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
509 def build_regression_train_val_plots(train_stats_path: str) -> List[Dict[str, str]]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
510 """Generate regression Train/Validation learning curve plots from training_statistics.json."""
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
511 if not train_stats_path or not Path(train_stats_path).exists():
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
512 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
513 try:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
514 with open(train_stats_path, "r") as f:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
515 train_stats = json.load(f)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
516 except Exception as exc:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
517 print(f"Warning: Unable to read training statistics: {exc}")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
518 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
519
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
520 label_train = (train_stats.get("training") or {}).get("label", {})
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
521 label_val = (train_stats.get("validation") or {}).get("label", {})
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
522 if not label_train and not label_val:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
523 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
524
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
525 plots: List[Dict[str, str]] = []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
526 include_js = True
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
527 for metric_key, title, ytitle in [
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
528 ("mean_absolute_error", "Mean Absolute Error across epochs", "MAE"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
529 ("root_mean_squared_error", "Root Mean Squared Error across epochs", "RMSE"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
530 ("mean_absolute_percentage_error", "Mean Absolute Percentage Error across epochs", "MAPE"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
531 ("r2", "R² across epochs", "R²"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
532 ("loss", "Loss across epochs", "Loss"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
533 ]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
534 plot = _regression_line_plot(label_train, label_val, metric_key, title, ytitle, include_js)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
535 if plot:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
536 plots.append(plot)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
537 include_js = False
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
538 return plots
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
539
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
540
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
541 def build_regression_test_plots(train_stats_path: str) -> List[Dict[str, str]]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
542 """Generate regression Test learning curves from training_statistics.json."""
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
543 if not train_stats_path or not Path(train_stats_path).exists():
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
544 return []
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
545 try:
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
546 with open(train_stats_path, "r") as f:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
547 train_stats = json.load(f)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
548 except Exception as exc:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
549 print(f"Warning: Unable to read training statistics: {exc}")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
550 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
551
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
552 label_test = (train_stats.get("test") or {}).get("label", {})
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
553 if not label_test:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
554 return []
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
555
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
556 plots: List[Dict[str, str]] = []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
557 include_js = True
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
558 metrics = [
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
559 ("mean_absolute_error", "Mean Absolute Error Across Epochs", "MAE"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
560 ("root_mean_squared_error", "Root Mean Squared Error Across Epochs", "RMSE"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
561 ("mean_absolute_percentage_error", "Mean Absolute Percentage Error Across Epochs", "MAPE"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
562 ("r2", "R² Across Epochs", "R²"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
563 ("loss", "Loss Across Epochs", "Loss"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
564 ]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
565 for metric_key, title, ytitle in metrics:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
566 series = _get_regression_series(label_test, metric_key)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
567 if not series:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
568 continue
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
569 fig = _line_chart(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
570 [("Test", series)],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
571 title=title,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
572 yaxis_title=ytitle,
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
573 )
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
574 plots.append(_wrap_plot(title, fig, include_js=include_js))
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
575 include_js = False
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
576 return plots
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
577
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
578
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
579 def _build_static_roc_plot(
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
580 label_stats: dict,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
581 config: dict,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
582 friendly_labels: Optional[List[str]] = None,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
583 threshold: Optional[float] = None,
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
584 ) -> Optional[Dict[str, str]]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
585 """Build ROC curve directly from test_statistics.json (single curve)."""
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
586 roc_data = label_stats.get("roc_curve")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
587 if not isinstance(roc_data, dict):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
588 return None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
589
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
590 fpr = roc_data.get("false_positive_rate")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
591 tpr = roc_data.get("true_positive_rate")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
592 if not fpr or not tpr or len(fpr) != len(tpr):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
593 return None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
594
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
595 try:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
596 fig = go.Figure()
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
597 fig.add_trace(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
598 go.Scatter(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
599 x=fpr,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
600 y=tpr,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
601 mode="lines+markers",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
602 name="ROC Curve",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
603 line=dict(color="#1f77b4", width=4),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
604 hovertemplate="FPR: %{x:.3f}<br>TPR: %{y:.3f}<extra></extra>",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
605 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
606 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
607 fig.add_trace(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
608 go.Scatter(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
609 x=[0, 1],
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
610 y=[0, 1],
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
611 mode="lines",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
612 name="Random Classifier",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
613 line=dict(color="gray", width=2, dash="dash"),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
614 hovertemplate="Random Classifier<extra></extra>",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
615 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
616 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
617
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
618 auc_val = label_stats.get("roc_auc") or label_stats.get("roc_auc_macro") or label_stats.get("roc_auc_micro")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
619 auc_txt = f" (AUC = {auc_val:.3f})" if isinstance(auc_val, (int, float)) else ""
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
620
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
621 # Determine which label is treated as positive for the curve
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
622 label_list: List = []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
623 pcs = label_stats.get("per_class_stats", {})
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
624 if pcs:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
625 label_list = list(pcs.keys())
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
626 if not label_list:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
627 labels_from_stats = label_stats.get("labels")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
628 if isinstance(labels_from_stats, list):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
629 label_list = labels_from_stats
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
630
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
631 # Try to resolve index of the positive label explicitly provided by Ludwig
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
632 pos_label_raw = (
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
633 roc_data.get("positive_label")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
634 or roc_data.get("positive_class")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
635 or label_stats.get("positive_label")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
636 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
637 pos_label_idx = None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
638 if pos_label_raw is not None and isinstance(label_list, list):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
639 try:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
640 pos_label_idx = label_list.index(pos_label_raw)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
641 except ValueError:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
642 pos_label_idx = None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
643
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
644 # Fallback: use the second label if available, otherwise the first
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
645 if pos_label_idx is None:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
646 if isinstance(label_list, list) and len(label_list) >= 2:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
647 pos_label_idx = 1
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
648 elif isinstance(label_list, list) and label_list:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
649 pos_label_idx = 0
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
650
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
651 if pos_label_raw is None and isinstance(label_list, list) and pos_label_idx is not None:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
652 pos_label_raw = label_list[pos_label_idx]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
653
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
654 # Map to friendly label if we have one from metadata/CSV
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
655 pos_label_display = pos_label_raw
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
656 if (
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
657 friendly_labels
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
658 and isinstance(pos_label_idx, int)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
659 and 0 <= pos_label_idx < len(friendly_labels)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
660 ):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
661 pos_label_display = friendly_labels[pos_label_idx]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
662
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
663 pos_label_txt = (
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
664 f"Positive class: {pos_label_display}"
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
665 if pos_label_display is not None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
666 else "Positive class: (not available)"
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
667 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
668
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
669 title_label = f"ROC Curve{auc_txt}"
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
670 if pos_label_display is not None:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
671 title_label = f"ROC Curve (Positive Class: {pos_label_display}){auc_txt}"
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
672
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
673 fig.update_layout(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
674 title=dict(text=title_label, x=0.5),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
675 xaxis_title="False Positive Rate",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
676 yaxis_title="True Positive Rate",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
677 width=700,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
678 height=600,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
679 margin=dict(t=80, l=80, r=80, b=110),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
680 hovermode="closest",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
681 legend=dict(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
682 x=0.6,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
683 y=0.1,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
684 bgcolor="rgba(255,255,255,0.9)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
685 bordercolor="rgba(0,0,0,0.2)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
686 borderwidth=1,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
687 ),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
688 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
689 _style_fig(fig)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
690 fig.update_xaxes(range=[0, 1.0])
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
691 fig.update_yaxes(range=[0, 1.05])
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
692
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
693 roc_thresholds = roc_data.get("thresholds")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
694 if threshold is not None and isinstance(roc_thresholds, list) and len(roc_thresholds) == len(fpr):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
695 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
696 diffs = [abs(th - threshold) for th in roc_thresholds]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
697 best_idx = int(np.argmin(diffs))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
698 # dashed guides through the chosen point
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
699 fig.add_shape(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
700 type="line",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
701 x0=fpr[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
702 x1=fpr[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
703 y0=0,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
704 y1=tpr[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
705 line=dict(color="gray", width=2, dash="dash"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
706 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
707 fig.add_shape(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
708 type="line",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
709 x0=0,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
710 x1=fpr[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
711 y0=tpr[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
712 y1=tpr[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
713 line=dict(color="gray", width=2, dash="dash"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
714 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
715 fig.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
716 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
717 x=[fpr[best_idx]],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
718 y=[tpr[best_idx]],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
719 mode="markers",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
720 marker=dict(color="black", size=10, symbol="x"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
721 name=f"Threshold={threshold}",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
722 hovertemplate="FPR: %{x:.3f}<br>TPR: %{y:.3f}<br>Threshold: %{text}<extra></extra>",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
723 text=[f"{threshold}"],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
724 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
725 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
726 except Exception as exc:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
727 print(f"Warning: could not add threshold marker to ROC: {exc}")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
728
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
729 fig.add_annotation(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
730 x=0.5,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
731 y=-0.15,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
732 xref="paper",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
733 yref="paper",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
734 showarrow=False,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
735 text=f"<span style='font-size:12px;color:#555;'>{pos_label_txt}</span>",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
736 xanchor="center",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
737 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
738
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
739 return _wrap_plot("ROC Curve", fig, config=config)
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
740 except Exception as e:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
741 print(f"Error building ROC plot: {e}")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
742 return None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
743
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
744
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
745 def _build_precision_recall_plot(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
746 label_stats: dict,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
747 config: dict,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
748 threshold: Optional[float] = None,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
749 ) -> Optional[Dict[str, str]]:
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
750 """Build Precision-Recall curve directly from test_statistics.json."""
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
751 pr_data = label_stats.get("precision_recall_curve")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
752 if not isinstance(pr_data, dict):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
753 return None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
754
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
755 precisions = pr_data.get("precisions")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
756 recalls = pr_data.get("recalls")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
757 if not precisions or not recalls or len(precisions) != len(recalls):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
758 return None
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
759
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
760 thresholds = pr_data.get("thresholds")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
761
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
762 try:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
763 fig = go.Figure()
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
764 fig.add_trace(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
765 go.Scatter(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
766 x=recalls,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
767 y=precisions,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
768 mode="lines+markers",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
769 name="Precision-Recall",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
770 line=dict(color="#d62728", width=4),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
771 hovertemplate="Recall: %{x:.3f}<br>Precision: %{y:.3f}<extra></extra>",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
772 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
773 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
774
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
775 ap_val = (
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
776 label_stats.get("average_precision_macro")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
777 or label_stats.get("average_precision_micro")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
778 or label_stats.get("average_precision_samples")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
779 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
780 ap_txt = f" (AP = {ap_val:.3f})" if isinstance(ap_val, (int, float)) else ""
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
781
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
782 fig.update_layout(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
783 title=dict(text=f"Precision-Recall Curve{ap_txt}", x=0.5),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
784 xaxis_title="Recall",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
785 yaxis_title="Precision",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
786 width=700,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
787 height=600,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
788 margin=dict(t=80, l=80, r=80, b=80),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
789 hovermode="closest",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
790 legend=dict(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
791 x=0.6,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
792 y=0.1,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
793 bgcolor="rgba(255,255,255,0.9)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
794 bordercolor="rgba(0,0,0,0.2)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
795 borderwidth=1,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
796 ),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
797 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
798 _style_fig(fig)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
799 fig.update_xaxes(range=[0, 1.0])
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
800 fig.update_yaxes(range=[0, 1.05])
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
801
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
802 if threshold is not None and isinstance(thresholds, list) and len(thresholds) == len(recalls):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
803 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
804 diffs = [abs(th - threshold) for th in thresholds]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
805 best_idx = int(np.argmin(diffs))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
806 fig.add_shape(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
807 type="line",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
808 x0=recalls[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
809 x1=recalls[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
810 y0=0,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
811 y1=precisions[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
812 line=dict(color="gray", width=2, dash="dash"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
813 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
814 fig.add_shape(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
815 type="line",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
816 x0=0,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
817 x1=recalls[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
818 y0=precisions[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
819 y1=precisions[best_idx],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
820 line=dict(color="gray", width=2, dash="dash"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
821 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
822 fig.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
823 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
824 x=[recalls[best_idx]],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
825 y=[precisions[best_idx]],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
826 mode="markers",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
827 marker=dict(color="black", size=10, symbol="x"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
828 name=f"Threshold={threshold}",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
829 hovertemplate="Recall: %{x:.3f}<br>Precision: %{y:.3f}<br>Threshold: %{text}<extra></extra>",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
830 text=[f"{threshold}"],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
831 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
832 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
833 except Exception as exc:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
834 print(f"Warning: could not add threshold marker to PR: {exc}")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
835
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
836 return _wrap_plot("Precision-Recall Curve", fig, config=config)
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
837 except Exception as e:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
838 print(f"Error building Precision-Recall plot: {e}")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
839 return None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
840
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
841
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
842 def build_prediction_diagnostics(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
843 predictions_path: str,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
844 label_data_path: Optional[str] = None,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
845 split_value: int = 2,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
846 ) -> List[Dict[str, str]]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
847 """Generate diagnostic plots from predictions.csv for classification tasks."""
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
848 preds_file = Path(predictions_path)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
849 if not preds_file.exists():
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
850 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
851
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
852 try:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
853 df_pred = pd.read_csv(predictions_path)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
854 except Exception as exc:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
855 print(f"Warning: Unable to read predictions CSV: {exc}")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
856 return []
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
857
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
858 plots: List[Dict[str, str]] = []
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
859 labels_from_dataset: Optional[pd.Series] = None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
860
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
861 filtered_by_split = False
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
862
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
863 # If a split column exists, focus on the requested split (e.g., validation=1, test=2).
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
864 # If not, but label_data_path is available and matches row count, use it to filter predictions.
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
865 if SPLIT_COLUMN_NAME in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
866 df_pred = df_pred[df_pred[SPLIT_COLUMN_NAME] == split_value].reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
867 if df_pred.empty:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
868 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
869 filtered_by_split = True
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
870 elif label_data_path and Path(label_data_path).exists():
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
871 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
872 df_labels_all = pd.read_csv(label_data_path)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
873 if SPLIT_COLUMN_NAME in df_labels_all.columns and len(df_labels_all) == len(df_pred):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
874 split_mask = pd.to_numeric(df_labels_all[SPLIT_COLUMN_NAME], errors="coerce") == split_value
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
875 labels_from_dataset = df_labels_all.loc[split_mask, LABEL_COLUMN_NAME].reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
876 df_pred = df_pred.loc[split_mask].reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
877 if df_pred.empty:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
878 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
879 filtered_by_split = True
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
880 except Exception as exc:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
881 print(f"Warning: Unable to filter predictions by split from label data: {exc}")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
882
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
883 # Fallback: no split info available. Assume the predictions file is already filtered
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
884 # (common for test-only exports) and avoid heuristic slicing that could discard rows.
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
885 if not filtered_by_split:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
886 if split_value != 2:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
887 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
888
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
889 def _strip_prob_prefix(col: str) -> str:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
890 if col.startswith("label_probabilities_"):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
891 return col.replace("label_probabilities_", "")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
892 if col.startswith("probabilities_"):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
893 return col.replace("probabilities_", "")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
894 return col
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
895
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
896 def _maybe_expand_probabilities_column(df: pd.DataFrame, labels_guess: List[str]) -> List[str]:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
897 """If only a single 'probabilities' column exists (list-like), expand it into per-class columns."""
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
898 if "probabilities" not in df.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
899 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
900 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
901 # Parse first non-null entry to infer length
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
902 first_val = df["probabilities"].dropna().iloc[0]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
903 parsed = first_val
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
904 if isinstance(first_val, str):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
905 parsed = json.loads(first_val)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
906 probs = list(parsed)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
907 n = len(probs)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
908 if n == 0:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
909 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
910 # Build labels: prefer provided guess; otherwise numeric
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
911 if labels_guess and len(labels_guess) == n:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
912 labels_use = labels_guess
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
913 else:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
914 labels_use = [str(i) for i in range(n)]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
915 # Expand column
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
916 for idx, lbl in enumerate(labels_use):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
917 df[f"probabilities_{lbl}"] = df["probabilities"].apply(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
918 lambda v: (json.loads(v)[idx] if isinstance(v, str) else list(v)[idx]) if pd.notnull(v) else np.nan
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
919 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
920 return [f"probabilities_{lbl}" for lbl in labels_use]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
921 except Exception:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
922 return []
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
923
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
924 # Identify probability columns
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
925 prob_cols = [
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
926 c
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
927 for c in df_pred.columns
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
928 if (
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
929 (c.startswith("label_probabilities_") or c.startswith("probabilities_"))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
930 and c != "label_probabilities"
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
931 )
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
932 ]
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
933 if not prob_cols and "label_probability" in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
934 prob_cols = ["label_probability"]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
935 if not prob_cols and "probability" in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
936 prob_cols = ["probability"]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
937 if not prob_cols and "prediction_probability" in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
938 prob_cols = ["prediction_probability"]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
939 if not prob_cols and "probabilities" in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
940 labels_guess = sorted([str(u) for u in pd.unique(df_pred[LABEL_COLUMN_NAME])])
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
941 prob_cols = _maybe_expand_probabilities_column(df_pred, labels_guess)
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
942 prob_cols_sorted = sorted(prob_cols)
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
943
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
944 def _select_positive_prob():
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
945 if not prob_cols_sorted:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
946 return None, None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
947 # Prefer a column indicating positive/event/true/1
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
948 preferred_keys = ("event", "true", "positive", "pos", "1")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
949 for col in prob_cols_sorted:
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
950 suffix = _strip_prob_prefix(col).lower()
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
951 if any(k in suffix for k in preferred_keys):
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
952 return col, suffix
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
953 if len(prob_cols_sorted) == 2:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
954 col = prob_cols_sorted[1]
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
955 return col, _strip_prob_prefix(col)
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
956 col = prob_cols_sorted[0]
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
957 return col, _strip_prob_prefix(col)
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
958
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
959 pos_prob_col, pos_label_hint = _select_positive_prob()
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
960 pos_prob_series = df_pred[pos_prob_col] if pos_prob_col and pos_prob_col in df_pred else None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
961
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
962 # Confidence series: prefer label_probability, otherwise positive prob, otherwise max prob
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
963 confidence_series = None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
964 if "label_probability" in df_pred.columns:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
965 confidence_series = df_pred["label_probability"]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
966 elif pos_prob_series is not None:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
967 confidence_series = pos_prob_series
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
968 elif prob_cols_sorted:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
969 confidence_series = df_pred[prob_cols_sorted].max(axis=1)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
970
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
971 # True labels
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
972 def _extract_labels():
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
973 if labels_from_dataset is not None:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
974 return labels_from_dataset
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
975 candidates = [
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
976 LABEL_COLUMN_NAME,
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
977 f"{LABEL_COLUMN_NAME}_ground_truth",
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
978 f"{LABEL_COLUMN_NAME}__ground_truth",
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
979 f"{LABEL_COLUMN_NAME}_target",
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
980 f"{LABEL_COLUMN_NAME}__target",
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
981 "label",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
982 "label_true",
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
983 ]
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
984 candidates.extend(
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
985 [
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
986 col
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
987 for col in df_pred.columns
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
988 if (col.startswith(f"{LABEL_COLUMN_NAME}_") or col.startswith(f"{LABEL_COLUMN_NAME}__"))
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
989 and "probabilities" not in col
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
990 and "predictions" not in col
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
991 ]
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
992 )
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
993 for col in candidates:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
994 if col in df_pred.columns and col not in prob_cols_sorted:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
995 return df_pred[col]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
996 if label_data_path and Path(label_data_path).exists():
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
997 try:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
998 df_all = pd.read_csv(label_data_path)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
999 if SPLIT_COLUMN_NAME in df_all.columns:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1000 df_all = df_all[df_all[SPLIT_COLUMN_NAME] == split_value].reset_index(drop=True)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1001 if LABEL_COLUMN_NAME in df_all.columns:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1002 return df_all[LABEL_COLUMN_NAME].reset_index(drop=True)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1003 except Exception as exc:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1004 print(f"Warning: Unable to load labels from dataset: {exc}")
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1005 return None
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
1006
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1007 labels_series = _extract_labels()
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
1008
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1009 # Plot 1: Confidence Histogram
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1010 if confidence_series is not None:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1011 fig_conf = go.Figure()
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1012 fig_conf.add_trace(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1013 go.Histogram(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1014 x=confidence_series,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1015 nbinsx=20,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1016 marker=dict(color="#1f77b4", line=dict(color="#ffffff", width=1)),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1017 opacity=0.8,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1018 histnorm="percent",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1019 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1020 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1021 fig_conf.update_layout(
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1022 title=dict(text="Prediction Confidence Distribution", x=0.5),
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1023 xaxis_title="Predicted probability (confidence)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1024 yaxis_title="Percentage (%)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1025 bargap=0.05,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1026 width=700,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1027 height=500,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1028 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1029 _style_fig(fig_conf)
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1030 plots.append(_wrap_plot("Prediction Confidence Distribution", fig_conf))
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
1031
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1032 # The remaining plots require true labels and a positive-class probability
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1033 if labels_series is None or pos_prob_series is None:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1034 return plots
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1035
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1036 # Align lengths
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1037 min_len = min(len(labels_series), len(pos_prob_series))
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1038 if min_len == 0:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1039 return plots
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1040 y_true_raw = labels_series.iloc[:min_len]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1041 y_score = np.array(pos_prob_series.iloc[:min_len], dtype=float)
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
1042
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1043 # Determine positive label
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1044 unique_labels = pd.unique(y_true_raw)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1045 unique_labels_list = list(unique_labels)
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1046 positive_label = None
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1047 if pos_label_hint and str(pos_label_hint) in [str(u) for u in unique_labels_list]:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1048 positive_label = pos_label_hint
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1049 elif len(unique_labels_list) == 2:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1050 positive_label = unique_labels_list[1]
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1051 else:
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1052 positive_label = unique_labels_list[0]
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
1053
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1054 y_true = (y_true_raw == positive_label).astype(int).values
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
1055
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1056 # Utility: compute calibration points
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1057 def _calibration_points(y_true_bin: np.ndarray, scores: np.ndarray):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1058 bins = np.linspace(0.0, 1.0, 11)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1059 bin_ids = np.digitize(scores, bins, right=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1060 bin_centers, frac_positives = [], []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1061 for b in range(1, len(bins)):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1062 mask = bin_ids == b
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1063 if not np.any(mask):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1064 continue
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1065 bin_centers.append(scores[mask].mean())
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1066 frac_positives.append(y_true_bin[mask].mean())
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1067 return bin_centers, frac_positives
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1068
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1069 # Plot 2: Calibration Curve (multi-class aware; one-vs-rest per label)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1070 label_prob_map = {}
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1071 for col in prob_cols_sorted:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1072 if col.startswith("label_probabilities_"):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1073 cls = col.replace("label_probabilities_", "")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1074 label_prob_map[cls] = col
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1075
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1076 unique_label_strs = [str(u) for u in unique_labels_list]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1077 if len(label_prob_map) > 1 and len(unique_label_strs) > 2:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1078 # Skip multi-class calibration curve for now (not informative in current report)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1079 pass
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1080 else:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1081 # Binary/unknown fallback (previous behavior)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1082 bin_centers, frac_positives = _calibration_points(y_true, y_score)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1083 if bin_centers and frac_positives:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1084 fig_cal = go.Figure()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1085 fig_cal.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1086 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1087 x=bin_centers,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1088 y=frac_positives,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1089 mode="lines+markers",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1090 name="Calibration",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1091 line=dict(color="#2ca02c", width=4),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1092 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1093 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1094 fig_cal.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1095 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1096 x=[0, 1],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1097 y=[0, 1],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1098 mode="lines",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1099 name="Perfect Calibration",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1100 line=dict(color="gray", width=2, dash="dash"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1101 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1102 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1103 fig_cal.update_layout(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1104 title=dict(text="Calibration Curve", x=0.5),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1105 xaxis_title="Predicted probability",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1106 yaxis_title="Observed frequency",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1107 width=700,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1108 height=500,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1109 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1110 _style_fig(fig_cal)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1111 plots.append(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1112 _wrap_plot(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1113 "Calibration Curve (Predicted Probability vs Observed Frequency)",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1114 fig_cal,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1115 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1116 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1117
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1118 return plots
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1119
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1120
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1121 def build_binary_threshold_plot(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1122 predictions_path: str,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1123 label_data_path: Optional[str] = None,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1124 split_value: int = 1,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1125 ) -> Optional[Dict[str, str]]:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1126 """Build a binary threshold sweep plot (accuracy, precision, recall, F1) for a given split."""
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1127 preds_file = Path(predictions_path)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1128 if not preds_file.exists():
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1129 return None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1130
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1131 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1132 df_pred = pd.read_csv(predictions_path)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1133 except Exception as exc:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1134 print(f"Warning: Unable to read predictions CSV for threshold plot: {exc}")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1135 return None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1136
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1137 labels_from_dataset: Optional[pd.Series] = None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1138 df_full = df_pred.copy()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1139
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1140 def _filter_by_split(df: pd.DataFrame, split_val: int) -> pd.DataFrame:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1141 if SPLIT_COLUMN_NAME in df.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1142 return df[df[SPLIT_COLUMN_NAME] == split_val].reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1143 return df
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1144
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1145 # Try preferred split, then fallback to others with data (val -> test -> train)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1146 candidate_splits = [split_value, 2, 0, 1] if split_value == 1 else [split_value, 1, 0, 2]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1147 df_candidate = pd.DataFrame()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1148 used_split: Optional[int] = None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1149 for sv in candidate_splits:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1150 df_candidate = _filter_by_split(df_full, sv)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1151 if not df_candidate.empty:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1152 used_split = sv
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1153 break
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1154 if used_split is None:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1155 df_candidate = df_full
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1156 df_pred = df_candidate.reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1157
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1158 # If still empty (e.g., split column exists but no rows for candidates), fall back to all rows
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1159 if df_pred.empty:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1160 df_pred = df_full.reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1161 labels_from_dataset = None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1162
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1163 if label_data_path and Path(label_data_path).exists():
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1164 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1165 df_labels_all = pd.read_csv(label_data_path)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1166 if SPLIT_COLUMN_NAME in df_labels_all.columns and len(df_labels_all) == len(df_full):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1167 mask = (
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1168 pd.to_numeric(df_labels_all[SPLIT_COLUMN_NAME], errors="coerce") == used_split
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1169 if used_split is not None and SPLIT_COLUMN_NAME in df_labels_all.columns
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1170 else pd.Series([True] * len(df_full))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1171 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1172 labels_from_dataset = df_labels_all.loc[mask, LABEL_COLUMN_NAME].reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1173 if len(labels_from_dataset) == len(df_pred):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1174 labels_from_dataset = labels_from_dataset.reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1175 except Exception as exc:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1176 print(f"Warning: Unable to align labels for threshold plot: {exc}")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1177
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1178 # Identify probability columns
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1179 prob_cols = [
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1180 c
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1181 for c in df_pred.columns
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1182 if (
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1183 (c.startswith("label_probabilities_") or c.startswith("probabilities_"))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1184 and c != "label_probabilities"
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1185 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1186 ]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1187 if not prob_cols and "probabilities" in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1188 labels_guess = sorted([str(u) for u in pd.unique(df_pred.get(LABEL_COLUMN_NAME, []))])
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1189 # reuse expansion logic from diagnostics
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1190 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1191 first_val = df_pred["probabilities"].dropna().iloc[0]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1192 parsed = json.loads(first_val) if isinstance(first_val, str) else list(first_val)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1193 n = len(parsed)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1194 if n > 0:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1195 if labels_guess and len(labels_guess) == n:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1196 labels_use = labels_guess
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1197 else:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1198 labels_use = [str(i) for i in range(n)]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1199 for idx, lbl in enumerate(labels_use):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1200 df_pred[f"probabilities_{lbl}"] = df_pred["probabilities"].apply(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1201 lambda v: (json.loads(v)[idx] if isinstance(v, str) else list(v)[idx]) if pd.notnull(v) else np.nan
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1202 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1203 prob_cols = [f"probabilities_{lbl}" for lbl in labels_use]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1204 except Exception:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1205 prob_cols = []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1206 prob_cols_sorted = sorted(prob_cols)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1207
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1208 def _strip_prob_prefix(col: str) -> str:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1209 if col.startswith("label_probabilities_"):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1210 return col.replace("label_probabilities_", "")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1211 if col.startswith("probabilities_"):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1212 return col.replace("probabilities_", "")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1213 return col
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1214
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1215 # True labels
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1216 def _extract_labels():
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1217 if labels_from_dataset is not None:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1218 return labels_from_dataset
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1219 for col in [
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1220 LABEL_COLUMN_NAME,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1221 f"{LABEL_COLUMN_NAME}_ground_truth",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1222 f"{LABEL_COLUMN_NAME}__ground_truth",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1223 f"{LABEL_COLUMN_NAME}_target",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1224 f"{LABEL_COLUMN_NAME}__target",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1225 "label",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1226 "label_true",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1227 "label_predictions",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1228 "prediction",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1229 ]:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1230 if col in df_pred.columns and col not in prob_cols_sorted:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1231 return df_pred[col]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1232 return None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1233
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1234 labels_series = _extract_labels()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1235 if labels_series is None or not prob_cols_sorted:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1236 return None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1237
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1238 # Positive prob column selection
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1239 preferred_keys = ("event", "true", "positive", "pos", "1")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1240 pos_prob_col = None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1241 for col in prob_cols_sorted:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1242 suffix = _strip_prob_prefix(col).lower()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1243 if any(k in suffix for k in preferred_keys):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1244 pos_prob_col = col
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1245 break
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1246 if pos_prob_col is None:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1247 pos_prob_col = prob_cols_sorted[-1]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1248
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1249 min_len = min(len(labels_series), len(df_pred[pos_prob_col]))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1250 if min_len == 0:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1251 return None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1252
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1253 y_true = np.array(labels_series.iloc[:min_len])
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1254 # map to binary 0/1
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1255 unique_labels = pd.unique(y_true)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1256 if len(unique_labels) < 2:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1257 return None
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1258 positive_label = unique_labels[1] if len(unique_labels) >= 2 else unique_labels[0]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1259 y_true_bin = (y_true == positive_label).astype(int)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1260 y_score = np.array(df_pred[pos_prob_col].iloc[:min_len], dtype=float)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1261
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1262 thresholds = np.linspace(0.0, 1.0, 101)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1263 accs: List[float] = []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1264 precs: List[float] = []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1265 recs: List[float] = []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1266 f1s: List[float] = []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1267 for t in thresholds:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1268 preds = (y_score >= t).astype(int)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1269 accs.append(accuracy_score(y_true_bin, preds))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1270 precs.append(precision_score(y_true_bin, preds, zero_division=0))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1271 recs.append(recall_score(y_true_bin, preds, zero_division=0))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1272 f1s.append(f1_score(y_true_bin, preds, zero_division=0))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1273
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1274 best_idx = int(np.argmax(f1s))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1275 best_thr = thresholds[best_idx]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1276
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1277 fig = go.Figure()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1278 fig.add_trace(go.Scatter(x=thresholds, y=accs, mode="lines", name="Accuracy", line=dict(width=4)))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1279 fig.add_trace(go.Scatter(x=thresholds, y=precs, mode="lines", name="Precision", line=dict(width=4)))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1280 fig.add_trace(go.Scatter(x=thresholds, y=recs, mode="lines", name="Recall", line=dict(width=4)))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1281 fig.add_trace(go.Scatter(x=thresholds, y=f1s, mode="lines", name="F1-Score", line=dict(width=4)))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1282 fig.add_shape(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1283 type="line",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1284 x0=best_thr,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1285 x1=best_thr,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1286 y0=0,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1287 y1=1,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1288 line=dict(color="gray", width=2, dash="dash"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1289 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1290 fig.update_layout(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1291 title=dict(text="Threshold plot", x=0.5),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1292 xaxis_title="Threshold",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1293 yaxis_title="Metric value",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1294 yaxis=dict(range=[0, 1]),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1295 width=760,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1296 height=520,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1297 legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1298 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1299 _style_fig(fig)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1300 return _wrap_plot("Threshold plot", fig, include_js=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1301
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1302
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1303 def build_multiclass_roc_pr_plots(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1304 predictions_path: str,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1305 split_value: int = 2,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1306 ) -> List[Dict[str, str]]:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1307 """Build one-vs-rest ROC and PR curves for multi-class classification from predictions."""
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1308 preds_file = Path(predictions_path)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1309 if not preds_file.exists():
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1310 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1311 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1312 df_pred = pd.read_csv(predictions_path)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1313 except Exception as exc:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1314 print(f"Warning: Unable to read predictions CSV: {exc}")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1315 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1316
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1317 if SPLIT_COLUMN_NAME in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1318 df_pred = df_pred[df_pred[SPLIT_COLUMN_NAME] == split_value].reset_index(drop=True)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1319 if df_pred.empty:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1320 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1321
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1322 if LABEL_COLUMN_NAME not in df_pred.columns:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1323 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1324
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1325 # Identify per-class probability columns
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1326 prob_cols = [
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1327 c
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1328 for c in df_pred.columns
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1329 if (
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1330 (c.startswith("label_probabilities_") or c.startswith("probabilities_"))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1331 and c != "label_probabilities"
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1332 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1333 ]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1334 if not prob_cols:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1335 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1336 labels = [c.replace("label_probabilities_", "").replace("probabilities_", "") for c in prob_cols]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1337 labels_sorted = sorted(labels)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1338
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1339 # Ensure all labels are present as probability columns
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1340 prob_map = {
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1341 c.replace("label_probabilities_", "").replace("probabilities_", ""): c
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1342 for c in prob_cols
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1343 }
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1344 if len(labels_sorted) < 3:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1345 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1346
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1347 y_true_raw = df_pred[LABEL_COLUMN_NAME].astype(str)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1348 # Drop rows with NaN probabilities across any class to avoid metric errors
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1349 prob_matrix = df_pred[[prob_map[lbl] for lbl in labels_sorted]].astype(float)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1350 mask_valid = ~prob_matrix.isnull().any(axis=1)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1351 prob_matrix = prob_matrix[mask_valid]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1352 y_true_raw = y_true_raw[mask_valid]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1353 if prob_matrix.empty:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1354 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1355
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1356 y_true_bin = label_binarize(y_true_raw, classes=labels_sorted)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1357 y_score = prob_matrix.to_numpy()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1358
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1359 plots: List[Dict[str, str]] = []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1360
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1361 # ROC: one-vs-rest + micro
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1362 fig_roc = go.Figure()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1363 added_any = False
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1364 for idx, lbl in enumerate(labels_sorted):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1365 if y_true_bin[:, idx].sum() == 0 or y_true_bin[:, idx].sum() == len(y_true_bin):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1366 continue # skip classes without both positives and negatives
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1367 fpr, tpr, _ = roc_curve(y_true_bin[:, idx], y_score[:, idx])
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1368 fig_roc.add_trace(
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1369 go.Scatter(
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1370 x=fpr,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1371 y=tpr,
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1372 mode="lines",
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1373 name=f"{lbl} (AUC={auc(fpr, tpr):.3f})",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1374 line=dict(width=3),
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1375 )
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1376 )
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1377 added_any = True
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1378 # Micro-average only if we have mixed labels
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1379 if y_true_bin.sum() > 0 and y_true_bin.sum() < y_true_bin.size:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1380 fpr_micro, tpr_micro, _ = roc_curve(y_true_bin.ravel(), y_score.ravel())
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1381 fig_roc.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1382 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1383 x=fpr_micro,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1384 y=tpr_micro,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1385 mode="lines",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1386 name=f"Micro-average (AUC={auc(fpr_micro, tpr_micro):.3f})",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1387 line=dict(width=3, dash="dash"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1388 )
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1389 )
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1390 added_any = True
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1391 if not added_any:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1392 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1393 fig_roc.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1394 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1395 x=[0, 1],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1396 y=[0, 1],
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1397 mode="lines",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1398 name="Random",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1399 line=dict(color="gray", width=2, dash="dot"),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1400 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1401 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1402 fig_roc.update_layout(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1403 title=dict(text="Multi-class ROC-AUC (one-vs-rest)", x=0.5),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1404 xaxis_title="False Positive Rate",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1405 yaxis_title="True Positive Rate",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1406 width=820,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1407 height=620,
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1408 legend=dict(
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1409 x=0.62,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1410 y=0.05,
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1411 bgcolor="rgba(255,255,255,0.9)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1412 bordercolor="rgba(0,0,0,0.2)",
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1413 borderwidth=1,
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1414 ),
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1415 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1416 _style_fig(fig_roc)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1417 plots.append(_wrap_plot("Multi-class ROC-AUC (one-vs-rest)", fig_roc))
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1418
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1419 # PR: one-vs-rest + micro AP
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1420 fig_pr = go.Figure()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1421 added_pr = False
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1422 for idx, lbl in enumerate(labels_sorted):
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1423 if y_true_bin[:, idx].sum() == 0:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1424 continue
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1425 prec, rec, _ = precision_recall_curve(y_true_bin[:, idx], y_score[:, idx])
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1426 ap = average_precision_score(y_true_bin[:, idx], y_score[:, idx])
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1427 fig_pr.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1428 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1429 x=rec,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1430 y=prec,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1431 mode="lines",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1432 name=f"{lbl} (AP={ap:.3f})",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1433 line=dict(width=3),
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1434 )
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1435 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1436 added_pr = True
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1437 if y_true_bin.sum() > 0:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1438 prec_micro, rec_micro, _ = precision_recall_curve(y_true_bin.ravel(), y_score.ravel())
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1439 ap_micro = average_precision_score(y_true_bin, y_score, average="micro")
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1440 fig_pr.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1441 go.Scatter(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1442 x=rec_micro,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1443 y=prec_micro,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1444 mode="lines",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1445 name=f"Micro-average (AP={ap_micro:.3f})",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1446 line=dict(width=3, dash="dash"),
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1447 )
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1448 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1449 added_pr = True
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1450 if not added_pr:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1451 return plots
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1452 fig_pr.update_layout(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1453 title=dict(text="Multi-class Precision-Recall (one-vs-rest)", x=0.5),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1454 xaxis_title="Recall",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1455 yaxis_title="Precision",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1456 width=820,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1457 height=620,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1458 legend=dict(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1459 x=0.62,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1460 y=0.05,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1461 bgcolor="rgba(255,255,255,0.9)",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1462 bordercolor="rgba(0,0,0,0.2)",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1463 borderwidth=1,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1464 ),
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1465 )
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1466 _style_fig(fig_pr)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1467 plots.append(_wrap_plot("Multi-class Precision-Recall (one-vs-rest)", fig_pr))
11
c5150cceab47 planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
goeckslab
parents: 8
diff changeset
1468
15
d17e3a1b8659 planemo upload for repository https://github.com/goeckslab/gleam.git commit bc50fef8acb44aca15d0a1746e6c0c967da5bb17
goeckslab
parents: 11
diff changeset
1469 return plots
17
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1470
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1471
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1472 def build_multiclass_metric_plots(test_stats_path: str) -> List[Dict[str, str]]:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1473 """Alternative multi-class transparency plots using test_statistics.json per-class stats."""
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1474 ts_path = Path(test_stats_path)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1475 if not ts_path.exists():
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1476 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1477 try:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1478 with open(ts_path, "r") as f:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1479 test_stats = json.load(f)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1480 except Exception:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1481 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1482
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1483 label_stats = test_stats.get("label", {})
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1484 pcs = label_stats.get("per_class_stats", {})
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1485 if not pcs:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1486 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1487 classes = list(pcs.keys())
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1488 if not classes:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1489 return []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1490
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1491 metrics = ["precision", "recall", "f1_score", "specificity", "accuracy"]
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1492 fig_bar = go.Figure()
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1493 for metric in metrics:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1494 values = []
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1495 for cls in classes:
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1496 v = pcs.get(cls, {}).get(metric)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1497 values.append(v if isinstance(v, (int, float)) else 0)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1498 fig_bar.add_trace(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1499 go.Bar(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1500 x=classes,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1501 y=values,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1502 name=metric.replace("_", " ").title(),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1503 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1504 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1505 fig_bar.update_layout(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1506 title=dict(text="Per-Class Metrics (Test)", x=0.5),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1507 xaxis_title="Class",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1508 yaxis_title="Metric value",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1509 barmode="group",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1510 width=900,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1511 height=600,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1512 legend=dict(
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1513 x=1.02,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1514 y=1.0,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1515 bgcolor="rgba(255,255,255,0.9)",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1516 bordercolor="rgba(0,0,0,0.2)",
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1517 borderwidth=1,
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1518 ),
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1519 )
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1520 _style_fig(fig_bar)
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1521
db9be962dc13 planemo upload for repository https://github.com/goeckslab/gleam.git commit 9db874612b0c3e4f53d639459fe789b762660cd6
goeckslab
parents: 15
diff changeset
1522 return [_wrap_plot("Per-Class Metrics (Test)", fig_bar)]