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annotate ml_visualization_ex.py @ 31:7ae443e6217d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author bgruening
date Mon, 02 Oct 2023 09:51:35 +0000
parents 4db563e8d453
children
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1 import argparse
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2 import json
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3 import os
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4 import warnings
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5
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6 import matplotlib
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7 import matplotlib.pyplot as plt
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8 import numpy as np
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9 import pandas as pd
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10 import plotly
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11 import plotly.graph_objs as go
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12 from galaxy_ml.model_persist import load_model_from_h5
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13 from galaxy_ml.utils import read_columns, SafeEval
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14 from sklearn.feature_selection._base import SelectorMixin
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15 from sklearn.metrics import (
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16 auc,
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17 average_precision_score,
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18 confusion_matrix,
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19 precision_recall_curve,
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20 roc_curve,
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21 )
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22 from sklearn.pipeline import Pipeline
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23 from tensorflow.keras.models import model_from_json
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24 from tensorflow.keras.utils import plot_model
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26 safe_eval = SafeEval()
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28 # plotly default colors
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29 default_colors = [
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30 "#1f77b4", # muted blue
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31 "#ff7f0e", # safety orange
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32 "#2ca02c", # cooked asparagus green
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33 "#d62728", # brick red
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34 "#9467bd", # muted purple
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35 "#8c564b", # chestnut brown
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36 "#e377c2", # raspberry yogurt pink
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37 "#7f7f7f", # middle gray
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38 "#bcbd22", # curry yellow-green
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39 "#17becf", # blue-teal
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40 ]
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43 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None):
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44 """output pr-curve in html using plotly
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46 df1 : pandas.DataFrame
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47 Containing y_true
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48 df2 : pandas.DataFrame
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49 Containing y_score
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50 pos_label : None
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51 The label of positive class
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52 title : str
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53 Plot title
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54 """
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55 data = []
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56 for idx in range(df1.shape[1]):
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57 y_true = df1.iloc[:, idx].values
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58 y_score = df2.iloc[:, idx].values
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59
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60 precision, recall, _ = precision_recall_curve(
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61 y_true, y_score, pos_label=pos_label
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62 )
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63 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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64
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65 trace = go.Scatter(
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66 x=recall,
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67 y=precision,
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68 mode="lines",
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69 marker=dict(color=default_colors[idx % len(default_colors)]),
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70 name="%s (area = %.3f)" % (idx, ap),
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71 )
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72 data.append(trace)
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74 layout = go.Layout(
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75 xaxis=dict(title="Recall", linecolor="lightslategray", linewidth=1),
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76 yaxis=dict(title="Precision", linecolor="lightslategray", linewidth=1),
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77 title=dict(
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78 text=title or "Precision-Recall Curve",
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79 x=0.5,
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80 y=0.92,
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81 xanchor="center",
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82 yanchor="top",
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83 ),
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84 font=dict(family="sans-serif", size=11),
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85 # control backgroud colors
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86 plot_bgcolor="rgba(255,255,255,0)",
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87 )
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88 """
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89 legend=dict(
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90 x=0.95,
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91 y=0,
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92 traceorder="normal",
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93 font=dict(
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94 family="sans-serif",
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95 size=9,
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96 color="black"
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97 ),
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98 bgcolor="LightSteelBlue",
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99 bordercolor="Black",
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100 borderwidth=2
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101 ),"""
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102
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103 fig = go.Figure(data=data, layout=layout)
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104
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105 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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106 # to be discovered by `from_work_dir`
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107 os.rename("output.html", "output")
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108
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109
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110 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
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111 """visualize pr-curve using matplotlib and output svg image"""
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112 backend = matplotlib.get_backend()
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113 if "inline" not in backend:
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114 matplotlib.use("SVG")
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115 plt.style.use("seaborn-colorblind")
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116 plt.figure()
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117
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118 for idx in range(df1.shape[1]):
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119 y_true = df1.iloc[:, idx].values
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120 y_score = df2.iloc[:, idx].values
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121
23
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122 precision, recall, _ = precision_recall_curve(
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123 y_true, y_score, pos_label=pos_label
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124 )
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125 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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126
21
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127 plt.step(
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128 recall,
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129 precision,
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130 "r-",
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131 color="black",
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132 alpha=0.3,
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133 lw=1,
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134 where="post",
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135 label="%s (area = %.3f)" % (idx, ap),
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136 )
17
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137
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138 plt.xlim([0.0, 1.0])
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139 plt.ylim([0.0, 1.05])
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140 plt.xlabel("Recall")
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141 plt.ylabel("Precision")
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142 title = title or "Precision-Recall Curve"
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143 plt.title(title)
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144 folder = os.getcwd()
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145 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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146 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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147
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148
21
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149 def visualize_roc_curve_plotly(df1, df2, pos_label, drop_intermediate=True, title=None):
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150 """output roc-curve in html using plotly
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151
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152 df1 : pandas.DataFrame
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153 Containing y_true
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154 df2 : pandas.DataFrame
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155 Containing y_score
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156 pos_label : None
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157 The label of positive class
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158 drop_intermediate : bool
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159 Whether to drop some suboptimal thresholds
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160 title : str
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161 Plot title
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162 """
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163 data = []
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164 for idx in range(df1.shape[1]):
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165 y_true = df1.iloc[:, idx].values
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166 y_score = df2.iloc[:, idx].values
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167
23
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168 fpr, tpr, _ = roc_curve(
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169 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
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170 )
17
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171 roc_auc = auc(fpr, tpr)
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172
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173 trace = go.Scatter(
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174 x=fpr,
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175 y=tpr,
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176 mode="lines",
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177 marker=dict(color=default_colors[idx % len(default_colors)]),
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178 name="%s (area = %.3f)" % (idx, roc_auc),
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179 )
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180 data.append(trace)
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181
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182 layout = go.Layout(
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183 xaxis=dict(
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184 title="False Positive Rate", linecolor="lightslategray", linewidth=1
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185 ),
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186 yaxis=dict(title="True Positive Rate", linecolor="lightslategray", linewidth=1),
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187 title=dict(
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188 text=title or "Receiver Operating Characteristic (ROC) Curve",
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189 x=0.5,
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190 y=0.92,
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191 xanchor="center",
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192 yanchor="top",
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193 ),
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194 font=dict(family="sans-serif", size=11),
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195 # control backgroud colors
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196 plot_bgcolor="rgba(255,255,255,0)",
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197 )
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198 """
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199 # legend=dict(
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200 # x=0.95,
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201 # y=0,
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202 # traceorder="normal",
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203 # font=dict(
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204 # family="sans-serif",
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205 # size=9,
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206 # color="black"
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207 # ),
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208 # bgcolor="LightSteelBlue",
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209 # bordercolor="Black",
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210 # borderwidth=2
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211 # ),
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212 """
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213
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214 fig = go.Figure(data=data, layout=layout)
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215
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216 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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217 # to be discovered by `from_work_dir`
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218 os.rename("output.html", "output")
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219
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220
23
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221 def visualize_roc_curve_matplotlib(
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222 df1, df2, pos_label, drop_intermediate=True, title=None
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223 ):
21
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224 """visualize roc-curve using matplotlib and output svg image"""
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225 backend = matplotlib.get_backend()
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226 if "inline" not in backend:
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227 matplotlib.use("SVG")
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228 plt.style.use("seaborn-colorblind")
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229 plt.figure()
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230
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231 for idx in range(df1.shape[1]):
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232 y_true = df1.iloc[:, idx].values
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233 y_score = df2.iloc[:, idx].values
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234
23
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235 fpr, tpr, _ = roc_curve(
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236 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
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237 )
17
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238 roc_auc = auc(fpr, tpr)
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239
21
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240 plt.step(
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241 fpr,
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242 tpr,
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243 "r-",
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244 color="black",
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245 alpha=0.3,
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246 lw=1,
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247 where="post",
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248 label="%s (area = %.3f)" % (idx, roc_auc),
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249 )
17
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250
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251 plt.xlim([0.0, 1.0])
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252 plt.ylim([0.0, 1.05])
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253 plt.xlabel("False Positive Rate")
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254 plt.ylabel("True Positive Rate")
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255 title = title or "Receiver Operating Characteristic (ROC) Curve"
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256 plt.title(title)
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257 folder = os.getcwd()
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258 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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259 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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260
13
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261
30
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262 def get_dataframe(file_path, plot_selection, header_name, column_name):
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263 header = "infer" if plot_selection[header_name] else None
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264 column_option = plot_selection[column_name]["selected_column_selector_option"]
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265 if column_option in [
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266 "by_index_number",
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267 "all_but_by_index_number",
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268 "by_header_name",
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269 "all_but_by_header_name",
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270 ]:
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271 col = plot_selection[column_name]["col1"]
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272 else:
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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273 col = None
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274 _, input_df = read_columns(
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275 file_path,
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276 c=col,
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277 c_option=column_option,
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278 return_df=True,
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279 sep="\t",
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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280 header=header,
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281 parse_dates=True,
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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282 )
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283 return input_df
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284
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285
21
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286 def main(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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287 inputs,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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288 infile_estimator=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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289 infile1=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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290 infile2=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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291 outfile_result=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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292 outfile_object=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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293 groups=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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294 ref_seq=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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295 intervals=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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296 targets=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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297 fasta_path=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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298 model_config=None,
30
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299 true_labels=None,
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300 predicted_labels=None,
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301 plot_color=None,
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302 title=None,
21
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303 ):
13
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304 """
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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305 Parameter
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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306 ---------
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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307 inputs : str
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308 File path to galaxy tool parameter
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309
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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310 infile_estimator : str, default is None
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311 File path to estimator
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312
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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313 infile1 : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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314 File path to dataset containing features or true labels.
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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315
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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316 infile2 : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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317 File path to dataset containing target values or predicted
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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318 probabilities.
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319
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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320 outfile_result : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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321 File path to save the results, either cv_results or test result
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322
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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323 outfile_object : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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324 File path to save searchCV object
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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325
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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326 groups : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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327 File path to dataset containing groups labels
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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328
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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329 ref_seq : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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330 File path to dataset containing genome sequence file
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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331
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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332 intervals : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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333 File path to dataset containing interval file
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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334
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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335 targets : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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336 File path to dataset compressed target bed file
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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337
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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338 fasta_path : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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339 File path to dataset containing fasta file
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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340
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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341 model_config : str, default is None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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342 File path to dataset containing JSON config for neural networks
30
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343
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344 true_labels : str, default is None
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345 File path to dataset containing true labels
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346
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347 predicted_labels : str, default is None
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348 File path to dataset containing true predicted labels
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349
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350 plot_color : str, default is None
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351 Color of the confusion matrix heatmap
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352
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353 title : str, default is None
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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354 Title of the confusion matrix heatmap
13
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355 """
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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356 warnings.simplefilter("ignore")
13
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357
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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358 with open(inputs, "r") as param_handler:
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359 params = json.load(param_handler)
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360
21
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361 title = params["plotting_selection"]["title"].strip()
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362 plot_type = params["plotting_selection"]["plot_type"]
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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363 plot_format = params["plotting_selection"]["plot_format"]
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
364
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
365 if plot_type == "feature_importances":
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 23
diff changeset
366 estimator = load_model_from_h5(infile_estimator)
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
367
23
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
368 column_option = params["plotting_selection"]["column_selector_options"][
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
369 "selected_column_selector_option"
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
370 ]
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
371 if column_option in [
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
372 "by_index_number",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
373 "all_but_by_index_number",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
374 "by_header_name",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
375 "all_but_by_header_name",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
376 ]:
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
377 c = params["plotting_selection"]["column_selector_options"]["col1"]
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
378 else:
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
379 c = None
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
380
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
381 _, input_df = read_columns(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
382 infile1,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
383 c=c,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
384 c_option=column_option,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
385 return_df=True,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
386 sep="\t",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
387 header="infer",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
388 parse_dates=True,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
389 )
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
390
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
391 feature_names = input_df.columns.values
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
392
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
393 if isinstance(estimator, Pipeline):
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
394 for st in estimator.steps[:-1]:
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
395 if isinstance(st[-1], SelectorMixin):
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
396 mask = st[-1].get_support()
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
397 feature_names = feature_names[mask]
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
398 estimator = estimator.steps[-1][-1]
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
399
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
400 if hasattr(estimator, "coef_"):
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
401 coefs = estimator.coef_
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
402 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
403 coefs = getattr(estimator, "feature_importances_", None)
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
404 if coefs is None:
23
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
405 raise RuntimeError(
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
406 "The classifier does not expose "
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
407 '"coef_" or "feature_importances_" '
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
408 "attributes"
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
409 )
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
410
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
411 threshold = params["plotting_selection"]["threshold"]
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
412 if threshold is not None:
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
413 mask = (coefs > threshold) | (coefs < -threshold)
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
414 coefs = coefs[mask]
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
415 feature_names = feature_names[mask]
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
416
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
417 # sort
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
418 indices = np.argsort(coefs)[::-1]
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
419
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
420 trace = go.Bar(x=feature_names[indices], y=coefs[indices])
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
421 layout = go.Layout(title=title or "Feature Importances")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
422 fig = go.Figure(data=[trace], layout=layout)
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
423
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
424 plotly.offline.plot(fig, filename="output.html", auto_open=False)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
425 # to be discovered by `from_work_dir`
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
426 os.rename("output.html", "output")
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
427
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
428 return 0
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
429
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
430 elif plot_type in ("pr_curve", "roc_curve"):
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
431 df1 = pd.read_csv(infile1, sep="\t", header="infer")
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
432 df2 = pd.read_csv(infile2, sep="\t", header="infer").astype(np.float32)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
433
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
434 minimum = params["plotting_selection"]["report_minimum_n_positives"]
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
435 # filter out columns whose n_positives is beblow the threhold
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
436 if minimum:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
437 mask = df1.sum(axis=0) >= minimum
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
438 df1 = df1.loc[:, mask]
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
439 df2 = df2.loc[:, mask]
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
440
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
441 pos_label = params["plotting_selection"]["pos_label"].strip() or None
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
442
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
443 if plot_type == "pr_curve":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
444 if plot_format == "plotly_html":
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
445 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
446 else:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
447 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
448 else: # 'roc_curve'
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
449 drop_intermediate = params["plotting_selection"]["drop_intermediate"]
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
450 if plot_format == "plotly_html":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
451 visualize_roc_curve_plotly(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
452 df1,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
453 df2,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
454 pos_label,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
455 drop_intermediate=drop_intermediate,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
456 title=title,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
457 )
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
458 else:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
459 visualize_roc_curve_matplotlib(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
460 df1,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
461 df2,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
462 pos_label,
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
463 drop_intermediate=drop_intermediate,
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
464 title=title,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
465 )
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
466
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
467 return 0
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
468
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
469 elif plot_type == "rfecv_gridscores":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
470 input_df = pd.read_csv(infile1, sep="\t", header="infer")
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
471 scores = input_df.iloc[:, 0]
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
472 steps = params["plotting_selection"]["steps"].strip()
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
473 steps = safe_eval(steps)
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
474
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
475 data = go.Scatter(
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
476 x=list(range(len(scores))),
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
477 y=scores,
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
478 text=[str(_) for _ in steps] if steps else None,
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
479 mode="lines",
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
480 )
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
481 layout = go.Layout(
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
482 xaxis=dict(title="Number of features selected"),
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
483 yaxis=dict(title="Cross validation score"),
23
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
484 title=dict(
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
485 text=title or None, x=0.5, y=0.92, xanchor="center", yanchor="top"
823ecc0bce45 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 22
diff changeset
486 ),
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
487 font=dict(family="sans-serif", size=11),
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
488 # control backgroud colors
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
489 plot_bgcolor="rgba(255,255,255,0)",
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
490 )
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
491 """
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
492 # legend=dict(
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
493 # x=0.95,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
494 # y=0,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
495 # traceorder="normal",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
496 # font=dict(
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
497 # family="sans-serif",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
498 # size=9,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
499 # color="black"
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
500 # ),
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
501 # bgcolor="LightSteelBlue",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
502 # bordercolor="Black",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
503 # borderwidth=2
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
504 # ),
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
505 """
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
506
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
507 fig = go.Figure(data=[data], layout=layout)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
508 plotly.offline.plot(fig, filename="output.html", auto_open=False)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
509 # to be discovered by `from_work_dir`
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
510 os.rename("output.html", "output")
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
511
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
512 return 0
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
513
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
514 elif plot_type == "learning_curve":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
515 input_df = pd.read_csv(infile1, sep="\t", header="infer")
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
516 plot_std_err = params["plotting_selection"]["plot_std_err"]
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
517 data1 = go.Scatter(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
518 x=input_df["train_sizes_abs"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
519 y=input_df["mean_train_scores"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
520 error_y=dict(array=input_df["std_train_scores"]) if plot_std_err else None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
521 mode="lines",
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
522 name="Train Scores",
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
523 )
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
524 data2 = go.Scatter(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
525 x=input_df["train_sizes_abs"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
526 y=input_df["mean_test_scores"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
527 error_y=dict(array=input_df["std_test_scores"]) if plot_std_err else None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
528 mode="lines",
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
529 name="Test Scores",
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
530 )
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
531 layout = dict(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
532 xaxis=dict(title="No. of samples"),
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
533 yaxis=dict(title="Performance Score"),
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
534 # modify these configurations to customize image
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
535 title=dict(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
536 text=title or "Learning Curve",
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
537 x=0.5,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
538 y=0.92,
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
539 xanchor="center",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
540 yanchor="top",
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
541 ),
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
542 font=dict(family="sans-serif", size=11),
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
543 # control backgroud colors
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
544 plot_bgcolor="rgba(255,255,255,0)",
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
545 )
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
546 """
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
547 # legend=dict(
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
548 # x=0.95,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
549 # y=0,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
550 # traceorder="normal",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
551 # font=dict(
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
552 # family="sans-serif",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
553 # size=9,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
554 # color="black"
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
555 # ),
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
556 # bgcolor="LightSteelBlue",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
557 # bordercolor="Black",
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
558 # borderwidth=2
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
559 # ),
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
560 """
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
561
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
562 fig = go.Figure(data=[data1, data2], layout=layout)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
563 plotly.offline.plot(fig, filename="output.html", auto_open=False)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
564 # to be discovered by `from_work_dir`
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
565 os.rename("output.html", "output")
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
566
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
567 return 0
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
568
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
569 elif plot_type == "keras_plot_model":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
570 with open(model_config, "r") as f:
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
571 model_str = f.read()
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
572 model = model_from_json(model_str)
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
573 plot_model(model, to_file="output.png")
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
574 os.rename("output.png", "output")
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
575
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
576 return 0
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
577
30
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
578 elif plot_type == "classification_confusion_matrix":
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
579 plot_selection = params["plotting_selection"]
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
580 input_true = get_dataframe(
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
581 true_labels, plot_selection, "header_true", "column_selector_options_true"
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
582 )
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
583 header_predicted = "infer" if plot_selection["header_predicted"] else None
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
584 input_predicted = pd.read_csv(
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
585 predicted_labels, sep="\t", parse_dates=True, header=header_predicted
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
586 )
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
587 true_classes = input_true.iloc[:, -1].copy()
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
588 predicted_classes = input_predicted.iloc[:, -1].copy()
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
589 axis_labels = list(set(true_classes))
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
590 c_matrix = confusion_matrix(true_classes, predicted_classes)
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
591 fig, ax = plt.subplots(figsize=(7, 7))
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
592 im = plt.imshow(c_matrix, cmap=plot_color)
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
593 for i in range(len(c_matrix)):
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
594 for j in range(len(c_matrix)):
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
595 ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k")
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
596 ax.set_ylabel("True class labels")
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
597 ax.set_xlabel("Predicted class labels")
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
598 ax.set_title(title)
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
599 ax.set_xticks(axis_labels)
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
600 ax.set_yticks(axis_labels)
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
601 fig.colorbar(im, ax=ax)
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
602 fig.tight_layout()
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
603 plt.savefig("output.png", dpi=125)
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
604 os.rename("output.png", "output")
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
605
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
606 return 0
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
607
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
608 # save pdf file to disk
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
609 # fig.write_image("image.pdf", format='pdf')
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 14
diff changeset
610 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
611
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
612
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 19
diff changeset
613 if __name__ == "__main__":
13
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
614 aparser = argparse.ArgumentParser()
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
615 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
616 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
617 aparser.add_argument("-X", "--infile1", dest="infile1")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
618 aparser.add_argument("-y", "--infile2", dest="infile2")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
619 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
620 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
621 aparser.add_argument("-g", "--groups", dest="groups")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
622 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
623 aparser.add_argument("-b", "--intervals", dest="intervals")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
624 aparser.add_argument("-t", "--targets", dest="targets")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
625 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
626 aparser.add_argument("-c", "--model_config", dest="model_config")
30
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
627 aparser.add_argument("-tl", "--true_labels", dest="true_labels")
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
628 aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels")
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents: 27
diff changeset
629 aparser.add_argument("-pc", "--plot_color", dest="plot_color")
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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630 aparser.add_argument("-pt", "--title", dest="title")
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631 args = aparser.parse_args()
fbc38059bb8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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632
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633 main(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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634 args.inputs,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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635 args.infile_estimator,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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636 args.infile1,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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637 args.infile2,
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638 args.outfile_result,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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639 outfile_object=args.outfile_object,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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640 groups=args.groups,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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641 ref_seq=args.ref_seq,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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642 intervals=args.intervals,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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643 targets=args.targets,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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644 fasta_path=args.fasta_path,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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645 model_config=args.model_config,
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646 true_labels=args.true_labels,
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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647 predicted_labels=args.predicted_labels,
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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648 plot_color=args.plot_color,
4db563e8d453 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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649 title=args.title,
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650 )