Mercurial > repos > bgruening > sklearn_svm_classifier

annotate ml_visualization_ex.py @ 22:cefbe0fe1bbb draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8850f42c2c3763e614f7454c9c006f3d2ff572c0
author bgruening
date Fri, 27 May 2022 11:25:59 +0000
parents 9cff519e0d13
children 0be7886106fb
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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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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.utils import load_model, read_columns, SafeEval
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13 from keras.models import model_from_json
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14 from keras.utils import plot_model
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15 from sklearn.feature_selection.base import SelectorMixin
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16 from sklearn.metrics import (auc, average_precision_score, confusion_matrix,
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17 precision_recall_curve, roc_curve)
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18 from sklearn.pipeline import Pipeline
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20 safe_eval = SafeEval()
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22 # plotly default colors
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23 default_colors = [
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24 "#1f77b4", # muted blue
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25 "#ff7f0e", # safety orange
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26 "#2ca02c", # cooked asparagus green
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27 "#d62728", # brick red
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28 "#9467bd", # muted purple
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29 "#8c564b", # chestnut brown
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30 "#e377c2", # raspberry yogurt pink
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31 "#7f7f7f", # middle gray
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32 "#bcbd22", # curry yellow-green
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33 "#17becf", # blue-teal
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34 ]
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37 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None):
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38 """output pr-curve in html using plotly
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40 df1 : pandas.DataFrame
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41 Containing y_true
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42 df2 : pandas.DataFrame
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43 Containing y_score
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44 pos_label : None
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45 The label of positive class
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46 title : str
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47 Plot title
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48 """
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49 data = []
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50 for idx in range(df1.shape[1]):
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51 y_true = df1.iloc[:, idx].values
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52 y_score = df2.iloc[:, idx].values
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53
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54 precision, recall, _ = precision_recall_curve(
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55 y_true, y_score, pos_label=pos_label
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56 )
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57 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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59 trace = go.Scatter(
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60 x=recall,
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61 y=precision,
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62 mode="lines",
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63 marker=dict(color=default_colors[idx % len(default_colors)]),
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64 name="%s (area = %.3f)" % (idx, ap),
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65 )
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66 data.append(trace)
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67
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68 layout = go.Layout(
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69 xaxis=dict(title="Recall", linecolor="lightslategray", linewidth=1),
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70 yaxis=dict(title="Precision", linecolor="lightslategray", linewidth=1),
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71 title=dict(
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72 text=title or "Precision-Recall Curve",
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73 x=0.5,
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74 y=0.92,
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75 xanchor="center",
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76 yanchor="top",
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77 ),
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78 font=dict(family="sans-serif", size=11),
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79 # control backgroud colors
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80 plot_bgcolor="rgba(255,255,255,0)",
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81 )
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82 """
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83 legend=dict(
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84 x=0.95,
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85 y=0,
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86 traceorder="normal",
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87 font=dict(
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88 family="sans-serif",
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89 size=9,
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90 color="black"
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91 ),
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92 bgcolor="LightSteelBlue",
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93 bordercolor="Black",
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94 borderwidth=2
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95 ),"""
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96
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97 fig = go.Figure(data=data, layout=layout)
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98
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99 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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100 # to be discovered by `from_work_dir`
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101 os.rename("output.html", "output")
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102
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103
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104 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
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105 """visualize pr-curve using matplotlib and output svg image"""
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106 backend = matplotlib.get_backend()
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107 if "inline" not in backend:
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108 matplotlib.use("SVG")
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109 plt.style.use("seaborn-colorblind")
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110 plt.figure()
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111
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112 for idx in range(df1.shape[1]):
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113 y_true = df1.iloc[:, idx].values
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114 y_score = df2.iloc[:, idx].values
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115
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116 precision, recall, _ = precision_recall_curve(
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117 y_true, y_score, pos_label=pos_label
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118 )
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119 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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120
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121 plt.step(
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122 recall,
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123 precision,
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124 "r-",
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125 color="black",
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126 alpha=0.3,
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127 lw=1,
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128 where="post",
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129 label="%s (area = %.3f)" % (idx, ap),
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130 )
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131
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132 plt.xlim([0.0, 1.0])
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133 plt.ylim([0.0, 1.05])
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134 plt.xlabel("Recall")
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135 plt.ylabel("Precision")
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136 title = title or "Precision-Recall Curve"
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137 plt.title(title)
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138 folder = os.getcwd()
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139 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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140 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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141
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142
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143 def visualize_roc_curve_plotly(df1, df2, pos_label, drop_intermediate=True, title=None):
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144 """output roc-curve in html using plotly
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145
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146 df1 : pandas.DataFrame
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147 Containing y_true
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148 df2 : pandas.DataFrame
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149 Containing y_score
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150 pos_label : None
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151 The label of positive class
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152 drop_intermediate : bool
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153 Whether to drop some suboptimal thresholds
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154 title : str
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155 Plot title
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156 """
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157 data = []
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158 for idx in range(df1.shape[1]):
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159 y_true = df1.iloc[:, idx].values
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160 y_score = df2.iloc[:, idx].values
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161
20
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162 fpr, tpr, _ = roc_curve(
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163 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
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164 )
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165 roc_auc = auc(fpr, tpr)
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166
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167 trace = go.Scatter(
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168 x=fpr,
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169 y=tpr,
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170 mode="lines",
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171 marker=dict(color=default_colors[idx % len(default_colors)]),
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172 name="%s (area = %.3f)" % (idx, roc_auc),
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173 )
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174 data.append(trace)
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175
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176 layout = go.Layout(
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177 xaxis=dict(
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178 title="False Positive Rate", linecolor="lightslategray", linewidth=1
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179 ),
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180 yaxis=dict(title="True Positive Rate", linecolor="lightslategray", linewidth=1),
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181 title=dict(
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182 text=title or "Receiver Operating Characteristic (ROC) Curve",
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183 x=0.5,
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184 y=0.92,
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185 xanchor="center",
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186 yanchor="top",
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187 ),
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188 font=dict(family="sans-serif", size=11),
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189 # control backgroud colors
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190 plot_bgcolor="rgba(255,255,255,0)",
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191 )
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192 """
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193 # legend=dict(
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194 # x=0.95,
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195 # y=0,
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196 # traceorder="normal",
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197 # font=dict(
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198 # family="sans-serif",
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199 # size=9,
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200 # color="black"
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201 # ),
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202 # bgcolor="LightSteelBlue",
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203 # bordercolor="Black",
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204 # borderwidth=2
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205 # ),
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206 """
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207
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208 fig = go.Figure(data=data, layout=layout)
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209
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210 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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211 # to be discovered by `from_work_dir`
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212 os.rename("output.html", "output")
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213
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214
20
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215 def visualize_roc_curve_matplotlib(
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216 df1, df2, pos_label, drop_intermediate=True, title=None
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217 ):
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218 """visualize roc-curve using matplotlib and output svg image"""
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219 backend = matplotlib.get_backend()
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220 if "inline" not in backend:
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221 matplotlib.use("SVG")
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222 plt.style.use("seaborn-colorblind")
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223 plt.figure()
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224
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225 for idx in range(df1.shape[1]):
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226 y_true = df1.iloc[:, idx].values
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227 y_score = df2.iloc[:, idx].values
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228
20
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229 fpr, tpr, _ = roc_curve(
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230 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
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231 )
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232 roc_auc = auc(fpr, tpr)
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233
18
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234 plt.step(
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235 fpr,
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236 tpr,
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237 "r-",
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238 color="black",
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239 alpha=0.3,
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240 lw=1,
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241 where="post",
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242 label="%s (area = %.3f)" % (idx, roc_auc),
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243 )
15
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244
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245 plt.xlim([0.0, 1.0])
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246 plt.ylim([0.0, 1.05])
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247 plt.xlabel("False Positive Rate")
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248 plt.ylabel("True Positive Rate")
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249 title = title or "Receiver Operating Characteristic (ROC) Curve"
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250 plt.title(title)
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251 folder = os.getcwd()
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252 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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253 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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254
11
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255
17
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256 def get_dataframe(file_path, plot_selection, header_name, column_name):
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257 header = "infer" if plot_selection[header_name] else None
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258 column_option = plot_selection[column_name]["selected_column_selector_option"]
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259 if column_option in [
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260 "by_index_number",
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261 "all_but_by_index_number",
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262 "by_header_name",
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263 "all_but_by_header_name",
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264 ]:
17
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265 col = plot_selection[column_name]["col1"]
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266 else:
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267 col = None
20
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268 _, input_df = read_columns(
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269 file_path,
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270 c=col,
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271 c_option=column_option,
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272 return_df=True,
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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diff changeset
273 sep="\t",
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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274 header=header,
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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275 parse_dates=True,
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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276 )
17
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277 return input_df
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278
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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279
18
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280 def main(
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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281 inputs,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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282 infile_estimator=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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283 infile1=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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284 infile2=None,
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285 outfile_result=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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286 outfile_object=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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287 groups=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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288 ref_seq=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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289 intervals=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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290 targets=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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291 fasta_path=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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292 model_config=None,
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293 true_labels=None,
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294 predicted_labels=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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295 plot_color=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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296 title=None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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297 ):
11
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298 """
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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299 Parameter
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300 ---------
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301 inputs : str
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302 File path to galaxy tool parameter
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303
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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304 infile_estimator : str, default is None
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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305 File path to estimator
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306
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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307 infile1 : str, default is None
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308 File path to dataset containing features or true labels.
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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309
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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310 infile2 : str, default is None
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311 File path to dataset containing target values or predicted
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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312 probabilities.
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313
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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314 outfile_result : str, default is None
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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315 File path to save the results, either cv_results or test result
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316
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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317 outfile_object : str, default is None
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318 File path to save searchCV object
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319
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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320 groups : str, default is None
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321 File path to dataset containing groups labels
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322
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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323 ref_seq : str, default is None
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324 File path to dataset containing genome sequence file
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325
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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326 intervals : str, default is None
a14fb713aaad "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 interval file
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328
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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329 targets : str, default is None
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330 File path to dataset compressed target bed file
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331
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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332 fasta_path : str, default is None
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333 File path to dataset containing fasta file
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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334
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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335 model_config : str, default is None
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336 File path to dataset containing JSON config for neural networks
17
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337
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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338 true_labels : str, default is None
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339 File path to dataset containing true labels
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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340
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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341 predicted_labels : str, default is None
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342 File path to dataset containing true predicted labels
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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343
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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344 plot_color : str, default is None
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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345 Color of the confusion matrix heatmap
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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346
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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347 title : str, default is None
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
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348 Title of the confusion matrix heatmap
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349 """
18
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diff changeset
350 warnings.simplefilter("ignore")
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351
18
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352 with open(inputs, "r") as param_handler:
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353 params = json.load(param_handler)
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354
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355 title = params["plotting_selection"]["title"].strip()
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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356 plot_type = params["plotting_selection"]["plot_type"]
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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357 plot_format = params["plotting_selection"]["plot_format"]
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2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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358
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359 if plot_type == "feature_importances":
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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360 with open(infile_estimator, "rb") as estimator_handler:
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diff changeset
361 estimator = load_model(estimator_handler)
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
362
20
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
363 column_option = params["plotting_selection"]["column_selector_options"][
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
364 "selected_column_selector_option"
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
365 ]
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
366 if column_option in [
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
367 "by_index_number",
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
368 "all_but_by_index_number",
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
369 "by_header_name",
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
370 "all_but_by_header_name",
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
371 ]:
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
372 c = params["plotting_selection"]["column_selector_options"]["col1"]
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
373 else:
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
374 c = None
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
375
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
376 _, input_df = read_columns(
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
377 infile1,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
378 c=c,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
379 c_option=column_option,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
380 return_df=True,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
381 sep="\t",
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
382 header="infer",
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
383 parse_dates=True,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
384 )
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
385
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
386 feature_names = input_df.columns.values
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
387
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
388 if isinstance(estimator, Pipeline):
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
389 for st in estimator.steps[:-1]:
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
390 if isinstance(st[-1], SelectorMixin):
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
391 mask = st[-1].get_support()
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
392 feature_names = feature_names[mask]
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
393 estimator = estimator.steps[-1][-1]
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
394
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
395 if hasattr(estimator, "coef_"):
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
396 coefs = estimator.coef_
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
397 else:
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
398 coefs = getattr(estimator, "feature_importances_", None)
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
399 if coefs is None:
20
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
400 raise RuntimeError(
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
401 "The classifier does not expose "
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
402 '"coef_" or "feature_importances_" '
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
403 "attributes"
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
404 )
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
405
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
406 threshold = params["plotting_selection"]["threshold"]
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
407 if threshold is not None:
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
408 mask = (coefs > threshold) | (coefs < -threshold)
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
409 coefs = coefs[mask]
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
410 feature_names = feature_names[mask]
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
411
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
412 # sort
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
413 indices = np.argsort(coefs)[::-1]
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
414
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
415 trace = go.Bar(x=feature_names[indices], y=coefs[indices])
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
416 layout = go.Layout(title=title or "Feature Importances")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
417 fig = go.Figure(data=[trace], layout=layout)
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
418
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
419 plotly.offline.plot(fig, filename="output.html", auto_open=False)
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
420 # to be discovered by `from_work_dir`
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
421 os.rename("output.html", "output")
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
422
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
423 return 0
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
424
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
425 elif plot_type in ("pr_curve", "roc_curve"):
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
426 df1 = pd.read_csv(infile1, sep="\t", header="infer")
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
427 df2 = pd.read_csv(infile2, sep="\t", header="infer").astype(np.float32)
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
428
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
429 minimum = params["plotting_selection"]["report_minimum_n_positives"]
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
430 # filter out columns whose n_positives is beblow the threhold
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
431 if minimum:
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
432 mask = df1.sum(axis=0) >= minimum
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
433 df1 = df1.loc[:, mask]
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
434 df2 = df2.loc[:, mask]
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
435
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
436 pos_label = params["plotting_selection"]["pos_label"].strip() or None
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
437
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
438 if plot_type == "pr_curve":
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
439 if plot_format == "plotly_html":
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
440 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
441 else:
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
442 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
443 else: # 'roc_curve'
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
444 drop_intermediate = params["plotting_selection"]["drop_intermediate"]
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
445 if plot_format == "plotly_html":
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
446 visualize_roc_curve_plotly(
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
447 df1,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
448 df2,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
449 pos_label,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
450 drop_intermediate=drop_intermediate,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
451 title=title,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
452 )
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
453 else:
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
454 visualize_roc_curve_matplotlib(
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
455 df1,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
456 df2,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
457 pos_label,
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
458 drop_intermediate=drop_intermediate,
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
459 title=title,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
460 )
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
461
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
462 return 0
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
463
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
464 elif plot_type == "rfecv_gridscores":
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
465 input_df = pd.read_csv(infile1, sep="\t", header="infer")
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
466 scores = input_df.iloc[:, 0]
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
467 steps = params["plotting_selection"]["steps"].strip()
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
468 steps = safe_eval(steps)
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
469
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
470 data = go.Scatter(
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
471 x=list(range(len(scores))),
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
472 y=scores,
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
473 text=[str(_) for _ in steps] if steps else None,
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
474 mode="lines",
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
475 )
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
476 layout = go.Layout(
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
477 xaxis=dict(title="Number of features selected"),
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
478 yaxis=dict(title="Cross validation score"),
20
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
479 title=dict(
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
480 text=title or None, x=0.5, y=0.92, xanchor="center", yanchor="top"
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
481 ),
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
482 font=dict(family="sans-serif", size=11),
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
483 # control backgroud colors
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
484 plot_bgcolor="rgba(255,255,255,0)",
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
485 )
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
486 """
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
487 # legend=dict(
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
488 # x=0.95,
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
489 # y=0,
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
490 # traceorder="normal",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
491 # font=dict(
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
492 # family="sans-serif",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
493 # size=9,
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
494 # color="black"
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
495 # ),
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
496 # bgcolor="LightSteelBlue",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
497 # bordercolor="Black",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
498 # borderwidth=2
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
499 # ),
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
500 """
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
501
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
502 fig = go.Figure(data=[data], layout=layout)
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
503 plotly.offline.plot(fig, filename="output.html", auto_open=False)
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
504 # to be discovered by `from_work_dir`
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
505 os.rename("output.html", "output")
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
506
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
507 return 0
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
508
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
509 elif plot_type == "learning_curve":
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
510 input_df = pd.read_csv(infile1, sep="\t", header="infer")
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
511 plot_std_err = params["plotting_selection"]["plot_std_err"]
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
512 data1 = go.Scatter(
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
513 x=input_df["train_sizes_abs"],
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
514 y=input_df["mean_train_scores"],
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
515 error_y=dict(array=input_df["std_train_scores"]) if plot_std_err else None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
516 mode="lines",
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
517 name="Train Scores",
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
518 )
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
519 data2 = go.Scatter(
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
520 x=input_df["train_sizes_abs"],
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
521 y=input_df["mean_test_scores"],
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
522 error_y=dict(array=input_df["std_test_scores"]) if plot_std_err else None,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
523 mode="lines",
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
524 name="Test Scores",
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
525 )
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
526 layout = dict(
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
527 xaxis=dict(title="No. of samples"),
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
528 yaxis=dict(title="Performance Score"),
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
529 # modify these configurations to customize image
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
530 title=dict(
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
531 text=title or "Learning Curve",
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
532 x=0.5,
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
533 y=0.92,
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
534 xanchor="center",
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
535 yanchor="top",
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
536 ),
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
537 font=dict(family="sans-serif", size=11),
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
538 # control backgroud colors
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
539 plot_bgcolor="rgba(255,255,255,0)",
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
540 )
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
541 """
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
542 # legend=dict(
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
543 # x=0.95,
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
544 # y=0,
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
545 # traceorder="normal",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
546 # font=dict(
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
547 # family="sans-serif",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
548 # size=9,
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
549 # color="black"
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
550 # ),
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
551 # bgcolor="LightSteelBlue",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
552 # bordercolor="Black",
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
553 # borderwidth=2
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
554 # ),
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
555 """
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
556
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
557 fig = go.Figure(data=[data1, data2], layout=layout)
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
558 plotly.offline.plot(fig, filename="output.html", auto_open=False)
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
559 # to be discovered by `from_work_dir`
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
560 os.rename("output.html", "output")
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
561
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
562 return 0
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
563
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
564 elif plot_type == "keras_plot_model":
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
565 with open(model_config, "r") as f:
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
566 model_str = f.read()
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
567 model = model_from_json(model_str)
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
568 plot_model(model, to_file="output.png")
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
569 os.rename("output.png", "output")
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
570
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
571 return 0
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
572
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
573 elif plot_type == "classification_confusion_matrix":
17
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
574 plot_selection = params["plotting_selection"]
20
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
575 input_true = get_dataframe(
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
576 true_labels, plot_selection, "header_true", "column_selector_options_true"
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
577 )
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
578 header_predicted = "infer" if plot_selection["header_predicted"] else None
20
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
579 input_predicted = pd.read_csv(
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
580 predicted_labels, sep="\t", parse_dates=True, header=header_predicted
9cff519e0d13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 19
diff changeset
581 )
17
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
582 true_classes = input_true.iloc[:, -1].copy()
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
583 predicted_classes = input_predicted.iloc[:, -1].copy()
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
584 axis_labels = list(set(true_classes))
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
585 c_matrix = confusion_matrix(true_classes, predicted_classes)
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
586 fig, ax = plt.subplots(figsize=(7, 7))
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
587 im = plt.imshow(c_matrix, cmap=plot_color)
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
588 for i in range(len(c_matrix)):
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
589 for j in range(len(c_matrix)):
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
590 ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k")
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
591 ax.set_ylabel("True class labels")
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
592 ax.set_xlabel("Predicted class labels")
17
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
593 ax.set_title(title)
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
594 ax.set_xticks(axis_labels)
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
595 ax.set_yticks(axis_labels)
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
596 fig.colorbar(im, ax=ax)
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
597 fig.tight_layout()
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
598 plt.savefig("output.png", dpi=125)
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
599 os.rename("output.png", "output")
17
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
600
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
601 return 0
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
602
15
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
603 # save pdf file to disk
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
604 # fig.write_image("image.pdf", format='pdf')
2bbf0b17deab "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
605 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
606
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
607
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
608 if __name__ == "__main__":
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
609 aparser = argparse.ArgumentParser()
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
610 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
611 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
612 aparser.add_argument("-X", "--infile1", dest="infile1")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
613 aparser.add_argument("-y", "--infile2", dest="infile2")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
614 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
615 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
616 aparser.add_argument("-g", "--groups", dest="groups")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
617 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
618 aparser.add_argument("-b", "--intervals", dest="intervals")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
619 aparser.add_argument("-t", "--targets", dest="targets")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
620 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
621 aparser.add_argument("-c", "--model_config", dest="model_config")
17
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
622 aparser.add_argument("-tl", "--true_labels", dest="true_labels")
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
623 aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels")
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
624 aparser.add_argument("-pc", "--plot_color", dest="plot_color")
93d7a03efd83 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 15
diff changeset
625 aparser.add_argument("-pt", "--title", dest="title")
11
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
626 args = aparser.parse_args()
a14fb713aaad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
627
18
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
628 main(
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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629 args.inputs,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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630 args.infile_estimator,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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631 args.infile1,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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632 args.infile2,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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633 args.outfile_result,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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634 outfile_object=args.outfile_object,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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635 groups=args.groups,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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636 ref_seq=args.ref_seq,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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637 intervals=args.intervals,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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638 targets=args.targets,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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639 fasta_path=args.fasta_path,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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640 model_config=args.model_config,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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641 true_labels=args.true_labels,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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642 predicted_labels=args.predicted_labels,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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643 plot_color=args.plot_color,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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644 title=args.title,
aa5170605077 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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645 )