Mercurial > repos > bgruening > sklearn_svm_classifier

annotate ml_visualization_ex.py @ 15:2df8f5c30edc draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
author bgruening
date Mon, 16 Dec 2019 05:21:05 -0500
parents 73d2ef652879
children d2afc87db26b
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7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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1 import argparse
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2 import json
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3 import matplotlib
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4 import matplotlib.pyplot as plt
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5 import numpy as np
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6 import os
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7 import pandas as pd
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8 import plotly
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9 import plotly.graph_objs as go
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10 import warnings
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7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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12 from keras.models import model_from_json
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13 from keras.utils import plot_model
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14 from sklearn.feature_selection.base import SelectorMixin
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15 from sklearn.metrics import precision_recall_curve, average_precision_score
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16 from sklearn.metrics import roc_curve, auc
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17 from sklearn.pipeline import Pipeline
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18 from galaxy_ml.utils import load_model, read_columns, SafeEval
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21 safe_eval = SafeEval()
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22
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23 # plotly default colors
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24 default_colors = [
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25 '#1f77b4', # muted blue
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26 '#ff7f0e', # safety orange
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27 '#2ca02c', # cooked asparagus green
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28 '#d62728', # brick red
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29 '#9467bd', # muted purple
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30 '#8c564b', # chestnut brown
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31 '#e377c2', # raspberry yogurt pink
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32 '#7f7f7f', # middle gray
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33 '#bcbd22', # curry yellow-green
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34 '#17becf' # blue-teal
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35 ]
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37
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38 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None):
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39 """output pr-curve in html using plotly
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40
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41 df1 : pandas.DataFrame
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42 Containing y_true
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43 df2 : pandas.DataFrame
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44 Containing y_score
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45 pos_label : None
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46 The label of positive class
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47 title : str
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48 Plot title
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49 """
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50 data = []
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51 for idx in range(df1.shape[1]):
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52 y_true = df1.iloc[:, idx].values
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53 y_score = df2.iloc[:, idx].values
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54
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55 precision, recall, _ = precision_recall_curve(
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56 y_true, y_score, pos_label=pos_label)
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57 ap = average_precision_score(
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58 y_true, y_score, pos_label=pos_label or 1)
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59
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60 trace = go.Scatter(
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61 x=recall,
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62 y=precision,
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63 mode='lines',
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64 marker=dict(
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65 color=default_colors[idx % len(default_colors)]
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66 ),
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67 name='%s (area = %.3f)' % (idx, ap)
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68 )
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69 data.append(trace)
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70
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71 layout = go.Layout(
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72 xaxis=dict(
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73 title='Recall',
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74 linecolor='lightslategray',
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75 linewidth=1
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76 ),
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77 yaxis=dict(
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78 title='Precision',
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79 linecolor='lightslategray',
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80 linewidth=1
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81 ),
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82 title=dict(
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83 text=title or 'Precision-Recall Curve',
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84 x=0.5,
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85 y=0.92,
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86 xanchor='center',
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87 yanchor='top'
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88 ),
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89 font=dict(
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90 family="sans-serif",
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91 size=11
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92 ),
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93 # control backgroud colors
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94 plot_bgcolor='rgba(255,255,255,0)'
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95 )
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96 """
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97 legend=dict(
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98 x=0.95,
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99 y=0,
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100 traceorder="normal",
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101 font=dict(
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102 family="sans-serif",
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103 size=9,
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104 color="black"
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105 ),
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106 bgcolor="LightSteelBlue",
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107 bordercolor="Black",
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108 borderwidth=2
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109 ),"""
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110
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111 fig = go.Figure(data=data, layout=layout)
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112
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113 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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114 # to be discovered by `from_work_dir`
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115 os.rename('output.html', 'output')
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116
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117
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118 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
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119 """visualize pr-curve using matplotlib and output svg image
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120 """
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121 backend = matplotlib.get_backend()
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122 if "inline" not in backend:
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123 matplotlib.use("SVG")
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124 plt.style.use('seaborn-colorblind')
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125 plt.figure()
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126
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127 for idx in range(df1.shape[1]):
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128 y_true = df1.iloc[:, idx].values
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129 y_score = df2.iloc[:, idx].values
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130
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131 precision, recall, _ = precision_recall_curve(
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132 y_true, y_score, pos_label=pos_label)
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133 ap = average_precision_score(
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134 y_true, y_score, pos_label=pos_label or 1)
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135
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136 plt.step(recall, precision, 'r-', color="black", alpha=0.3,
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137 lw=1, where="post", label='%s (area = %.3f)' % (idx, ap))
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138
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139 plt.xlim([0.0, 1.0])
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140 plt.ylim([0.0, 1.05])
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141 plt.xlabel('Recall')
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142 plt.ylabel('Precision')
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143 title = title or 'Precision-Recall Curve'
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144 plt.title(title)
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145 folder = os.getcwd()
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146 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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147 os.rename(os.path.join(folder, "output.svg"),
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148 os.path.join(folder, "output"))
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149
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150
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151 def visualize_roc_curve_plotly(df1, df2, pos_label,
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152 drop_intermediate=True,
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153 title=None):
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154 """output roc-curve in html using plotly
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155
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156 df1 : pandas.DataFrame
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157 Containing y_true
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158 df2 : pandas.DataFrame
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159 Containing y_score
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160 pos_label : None
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161 The label of positive class
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162 drop_intermediate : bool
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163 Whether to drop some suboptimal thresholds
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164 title : str
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165 Plot title
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166 """
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167 data = []
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168 for idx in range(df1.shape[1]):
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169 y_true = df1.iloc[:, idx].values
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170 y_score = df2.iloc[:, idx].values
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171
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172 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label,
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173 drop_intermediate=drop_intermediate)
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174 roc_auc = auc(fpr, tpr)
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175
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176 trace = go.Scatter(
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177 x=fpr,
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178 y=tpr,
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179 mode='lines',
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180 marker=dict(
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181 color=default_colors[idx % len(default_colors)]
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182 ),
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183 name='%s (area = %.3f)' % (idx, roc_auc)
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184 )
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185 data.append(trace)
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186
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187 layout = go.Layout(
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188 xaxis=dict(
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189 title='False Positive Rate',
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190 linecolor='lightslategray',
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191 linewidth=1
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192 ),
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193 yaxis=dict(
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194 title='True Positive Rate',
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195 linecolor='lightslategray',
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196 linewidth=1
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197 ),
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198 title=dict(
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199 text=title or 'Receiver Operating Characteristic (ROC) Curve',
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200 x=0.5,
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201 y=0.92,
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202 xanchor='center',
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203 yanchor='top'
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204 ),
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205 font=dict(
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206 family="sans-serif",
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207 size=11
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208 ),
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209 # control backgroud colors
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210 plot_bgcolor='rgba(255,255,255,0)'
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211 )
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212 """
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213 # legend=dict(
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214 # x=0.95,
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215 # y=0,
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216 # traceorder="normal",
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217 # font=dict(
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218 # family="sans-serif",
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219 # size=9,
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220 # color="black"
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221 # ),
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222 # bgcolor="LightSteelBlue",
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223 # bordercolor="Black",
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224 # borderwidth=2
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225 # ),
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226 """
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227
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228 fig = go.Figure(data=data, layout=layout)
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229
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230 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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231 # to be discovered by `from_work_dir`
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232 os.rename('output.html', 'output')
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233
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234
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235 def visualize_roc_curve_matplotlib(df1, df2, pos_label,
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236 drop_intermediate=True,
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237 title=None):
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238 """visualize roc-curve using matplotlib and output svg image
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239 """
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240 backend = matplotlib.get_backend()
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241 if "inline" not in backend:
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242 matplotlib.use("SVG")
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243 plt.style.use('seaborn-colorblind')
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244 plt.figure()
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245
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246 for idx in range(df1.shape[1]):
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247 y_true = df1.iloc[:, idx].values
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248 y_score = df2.iloc[:, idx].values
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249
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250 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label,
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251 drop_intermediate=drop_intermediate)
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252 roc_auc = auc(fpr, tpr)
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253
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254 plt.step(fpr, tpr, 'r-', color="black", alpha=0.3, lw=1,
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255 where="post", label='%s (area = %.3f)' % (idx, roc_auc))
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256
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257 plt.xlim([0.0, 1.0])
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258 plt.ylim([0.0, 1.05])
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259 plt.xlabel('False Positive Rate')
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260 plt.ylabel('True Positive Rate')
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261 title = title or 'Receiver Operating Characteristic (ROC) Curve'
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262 plt.title(title)
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263 folder = os.getcwd()
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264 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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265 os.rename(os.path.join(folder, "output.svg"),
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266 os.path.join(folder, "output"))
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267
11
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268
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269 def main(inputs, infile_estimator=None, infile1=None,
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270 infile2=None, outfile_result=None,
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271 outfile_object=None, groups=None,
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bgruening
parents:
diff changeset
272 ref_seq=None, intervals=None,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
273 targets=None, fasta_path=None,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
274 model_config=None):
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
275 """
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
276 Parameter
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
277 ---------
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
278 inputs : str
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
279 File path to galaxy tool parameter
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
280
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
281 infile_estimator : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
282 File path to estimator
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
283
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
284 infile1 : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
285 File path to dataset containing features or true labels.
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
286
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
287 infile2 : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
288 File path to dataset containing target values or predicted
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
289 probabilities.
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
290
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
291 outfile_result : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
292 File path to save the results, either cv_results or test result
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
293
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
294 outfile_object : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
295 File path to save searchCV object
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
296
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
297 groups : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
298 File path to dataset containing groups labels
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
299
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
300 ref_seq : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
301 File path to dataset containing genome sequence file
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
302
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
303 intervals : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
304 File path to dataset containing interval file
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
305
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
306 targets : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
307 File path to dataset compressed target bed file
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
308
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
309 fasta_path : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
310 File path to dataset containing fasta file
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
311
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
312 model_config : str, default is None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
313 File path to dataset containing JSON config for neural networks
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
314 """
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
315 warnings.simplefilter('ignore')
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
316
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
317 with open(inputs, 'r') as param_handler:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
318 params = json.load(param_handler)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
319
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
320 title = params['plotting_selection']['title'].strip()
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
321 plot_type = params['plotting_selection']['plot_type']
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
322 plot_format = params['plotting_selection']['plot_format']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
323
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
324 if plot_type == 'feature_importances':
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
325 with open(infile_estimator, 'rb') as estimator_handler:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
326 estimator = load_model(estimator_handler)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
327
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
328 column_option = (params['plotting_selection']
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
329 ['column_selector_options']
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
330 ['selected_column_selector_option'])
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
331 if column_option in ['by_index_number', 'all_but_by_index_number',
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
332 'by_header_name', 'all_but_by_header_name']:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
333 c = (params['plotting_selection']
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
334 ['column_selector_options']['col1'])
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
335 else:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
336 c = None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
337
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
338 _, input_df = read_columns(infile1, c=c,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
339 c_option=column_option,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
340 return_df=True,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
341 sep='\t', header='infer',
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
342 parse_dates=True)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
343
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
344 feature_names = input_df.columns.values
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
345
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
346 if isinstance(estimator, Pipeline):
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
347 for st in estimator.steps[:-1]:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
348 if isinstance(st[-1], SelectorMixin):
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
349 mask = st[-1].get_support()
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
350 feature_names = feature_names[mask]
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
351 estimator = estimator.steps[-1][-1]
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
352
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
353 if hasattr(estimator, 'coef_'):
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
354 coefs = estimator.coef_
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
355 else:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
356 coefs = getattr(estimator, 'feature_importances_', None)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
357 if coefs is None:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
358 raise RuntimeError('The classifier does not expose '
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
359 '"coef_" or "feature_importances_" '
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
360 'attributes')
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
361
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
362 threshold = params['plotting_selection']['threshold']
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
363 if threshold is not None:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
364 mask = (coefs > threshold) | (coefs < -threshold)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
365 coefs = coefs[mask]
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
366 feature_names = feature_names[mask]
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
367
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
368 # sort
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
369 indices = np.argsort(coefs)[::-1]
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
370
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
371 trace = go.Bar(x=feature_names[indices],
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
372 y=coefs[indices])
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
373 layout = go.Layout(title=title or "Feature Importances")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
374 fig = go.Figure(data=[trace], layout=layout)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
375
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
376 plotly.offline.plot(fig, filename="output.html",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
377 auto_open=False)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
378 # to be discovered by `from_work_dir`
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
379 os.rename('output.html', 'output')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
380
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
381 return 0
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
382
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
383 elif plot_type in ('pr_curve', 'roc_curve'):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
384 df1 = pd.read_csv(infile1, sep='\t', header='infer')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
385 df2 = pd.read_csv(infile2, sep='\t', header='infer').astype(np.float32)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
386
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
387 minimum = params['plotting_selection']['report_minimum_n_positives']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
388 # filter out columns whose n_positives is beblow the threhold
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
389 if minimum:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
390 mask = df1.sum(axis=0) >= minimum
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
391 df1 = df1.loc[:, mask]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
392 df2 = df2.loc[:, mask]
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
393
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
394 pos_label = params['plotting_selection']['pos_label'].strip() \
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
395 or None
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
396
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
397 if plot_type == 'pr_curve':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
398 if plot_format == 'plotly_html':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
399 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
400 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
401 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
402 else: # 'roc_curve'
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
403 drop_intermediate = (params['plotting_selection']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
404 ['drop_intermediate'])
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
405 if plot_format == 'plotly_html':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
406 visualize_roc_curve_plotly(df1, df2, pos_label,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
407 drop_intermediate=drop_intermediate,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
408 title=title)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
409 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
410 visualize_roc_curve_matplotlib(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
411 df1, df2, pos_label,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
412 drop_intermediate=drop_intermediate,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
413 title=title)
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
414
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
415 return 0
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
416
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
417 elif plot_type == 'rfecv_gridscores':
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
418 input_df = pd.read_csv(infile1, sep='\t', header='infer')
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
419 scores = input_df.iloc[:, 0]
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
420 steps = params['plotting_selection']['steps'].strip()
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
421 steps = safe_eval(steps)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
422
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
423 data = go.Scatter(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
424 x=list(range(len(scores))),
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
425 y=scores,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
426 text=[str(_) for _ in steps] if steps else None,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
427 mode='lines'
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
428 )
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
429 layout = go.Layout(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
430 xaxis=dict(title="Number of features selected"),
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
431 yaxis=dict(title="Cross validation score"),
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
432 title=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
433 text=title or None,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
434 x=0.5,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
435 y=0.92,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
436 xanchor='center',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
437 yanchor='top'
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
438 ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
439 font=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
440 family="sans-serif",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
441 size=11
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
442 ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
443 # control backgroud colors
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
444 plot_bgcolor='rgba(255,255,255,0)'
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
445 )
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
446 """
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
447 # legend=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
448 # x=0.95,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
449 # y=0,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
450 # traceorder="normal",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
451 # font=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
452 # family="sans-serif",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
453 # size=9,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
454 # color="black"
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
455 # ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
456 # bgcolor="LightSteelBlue",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
457 # bordercolor="Black",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
458 # borderwidth=2
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
459 # ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
460 """
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
461
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
462 fig = go.Figure(data=[data], layout=layout)
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
463 plotly.offline.plot(fig, filename="output.html",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
464 auto_open=False)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
465 # to be discovered by `from_work_dir`
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
466 os.rename('output.html', 'output')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
467
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
468 return 0
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
469
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
470 elif plot_type == 'learning_curve':
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
471 input_df = pd.read_csv(infile1, sep='\t', header='infer')
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
472 plot_std_err = params['plotting_selection']['plot_std_err']
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
473 data1 = go.Scatter(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
474 x=input_df['train_sizes_abs'],
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
475 y=input_df['mean_train_scores'],
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
476 error_y=dict(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
477 array=input_df['std_train_scores']
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
478 ) if plot_std_err else None,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
479 mode='lines',
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
480 name="Train Scores",
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
481 )
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
482 data2 = go.Scatter(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
483 x=input_df['train_sizes_abs'],
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
484 y=input_df['mean_test_scores'],
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
485 error_y=dict(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
486 array=input_df['std_test_scores']
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
487 ) if plot_std_err else None,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
488 mode='lines',
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
489 name="Test Scores",
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
490 )
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
491 layout = dict(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
492 xaxis=dict(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
493 title='No. of samples'
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
494 ),
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
495 yaxis=dict(
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
496 title='Performance Score'
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
497 ),
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
498 # modify these configurations to customize image
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
499 title=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
500 text=title or 'Learning Curve',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
501 x=0.5,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
502 y=0.92,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
503 xanchor='center',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
504 yanchor='top'
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
505 ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
506 font=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
507 family="sans-serif",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
508 size=11
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
509 ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
510 # control backgroud colors
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
511 plot_bgcolor='rgba(255,255,255,0)'
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
512 )
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
513 """
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
514 # legend=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
515 # x=0.95,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
516 # y=0,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
517 # traceorder="normal",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
518 # font=dict(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
519 # family="sans-serif",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
520 # size=9,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
521 # color="black"
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
522 # ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
523 # bgcolor="LightSteelBlue",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
524 # bordercolor="Black",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
525 # borderwidth=2
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
526 # ),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
527 """
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
528
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
529 fig = go.Figure(data=[data1, data2], layout=layout)
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
530 plotly.offline.plot(fig, filename="output.html",
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
531 auto_open=False)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
532 # to be discovered by `from_work_dir`
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
533 os.rename('output.html', 'output')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
534
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
535 return 0
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
536
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
537 elif plot_type == 'keras_plot_model':
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
538 with open(model_config, 'r') as f:
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
539 model_str = f.read()
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
540 model = model_from_json(model_str)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
541 plot_model(model, to_file="output.png")
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
542 os.rename('output.png', 'output')
11
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
543
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
544 return 0
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
545
15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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546 # save pdf file to disk
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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547 # fig.write_image("image.pdf", format='pdf')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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548 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
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7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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549
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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550
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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551 if __name__ == '__main__':
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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552 aparser = argparse.ArgumentParser()
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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553 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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554 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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555 aparser.add_argument("-X", "--infile1", dest="infile1")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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556 aparser.add_argument("-y", "--infile2", dest="infile2")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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557 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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558 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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559 aparser.add_argument("-g", "--groups", dest="groups")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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560 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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561 aparser.add_argument("-b", "--intervals", dest="intervals")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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562 aparser.add_argument("-t", "--targets", dest="targets")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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563 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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564 aparser.add_argument("-c", "--model_config", dest="model_config")
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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565 args = aparser.parse_args()
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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566
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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567 main(args.inputs, args.infile_estimator, args.infile1, args.infile2,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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568 args.outfile_result, outfile_object=args.outfile_object,
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569 groups=args.groups, ref_seq=args.ref_seq, intervals=args.intervals,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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570 targets=args.targets, fasta_path=args.fasta_path,
7d7379dfef8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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571 model_config=args.model_config)