Mercurial > repos > bgruening > sklearn_numeric_clustering

annotate ml_visualization_ex.py @ 34:816b65d52c33 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author bgruening
date Tue, 13 Apr 2021 18:05:02 +0000
parents ad7e0b4291ee
children e7f047a9dca9
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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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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, confusion_matrix
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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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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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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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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(y_true, y_score, pos_label=pos_label)
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56 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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58 trace = go.Scatter(
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59 x=recall,
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60 y=precision,
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61 mode="lines",
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62 marker=dict(color=default_colors[idx % len(default_colors)]),
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63 name="%s (area = %.3f)" % (idx, ap),
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64 )
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65 data.append(trace)
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66
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67 layout = go.Layout(
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68 xaxis=dict(title="Recall", linecolor="lightslategray", linewidth=1),
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69 yaxis=dict(title="Precision", linecolor="lightslategray", linewidth=1),
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70 title=dict(
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71 text=title or "Precision-Recall Curve",
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72 x=0.5,
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73 y=0.92,
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74 xanchor="center",
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75 yanchor="top",
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76 ),
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77 font=dict(family="sans-serif", size=11),
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78 # control backgroud colors
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79 plot_bgcolor="rgba(255,255,255,0)",
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80 )
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81 """
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82 legend=dict(
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83 x=0.95,
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84 y=0,
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85 traceorder="normal",
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86 font=dict(
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87 family="sans-serif",
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88 size=9,
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89 color="black"
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90 ),
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91 bgcolor="LightSteelBlue",
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92 bordercolor="Black",
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93 borderwidth=2
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94 ),"""
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95
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96 fig = go.Figure(data=data, layout=layout)
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97
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98 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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99 # to be discovered by `from_work_dir`
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100 os.rename("output.html", "output")
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101
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102
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103 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
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104 """visualize pr-curve using matplotlib and output svg image"""
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105 backend = matplotlib.get_backend()
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106 if "inline" not in backend:
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107 matplotlib.use("SVG")
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108 plt.style.use("seaborn-colorblind")
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109 plt.figure()
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110
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111 for idx in range(df1.shape[1]):
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112 y_true = df1.iloc[:, idx].values
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113 y_score = df2.iloc[:, idx].values
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114
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115 precision, recall, _ = precision_recall_curve(y_true, y_score, pos_label=pos_label)
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116 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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117
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118 plt.step(
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119 recall,
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120 precision,
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121 "r-",
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122 color="black",
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123 alpha=0.3,
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124 lw=1,
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125 where="post",
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126 label="%s (area = %.3f)" % (idx, ap),
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127 )
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128
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129 plt.xlim([0.0, 1.0])
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130 plt.ylim([0.0, 1.05])
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131 plt.xlabel("Recall")
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132 plt.ylabel("Precision")
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133 title = title or "Precision-Recall Curve"
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134 plt.title(title)
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135 folder = os.getcwd()
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136 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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137 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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138
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139
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140 def visualize_roc_curve_plotly(df1, df2, pos_label, drop_intermediate=True, title=None):
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141 """output roc-curve in html using plotly
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142
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143 df1 : pandas.DataFrame
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144 Containing y_true
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145 df2 : pandas.DataFrame
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146 Containing y_score
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147 pos_label : None
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148 The label of positive class
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149 drop_intermediate : bool
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150 Whether to drop some suboptimal thresholds
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151 title : str
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152 Plot title
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153 """
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154 data = []
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155 for idx in range(df1.shape[1]):
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156 y_true = df1.iloc[:, idx].values
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157 y_score = df2.iloc[:, idx].values
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158
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159 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate)
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160 roc_auc = auc(fpr, tpr)
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161
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162 trace = go.Scatter(
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163 x=fpr,
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164 y=tpr,
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165 mode="lines",
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166 marker=dict(color=default_colors[idx % len(default_colors)]),
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167 name="%s (area = %.3f)" % (idx, roc_auc),
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168 )
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169 data.append(trace)
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170
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171 layout = go.Layout(
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172 xaxis=dict(title="False Positive Rate", linecolor="lightslategray", linewidth=1),
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173 yaxis=dict(title="True Positive Rate", linecolor="lightslategray", linewidth=1),
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174 title=dict(
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175 text=title or "Receiver Operating Characteristic (ROC) Curve",
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176 x=0.5,
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177 y=0.92,
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178 xanchor="center",
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179 yanchor="top",
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180 ),
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181 font=dict(family="sans-serif", size=11),
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182 # control backgroud colors
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183 plot_bgcolor="rgba(255,255,255,0)",
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184 )
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185 """
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186 # legend=dict(
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187 # x=0.95,
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188 # y=0,
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189 # traceorder="normal",
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190 # font=dict(
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191 # family="sans-serif",
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192 # size=9,
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193 # color="black"
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194 # ),
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195 # bgcolor="LightSteelBlue",
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196 # bordercolor="Black",
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197 # borderwidth=2
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198 # ),
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199 """
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200
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201 fig = go.Figure(data=data, layout=layout)
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202
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203 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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204 # to be discovered by `from_work_dir`
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205 os.rename("output.html", "output")
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206
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207
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208 def visualize_roc_curve_matplotlib(df1, df2, pos_label, drop_intermediate=True, title=None):
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209 """visualize roc-curve using matplotlib and output svg image"""
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210 backend = matplotlib.get_backend()
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211 if "inline" not in backend:
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212 matplotlib.use("SVG")
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213 plt.style.use("seaborn-colorblind")
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214 plt.figure()
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215
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216 for idx in range(df1.shape[1]):
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217 y_true = df1.iloc[:, idx].values
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218 y_score = df2.iloc[:, idx].values
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219
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220 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate)
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221 roc_auc = auc(fpr, tpr)
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222
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223 plt.step(
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224 fpr,
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225 tpr,
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226 "r-",
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227 color="black",
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228 alpha=0.3,
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229 lw=1,
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230 where="post",
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231 label="%s (area = %.3f)" % (idx, roc_auc),
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232 )
31
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233
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234 plt.xlim([0.0, 1.0])
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235 plt.ylim([0.0, 1.05])
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236 plt.xlabel("False Positive Rate")
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237 plt.ylabel("True Positive Rate")
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238 title = title or "Receiver Operating Characteristic (ROC) Curve"
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239 plt.title(title)
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240 folder = os.getcwd()
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241 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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242 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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243
27
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244
33
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245 def get_dataframe(file_path, plot_selection, header_name, column_name):
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246 header = "infer" if plot_selection[header_name] else None
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247 column_option = plot_selection[column_name]["selected_column_selector_option"]
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248 if column_option in [
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249 "by_index_number",
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250 "all_but_by_index_number",
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251 "by_header_name",
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252 "all_but_by_header_name",
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253 ]:
33
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254 col = plot_selection[column_name]["col1"]
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255 else:
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256 col = None
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257 _, input_df = read_columns(file_path, c=col,
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258 c_option=column_option,
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259 return_df=True,
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260 sep='\t', header=header,
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261 parse_dates=True)
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262 return input_df
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263
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264
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265 def main(
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266 inputs,
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267 infile_estimator=None,
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268 infile1=None,
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269 infile2=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
270 outfile_result=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
271 outfile_object=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
272 groups=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
273 ref_seq=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
274 intervals=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
275 targets=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
276 fasta_path=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
277 model_config=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
278 true_labels=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
279 predicted_labels=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
280 plot_color=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
281 title=None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
282 ):
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
283 """
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
284 Parameter
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
285 ---------
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
286 inputs : str
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
287 File path to galaxy tool parameter
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
288
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
289 infile_estimator : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
290 File path to estimator
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
291
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
292 infile1 : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
293 File path to dataset containing features or true labels.
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
294
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
295 infile2 : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
296 File path to dataset containing target values or predicted
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
297 probabilities.
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
298
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
299 outfile_result : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
300 File path to save the results, either cv_results or test result
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
301
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
302 outfile_object : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
303 File path to save searchCV object
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
304
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
305 groups : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
306 File path to dataset containing groups labels
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
307
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
308 ref_seq : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
309 File path to dataset containing genome sequence file
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
310
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
311 intervals : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
312 File path to dataset containing interval file
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
313
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
314 targets : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
315 File path to dataset compressed target bed file
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
316
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
317 fasta_path : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
318 File path to dataset containing fasta file
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
319
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
320 model_config : str, default is None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
321 File path to dataset containing JSON config for neural networks
33
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
322
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
323 true_labels : str, default is None
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
324 File path to dataset containing true labels
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
325
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
326 predicted_labels : str, default is None
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
327 File path to dataset containing true predicted labels
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
328
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
329 plot_color : str, default is None
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
330 Color of the confusion matrix heatmap
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
331
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
332 title : str, default is None
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
333 Title of the confusion matrix heatmap
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
334 """
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
335 warnings.simplefilter("ignore")
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
336
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
337 with open(inputs, "r") as param_handler:
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
338 params = json.load(param_handler)
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
339
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
340 title = params["plotting_selection"]["title"].strip()
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
341 plot_type = params["plotting_selection"]["plot_type"]
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
342 plot_format = params["plotting_selection"]["plot_format"]
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
343
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
344 if plot_type == "feature_importances":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
345 with open(infile_estimator, "rb") as estimator_handler:
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
346 estimator = load_model(estimator_handler)
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
347
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
348 column_option = params["plotting_selection"]["column_selector_options"]["selected_column_selector_option"]
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
349 if column_option in [
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
350 "by_index_number",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
351 "all_but_by_index_number",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
352 "by_header_name",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
353 "all_but_by_header_name",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
354 ]:
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
355 c = params["plotting_selection"]["column_selector_options"]["col1"]
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
356 else:
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
357 c = None
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
358
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
359 _, input_df = read_columns(
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
360 infile1,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
361 c=c,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
362 c_option=column_option,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
363 return_df=True,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
364 sep="\t",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
365 header="infer",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
366 parse_dates=True,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
367 )
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
368
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
369 feature_names = input_df.columns.values
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
370
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
371 if isinstance(estimator, Pipeline):
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
372 for st in estimator.steps[:-1]:
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
373 if isinstance(st[-1], SelectorMixin):
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
374 mask = st[-1].get_support()
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
375 feature_names = feature_names[mask]
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
376 estimator = estimator.steps[-1][-1]
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
377
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
378 if hasattr(estimator, "coef_"):
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
379 coefs = estimator.coef_
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
380 else:
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
381 coefs = getattr(estimator, "feature_importances_", None)
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
382 if coefs is None:
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
383 raise RuntimeError("The classifier does not expose " '"coef_" or "feature_importances_" ' "attributes")
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
384
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
385 threshold = params["plotting_selection"]["threshold"]
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
386 if threshold is not None:
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
387 mask = (coefs > threshold) | (coefs < -threshold)
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
388 coefs = coefs[mask]
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
389 feature_names = feature_names[mask]
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
390
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
391 # sort
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
392 indices = np.argsort(coefs)[::-1]
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
393
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
394 trace = go.Bar(x=feature_names[indices], y=coefs[indices])
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
395 layout = go.Layout(title=title or "Feature Importances")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
396 fig = go.Figure(data=[trace], layout=layout)
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
397
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
398 plotly.offline.plot(fig, filename="output.html", auto_open=False)
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
399 # to be discovered by `from_work_dir`
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
400 os.rename("output.html", "output")
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
401
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
402 return 0
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
403
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
404 elif plot_type in ("pr_curve", "roc_curve"):
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
405 df1 = pd.read_csv(infile1, sep="\t", header="infer")
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
406 df2 = pd.read_csv(infile2, sep="\t", header="infer").astype(np.float32)
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
407
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
408 minimum = params["plotting_selection"]["report_minimum_n_positives"]
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
409 # filter out columns whose n_positives is beblow the threhold
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
410 if minimum:
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
411 mask = df1.sum(axis=0) >= minimum
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
412 df1 = df1.loc[:, mask]
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
413 df2 = df2.loc[:, mask]
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
414
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
415 pos_label = params["plotting_selection"]["pos_label"].strip() or None
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
416
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
417 if plot_type == "pr_curve":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
418 if plot_format == "plotly_html":
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
419 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
420 else:
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
421 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
422 else: # 'roc_curve'
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
423 drop_intermediate = params["plotting_selection"]["drop_intermediate"]
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
424 if plot_format == "plotly_html":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
425 visualize_roc_curve_plotly(
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
426 df1,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
427 df2,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
428 pos_label,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
429 drop_intermediate=drop_intermediate,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
430 title=title,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
431 )
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
432 else:
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
433 visualize_roc_curve_matplotlib(
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
434 df1,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
435 df2,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
436 pos_label,
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
437 drop_intermediate=drop_intermediate,
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
438 title=title,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
439 )
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
440
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
441 return 0
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
442
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
443 elif plot_type == "rfecv_gridscores":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
444 input_df = pd.read_csv(infile1, sep="\t", header="infer")
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
445 scores = input_df.iloc[:, 0]
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
446 steps = params["plotting_selection"]["steps"].strip()
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
447 steps = safe_eval(steps)
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
448
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
449 data = go.Scatter(
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
450 x=list(range(len(scores))),
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
451 y=scores,
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
452 text=[str(_) for _ in steps] if steps else None,
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
453 mode="lines",
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
454 )
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
455 layout = go.Layout(
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
456 xaxis=dict(title="Number of features selected"),
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
457 yaxis=dict(title="Cross validation score"),
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
458 title=dict(text=title or None, x=0.5, y=0.92, xanchor="center", yanchor="top"),
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
459 font=dict(family="sans-serif", size=11),
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
460 # control backgroud colors
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
461 plot_bgcolor="rgba(255,255,255,0)",
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
462 )
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
463 """
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
464 # legend=dict(
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
465 # x=0.95,
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
466 # y=0,
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
467 # traceorder="normal",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
468 # font=dict(
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
469 # family="sans-serif",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
470 # size=9,
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
471 # color="black"
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
472 # ),
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
473 # bgcolor="LightSteelBlue",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
474 # bordercolor="Black",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
475 # borderwidth=2
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
476 # ),
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
477 """
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
478
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
479 fig = go.Figure(data=[data], layout=layout)
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
480 plotly.offline.plot(fig, filename="output.html", auto_open=False)
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
481 # to be discovered by `from_work_dir`
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
482 os.rename("output.html", "output")
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
483
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
484 return 0
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
485
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
486 elif plot_type == "learning_curve":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
487 input_df = pd.read_csv(infile1, sep="\t", header="infer")
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
488 plot_std_err = params["plotting_selection"]["plot_std_err"]
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
489 data1 = go.Scatter(
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
490 x=input_df["train_sizes_abs"],
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
491 y=input_df["mean_train_scores"],
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
492 error_y=dict(array=input_df["std_train_scores"]) if plot_std_err else None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
493 mode="lines",
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
494 name="Train Scores",
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
495 )
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
496 data2 = go.Scatter(
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
497 x=input_df["train_sizes_abs"],
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
498 y=input_df["mean_test_scores"],
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
499 error_y=dict(array=input_df["std_test_scores"]) if plot_std_err else None,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
500 mode="lines",
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
501 name="Test Scores",
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
502 )
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
503 layout = dict(
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
504 xaxis=dict(title="No. of samples"),
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
505 yaxis=dict(title="Performance Score"),
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
506 # modify these configurations to customize image
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
507 title=dict(
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
508 text=title or "Learning Curve",
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
509 x=0.5,
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
510 y=0.92,
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
511 xanchor="center",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
512 yanchor="top",
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
513 ),
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
514 font=dict(family="sans-serif", size=11),
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
515 # control backgroud colors
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
516 plot_bgcolor="rgba(255,255,255,0)",
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
517 )
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
518 """
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
519 # legend=dict(
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
520 # x=0.95,
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
521 # y=0,
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
522 # traceorder="normal",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
523 # font=dict(
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
524 # family="sans-serif",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
525 # size=9,
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
526 # color="black"
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
527 # ),
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
528 # bgcolor="LightSteelBlue",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
529 # bordercolor="Black",
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
530 # borderwidth=2
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
531 # ),
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
532 """
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
533
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
534 fig = go.Figure(data=[data1, data2], layout=layout)
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
535 plotly.offline.plot(fig, filename="output.html", auto_open=False)
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
536 # to be discovered by `from_work_dir`
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
537 os.rename("output.html", "output")
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
538
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
539 return 0
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
540
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
541 elif plot_type == "keras_plot_model":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
542 with open(model_config, "r") as f:
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
543 model_str = f.read()
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
544 model = model_from_json(model_str)
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
545 plot_model(model, to_file="output.png")
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
546 os.rename("output.png", "output")
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
547
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
548 return 0
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
549
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
550 elif plot_type == "classification_confusion_matrix":
33
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
551 plot_selection = params["plotting_selection"]
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
552 input_true = get_dataframe(true_labels, plot_selection, "header_true", "column_selector_options_true")
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
553 header_predicted = "infer" if plot_selection["header_predicted"] else None
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
554 input_predicted = pd.read_csv(predicted_labels, sep="\t", parse_dates=True, header=header_predicted)
33
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
555 true_classes = input_true.iloc[:, -1].copy()
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
556 predicted_classes = input_predicted.iloc[:, -1].copy()
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
557 axis_labels = list(set(true_classes))
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
558 c_matrix = confusion_matrix(true_classes, predicted_classes)
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
559 fig, ax = plt.subplots(figsize=(7, 7))
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
560 im = plt.imshow(c_matrix, cmap=plot_color)
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
561 for i in range(len(c_matrix)):
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
562 for j in range(len(c_matrix)):
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
563 ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k")
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
564 ax.set_ylabel("True class labels")
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
565 ax.set_xlabel("Predicted class labels")
33
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
566 ax.set_title(title)
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
567 ax.set_xticks(axis_labels)
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
568 ax.set_yticks(axis_labels)
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
569 fig.colorbar(im, ax=ax)
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
570 fig.tight_layout()
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
571 plt.savefig("output.png", dpi=125)
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
572 os.rename("output.png", "output")
33
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
573
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
574 return 0
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
575
31
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
576 # save pdf file to disk
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
577 # fig.write_image("image.pdf", format='pdf')
83938131dd46 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
578 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
579
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
580
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
581 if __name__ == "__main__":
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
582 aparser = argparse.ArgumentParser()
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
583 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
584 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
585 aparser.add_argument("-X", "--infile1", dest="infile1")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
586 aparser.add_argument("-y", "--infile2", dest="infile2")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
587 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
588 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
589 aparser.add_argument("-g", "--groups", dest="groups")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
590 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
591 aparser.add_argument("-b", "--intervals", dest="intervals")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
592 aparser.add_argument("-t", "--targets", dest="targets")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
593 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
594 aparser.add_argument("-c", "--model_config", dest="model_config")
33
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
595 aparser.add_argument("-tl", "--true_labels", dest="true_labels")
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
596 aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels")
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
597 aparser.add_argument("-pc", "--plot_color", dest="plot_color")
ad7e0b4291ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents: 31
diff changeset
598 aparser.add_argument("-pt", "--title", dest="title")
27
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
599 args = aparser.parse_args()
6edcaa8dbb9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
600
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
601 main(
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
602 args.inputs,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
603 args.infile_estimator,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
604 args.infile1,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
605 args.infile2,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
606 args.outfile_result,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
607 outfile_object=args.outfile_object,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
608 groups=args.groups,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
609 ref_seq=args.ref_seq,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
610 intervals=args.intervals,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
611 targets=args.targets,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
612 fasta_path=args.fasta_path,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
613 model_config=args.model_config,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
614 true_labels=args.true_labels,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
615 predicted_labels=args.predicted_labels,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
616 plot_color=args.plot_color,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
617 title=args.title,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 33
diff changeset
618 )