Mercurial > repos > bgruening > sklearn_train_test_eval

annotate ml_visualization_ex.py @ 10:a9e0b963b7bb draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
author bgruening
date Tue, 13 Apr 2021 22:04:06 +0000
parents ead7adad8d0e
children caf7d2b71a48
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cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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1 import argparse
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2 import json
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3 import os
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4 import warnings
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5
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6 import matplotlib
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7 import matplotlib.pyplot as plt
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8 import numpy as np
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9 import pandas as pd
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10 import plotly
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11 import plotly.graph_objs as go
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12 from galaxy_ml.utils import load_model, read_columns, SafeEval
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13 from keras.models import model_from_json
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14 from keras.utils import plot_model
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15 from sklearn.feature_selection.base import SelectorMixin
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16 from sklearn.metrics import auc, average_precision_score, confusion_matrix, precision_recall_curve, roc_curve
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17 from sklearn.pipeline import Pipeline
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20 safe_eval = SafeEval()
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22 # plotly default colors
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23 default_colors = [
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24 "#1f77b4", # muted blue
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25 "#ff7f0e", # safety orange
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26 "#2ca02c", # cooked asparagus green
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27 "#d62728", # brick red
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28 "#9467bd", # muted purple
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29 "#8c564b", # chestnut brown
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30 "#e377c2", # raspberry yogurt pink
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31 "#7f7f7f", # middle gray
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32 "#bcbd22", # curry yellow-green
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33 "#17becf", # blue-teal
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34 ]
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37 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None):
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38 """output pr-curve in html using plotly
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39
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40 df1 : pandas.DataFrame
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41 Containing y_true
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42 df2 : pandas.DataFrame
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43 Containing y_score
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44 pos_label : None
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45 The label of positive class
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46 title : str
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47 Plot title
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48 """
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49 data = []
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50 for idx in range(df1.shape[1]):
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51 y_true = df1.iloc[:, idx].values
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52 y_score = df2.iloc[:, idx].values
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53
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54 precision, recall, _ = precision_recall_curve(y_true, y_score, pos_label=pos_label)
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55 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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56
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57 trace = go.Scatter(
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58 x=recall,
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59 y=precision,
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60 mode="lines",
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61 marker=dict(color=default_colors[idx % len(default_colors)]),
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62 name="%s (area = %.3f)" % (idx, ap),
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63 )
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64 data.append(trace)
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65
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66 layout = go.Layout(
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67 xaxis=dict(title="Recall", linecolor="lightslategray", linewidth=1),
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68 yaxis=dict(title="Precision", linecolor="lightslategray", linewidth=1),
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69 title=dict(
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70 text=title or "Precision-Recall Curve",
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71 x=0.5,
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72 y=0.92,
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73 xanchor="center",
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74 yanchor="top",
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75 ),
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76 font=dict(family="sans-serif", size=11),
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77 # control backgroud colors
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78 plot_bgcolor="rgba(255,255,255,0)",
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79 )
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80 """
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81 legend=dict(
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82 x=0.95,
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83 y=0,
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84 traceorder="normal",
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85 font=dict(
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86 family="sans-serif",
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87 size=9,
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88 color="black"
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89 ),
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90 bgcolor="LightSteelBlue",
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91 bordercolor="Black",
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92 borderwidth=2
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93 ),"""
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94
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95 fig = go.Figure(data=data, layout=layout)
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96
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97 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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98 # to be discovered by `from_work_dir`
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99 os.rename("output.html", "output")
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100
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101
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102 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
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103 """visualize pr-curve using matplotlib and output svg image"""
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104 backend = matplotlib.get_backend()
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105 if "inline" not in backend:
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106 matplotlib.use("SVG")
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107 plt.style.use("seaborn-colorblind")
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108 plt.figure()
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109
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110 for idx in range(df1.shape[1]):
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111 y_true = df1.iloc[:, idx].values
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112 y_score = df2.iloc[:, idx].values
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113
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114 precision, recall, _ = precision_recall_curve(y_true, y_score, pos_label=pos_label)
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115 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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116
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117 plt.step(
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118 recall,
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119 precision,
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120 "r-",
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121 color="black",
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122 alpha=0.3,
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123 lw=1,
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124 where="post",
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125 label="%s (area = %.3f)" % (idx, ap),
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126 )
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127
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128 plt.xlim([0.0, 1.0])
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129 plt.ylim([0.0, 1.05])
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130 plt.xlabel("Recall")
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131 plt.ylabel("Precision")
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132 title = title or "Precision-Recall Curve"
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133 plt.title(title)
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134 folder = os.getcwd()
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135 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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136 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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137
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138
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139 def visualize_roc_curve_plotly(df1, df2, pos_label, drop_intermediate=True, title=None):
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140 """output roc-curve in html using plotly
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141
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142 df1 : pandas.DataFrame
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143 Containing y_true
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144 df2 : pandas.DataFrame
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145 Containing y_score
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146 pos_label : None
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147 The label of positive class
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148 drop_intermediate : bool
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149 Whether to drop some suboptimal thresholds
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150 title : str
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151 Plot title
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152 """
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153 data = []
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154 for idx in range(df1.shape[1]):
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155 y_true = df1.iloc[:, idx].values
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156 y_score = df2.iloc[:, idx].values
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157
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158 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate)
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159 roc_auc = auc(fpr, tpr)
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160
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161 trace = go.Scatter(
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162 x=fpr,
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163 y=tpr,
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164 mode="lines",
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165 marker=dict(color=default_colors[idx % len(default_colors)]),
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166 name="%s (area = %.3f)" % (idx, roc_auc),
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167 )
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168 data.append(trace)
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169
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170 layout = go.Layout(
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171 xaxis=dict(title="False Positive Rate", linecolor="lightslategray", linewidth=1),
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172 yaxis=dict(title="True Positive Rate", linecolor="lightslategray", linewidth=1),
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173 title=dict(
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174 text=title or "Receiver Operating Characteristic (ROC) Curve",
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175 x=0.5,
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176 y=0.92,
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177 xanchor="center",
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178 yanchor="top",
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179 ),
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180 font=dict(family="sans-serif", size=11),
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181 # control backgroud colors
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182 plot_bgcolor="rgba(255,255,255,0)",
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183 )
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184 """
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185 # legend=dict(
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186 # x=0.95,
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187 # y=0,
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188 # traceorder="normal",
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189 # font=dict(
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190 # family="sans-serif",
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191 # size=9,
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192 # color="black"
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193 # ),
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194 # bgcolor="LightSteelBlue",
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195 # bordercolor="Black",
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196 # borderwidth=2
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197 # ),
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198 """
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199
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200 fig = go.Figure(data=data, layout=layout)
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201
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202 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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203 # to be discovered by `from_work_dir`
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204 os.rename("output.html", "output")
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205
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206
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207 def visualize_roc_curve_matplotlib(df1, df2, pos_label, drop_intermediate=True, title=None):
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208 """visualize roc-curve using matplotlib and output svg image"""
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209 backend = matplotlib.get_backend()
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210 if "inline" not in backend:
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211 matplotlib.use("SVG")
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212 plt.style.use("seaborn-colorblind")
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213 plt.figure()
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214
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215 for idx in range(df1.shape[1]):
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216 y_true = df1.iloc[:, idx].values
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217 y_score = df2.iloc[:, idx].values
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218
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219 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate)
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220 roc_auc = auc(fpr, tpr)
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221
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222 plt.step(
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223 fpr,
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224 tpr,
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225 "r-",
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226 color="black",
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227 alpha=0.3,
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228 lw=1,
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229 where="post",
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230 label="%s (area = %.3f)" % (idx, roc_auc),
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231 )
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232
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233 plt.xlim([0.0, 1.0])
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234 plt.ylim([0.0, 1.05])
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235 plt.xlabel("False Positive Rate")
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236 plt.ylabel("True Positive Rate")
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237 title = title or "Receiver Operating Characteristic (ROC) Curve"
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238 plt.title(title)
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239 folder = os.getcwd()
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240 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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241 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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242
1
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243
7
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244 def get_dataframe(file_path, plot_selection, header_name, column_name):
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245 header = "infer" if plot_selection[header_name] else None
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246 column_option = plot_selection[column_name]["selected_column_selector_option"]
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247 if column_option in [
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248 "by_index_number",
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249 "all_but_by_index_number",
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250 "by_header_name",
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251 "all_but_by_header_name",
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252 ]:
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253 col = plot_selection[column_name]["col1"]
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254 else:
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255 col = None
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256 _, input_df = read_columns(file_path, c=col,
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257 c_option=column_option,
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258 return_df=True,
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259 sep='\t', header=header,
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260 parse_dates=True)
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261 return input_df
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262
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263
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264 def main(
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
265 inputs,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
266 infile_estimator=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
267 infile1=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
268 infile2=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
269 outfile_result=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
270 outfile_object=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
271 groups=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
272 ref_seq=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
273 intervals=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
274 targets=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
275 fasta_path=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
276 model_config=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
277 true_labels=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
278 predicted_labels=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
279 plot_color=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
280 title=None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
281 ):
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
282 """
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
283 Parameter
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
284 ---------
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
285 inputs : str
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
286 File path to galaxy tool parameter
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
287
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
288 infile_estimator : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
289 File path to estimator
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
290
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
291 infile1 : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
292 File path to dataset containing features or true labels.
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
293
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
294 infile2 : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
295 File path to dataset containing target values or predicted
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
296 probabilities.
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
297
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
298 outfile_result : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
299 File path to save the results, either cv_results or test result
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
300
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
301 outfile_object : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
302 File path to save searchCV object
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
303
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
304 groups : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
305 File path to dataset containing groups labels
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
306
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
307 ref_seq : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
308 File path to dataset containing genome sequence file
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
309
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
310 intervals : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
311 File path to dataset containing interval file
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
312
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
313 targets : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
314 File path to dataset compressed target bed file
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
315
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
316 fasta_path : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
317 File path to dataset containing fasta file
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
318
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
319 model_config : str, default is None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
320 File path to dataset containing JSON config for neural networks
7
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
321
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
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diff changeset
322 true_labels : str, default is None
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
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diff changeset
323 File path to dataset containing true labels
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
324
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
325 predicted_labels : str, default is None
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
326 File path to dataset containing true predicted labels
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
327
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
328 plot_color : str, default is None
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
329 Color of the confusion matrix heatmap
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
330
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
331 title : str, default is None
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
332 Title of the confusion matrix heatmap
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
333 """
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
334 warnings.simplefilter("ignore")
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
335
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
336 with open(inputs, "r") as param_handler:
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
337 params = json.load(param_handler)
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
338
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
339 title = params["plotting_selection"]["title"].strip()
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
340 plot_type = params["plotting_selection"]["plot_type"]
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
341 plot_format = params["plotting_selection"]["plot_format"]
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
342
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
343 if plot_type == "feature_importances":
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
344 with open(infile_estimator, "rb") as estimator_handler:
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
345 estimator = load_model(estimator_handler)
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
346
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
347 column_option = params["plotting_selection"]["column_selector_options"]["selected_column_selector_option"]
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
348 if column_option in [
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
349 "by_index_number",
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
350 "all_but_by_index_number",
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
351 "by_header_name",
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
352 "all_but_by_header_name",
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
353 ]:
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
354 c = params["plotting_selection"]["column_selector_options"]["col1"]
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
355 else:
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
356 c = None
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
357
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
358 _, input_df = read_columns(
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
359 infile1,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
360 c=c,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
361 c_option=column_option,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
362 return_df=True,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
363 sep="\t",
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
364 header="infer",
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
365 parse_dates=True,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
366 )
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
367
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
368 feature_names = input_df.columns.values
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
369
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
370 if isinstance(estimator, Pipeline):
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
371 for st in estimator.steps[:-1]:
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
372 if isinstance(st[-1], SelectorMixin):
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
373 mask = st[-1].get_support()
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
374 feature_names = feature_names[mask]
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
375 estimator = estimator.steps[-1][-1]
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
376
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
377 if hasattr(estimator, "coef_"):
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
378 coefs = estimator.coef_
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
379 else:
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
380 coefs = getattr(estimator, "feature_importances_", None)
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
381 if coefs is None:
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
382 raise RuntimeError("The classifier does not expose " '"coef_" or "feature_importances_" ' "attributes")
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
383
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
384 threshold = params["plotting_selection"]["threshold"]
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
385 if threshold is not None:
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
386 mask = (coefs > threshold) | (coefs < -threshold)
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
387 coefs = coefs[mask]
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
388 feature_names = feature_names[mask]
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
389
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
390 # sort
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
391 indices = np.argsort(coefs)[::-1]
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
392
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
393 trace = go.Bar(x=feature_names[indices], y=coefs[indices])
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
394 layout = go.Layout(title=title or "Feature Importances")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
395 fig = go.Figure(data=[trace], layout=layout)
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
396
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
397 plotly.offline.plot(fig, filename="output.html", auto_open=False)
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
398 # to be discovered by `from_work_dir`
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
399 os.rename("output.html", "output")
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
400
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
401 return 0
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
402
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
403 elif plot_type in ("pr_curve", "roc_curve"):
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
404 df1 = pd.read_csv(infile1, sep="\t", header="infer")
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
405 df2 = pd.read_csv(infile2, sep="\t", header="infer").astype(np.float32)
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
406
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
407 minimum = params["plotting_selection"]["report_minimum_n_positives"]
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
408 # filter out columns whose n_positives is beblow the threhold
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
409 if minimum:
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
410 mask = df1.sum(axis=0) >= minimum
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
411 df1 = df1.loc[:, mask]
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
412 df2 = df2.loc[:, mask]
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
413
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
414 pos_label = params["plotting_selection"]["pos_label"].strip() or None
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
415
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
416 if plot_type == "pr_curve":
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
417 if plot_format == "plotly_html":
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
418 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
419 else:
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
420 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
421 else: # 'roc_curve'
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
422 drop_intermediate = params["plotting_selection"]["drop_intermediate"]
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
423 if plot_format == "plotly_html":
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
424 visualize_roc_curve_plotly(
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
425 df1,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
426 df2,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
427 pos_label,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
428 drop_intermediate=drop_intermediate,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
429 title=title,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
430 )
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
431 else:
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
432 visualize_roc_curve_matplotlib(
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
433 df1,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
434 df2,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
435 pos_label,
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
436 drop_intermediate=drop_intermediate,
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
437 title=title,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
438 )
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
439
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
440 return 0
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
441
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
442 elif plot_type == "rfecv_gridscores":
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
443 input_df = pd.read_csv(infile1, sep="\t", header="infer")
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
444 scores = input_df.iloc[:, 0]
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
445 steps = params["plotting_selection"]["steps"].strip()
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
446 steps = safe_eval(steps)
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
447
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
448 data = go.Scatter(
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
449 x=list(range(len(scores))),
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
450 y=scores,
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
451 text=[str(_) for _ in steps] if steps else None,
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
452 mode="lines",
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
453 )
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
454 layout = go.Layout(
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
455 xaxis=dict(title="Number of features selected"),
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
456 yaxis=dict(title="Cross validation score"),
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
457 title=dict(text=title or None, x=0.5, y=0.92, xanchor="center", yanchor="top"),
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
458 font=dict(family="sans-serif", size=11),
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
459 # control backgroud colors
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
460 plot_bgcolor="rgba(255,255,255,0)",
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
461 )
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
462 """
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
463 # legend=dict(
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
464 # x=0.95,
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
465 # y=0,
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
466 # traceorder="normal",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
467 # font=dict(
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
468 # family="sans-serif",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
469 # size=9,
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
470 # color="black"
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
471 # ),
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
472 # bgcolor="LightSteelBlue",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
473 # bordercolor="Black",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
474 # borderwidth=2
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
475 # ),
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
476 """
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
477
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
478 fig = go.Figure(data=[data], layout=layout)
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
479 plotly.offline.plot(fig, filename="output.html", auto_open=False)
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
480 # to be discovered by `from_work_dir`
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
481 os.rename("output.html", "output")
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
482
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
483 return 0
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
484
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
485 elif plot_type == "learning_curve":
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
486 input_df = pd.read_csv(infile1, sep="\t", header="infer")
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
487 plot_std_err = params["plotting_selection"]["plot_std_err"]
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
488 data1 = go.Scatter(
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
489 x=input_df["train_sizes_abs"],
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
490 y=input_df["mean_train_scores"],
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
491 error_y=dict(array=input_df["std_train_scores"]) if plot_std_err else None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
492 mode="lines",
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
493 name="Train Scores",
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
494 )
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
495 data2 = go.Scatter(
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
496 x=input_df["train_sizes_abs"],
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
497 y=input_df["mean_test_scores"],
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
498 error_y=dict(array=input_df["std_test_scores"]) if plot_std_err else None,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
499 mode="lines",
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
500 name="Test Scores",
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
501 )
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
502 layout = dict(
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
503 xaxis=dict(title="No. of samples"),
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
504 yaxis=dict(title="Performance Score"),
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
505 # modify these configurations to customize image
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
506 title=dict(
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
507 text=title or "Learning Curve",
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
508 x=0.5,
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
509 y=0.92,
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
510 xanchor="center",
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
511 yanchor="top",
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
512 ),
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
513 font=dict(family="sans-serif", size=11),
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
514 # control backgroud colors
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
515 plot_bgcolor="rgba(255,255,255,0)",
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
516 )
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
517 """
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
518 # legend=dict(
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
519 # x=0.95,
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
520 # y=0,
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
521 # traceorder="normal",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
522 # font=dict(
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
523 # family="sans-serif",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
524 # size=9,
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
525 # color="black"
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
526 # ),
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
527 # bgcolor="LightSteelBlue",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
528 # bordercolor="Black",
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
529 # borderwidth=2
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
530 # ),
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
531 """
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
532
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
533 fig = go.Figure(data=[data1, data2], layout=layout)
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
534 plotly.offline.plot(fig, filename="output.html", auto_open=False)
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
535 # to be discovered by `from_work_dir`
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
536 os.rename("output.html", "output")
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
537
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
538 return 0
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
539
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
540 elif plot_type == "keras_plot_model":
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
541 with open(model_config, "r") as f:
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
542 model_str = f.read()
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
543 model = model_from_json(model_str)
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
544 plot_model(model, to_file="output.png")
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
545 os.rename("output.png", "output")
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
546
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
547 return 0
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
548
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
549 elif plot_type == "classification_confusion_matrix":
7
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
550 plot_selection = params["plotting_selection"]
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
551 input_true = get_dataframe(true_labels, plot_selection, "header_true", "column_selector_options_true")
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
552 header_predicted = "infer" if plot_selection["header_predicted"] else None
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
553 input_predicted = pd.read_csv(predicted_labels, sep="\t", parse_dates=True, header=header_predicted)
7
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
554 true_classes = input_true.iloc[:, -1].copy()
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
555 predicted_classes = input_predicted.iloc[:, -1].copy()
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
556 axis_labels = list(set(true_classes))
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
557 c_matrix = confusion_matrix(true_classes, predicted_classes)
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
558 fig, ax = plt.subplots(figsize=(7, 7))
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
559 im = plt.imshow(c_matrix, cmap=plot_color)
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
560 for i in range(len(c_matrix)):
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
561 for j in range(len(c_matrix)):
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
562 ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k")
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
563 ax.set_ylabel("True class labels")
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
564 ax.set_xlabel("Predicted class labels")
7
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
565 ax.set_title(title)
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
566 ax.set_xticks(axis_labels)
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
567 ax.set_yticks(axis_labels)
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
568 fig.colorbar(im, ax=ax)
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
569 fig.tight_layout()
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
570 plt.savefig("output.png", dpi=125)
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
571 os.rename("output.png", "output")
7
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
572
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
573 return 0
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
574
5
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
575 # save pdf file to disk
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
576 # fig.write_image("image.pdf", format='pdf')
2b8406e74f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 2
diff changeset
577 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
578
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
579
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
580 if __name__ == "__main__":
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
581 aparser = argparse.ArgumentParser()
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
582 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
583 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
584 aparser.add_argument("-X", "--infile1", dest="infile1")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
585 aparser.add_argument("-y", "--infile2", dest="infile2")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
586 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
cc49634df38f "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_object", dest="outfile_object")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
588 aparser.add_argument("-g", "--groups", dest="groups")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
589 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
590 aparser.add_argument("-b", "--intervals", dest="intervals")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
591 aparser.add_argument("-t", "--targets", dest="targets")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
592 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
593 aparser.add_argument("-c", "--model_config", dest="model_config")
7
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
594 aparser.add_argument("-tl", "--true_labels", dest="true_labels")
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
595 aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels")
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
596 aparser.add_argument("-pc", "--plot_color", dest="plot_color")
1b68acd5ac08 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
bgruening
parents: 5
diff changeset
597 aparser.add_argument("-pt", "--title", dest="title")
1
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
598 args = aparser.parse_args()
cc49634df38f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
599
9
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
600 main(
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
601 args.inputs,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
602 args.infile_estimator,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
603 args.infile1,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
604 args.infile2,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
605 args.outfile_result,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
606 outfile_object=args.outfile_object,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
607 groups=args.groups,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
608 ref_seq=args.ref_seq,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
609 intervals=args.intervals,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
610 targets=args.targets,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
611 fasta_path=args.fasta_path,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
612 model_config=args.model_config,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
613 true_labels=args.true_labels,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
614 predicted_labels=args.predicted_labels,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
615 plot_color=args.plot_color,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
616 title=args.title,
ead7adad8d0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
617 )