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annotate ml_visualization_ex.py @ 42:9fdff01a34b0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 12:37:34 +0000
parents ed7d6d7c6e93
children 21d05f8abca6
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1 import argparse
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2 import json
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3 import os
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4 import warnings
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5
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6 import matplotlib
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7 import matplotlib.pyplot as plt
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8 import numpy as np
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9 import pandas as pd
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10 import plotly
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11 import plotly.graph_objs as go
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12 from galaxy_ml.model_persist import load_model_from_h5
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13 from galaxy_ml.utils import read_columns, SafeEval
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14 from sklearn.feature_selection._base import SelectorMixin
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15 from sklearn.metrics import (
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16 auc,
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17 average_precision_score,
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18 precision_recall_curve,
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19 roc_curve,
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20 )
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21 from sklearn.pipeline import Pipeline
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22 from tensorflow.keras.models import model_from_json
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23 from tensorflow.keras.utils import plot_model
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25 safe_eval = SafeEval()
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27 # plotly default colors
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28 default_colors = [
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29 "#1f77b4", # muted blue
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30 "#ff7f0e", # safety orange
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31 "#2ca02c", # cooked asparagus green
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32 "#d62728", # brick red
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33 "#9467bd", # muted purple
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34 "#8c564b", # chestnut brown
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35 "#e377c2", # raspberry yogurt pink
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36 "#7f7f7f", # middle gray
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37 "#bcbd22", # curry yellow-green
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38 "#17becf", # blue-teal
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39 ]
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42 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None):
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43 """output pr-curve in html using plotly
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45 df1 : pandas.DataFrame
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46 Containing y_true
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47 df2 : pandas.DataFrame
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48 Containing y_score
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49 pos_label : None
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50 The label of positive class
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51 title : str
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52 Plot title
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53 """
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54 data = []
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55 for idx in range(df1.shape[1]):
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56 y_true = df1.iloc[:, idx].values
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57 y_score = df2.iloc[:, idx].values
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58
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59 precision, recall, _ = precision_recall_curve(
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60 y_true, y_score, pos_label=pos_label
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61 )
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62 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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64 trace = go.Scatter(
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65 x=recall,
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66 y=precision,
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67 mode="lines",
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68 marker=dict(color=default_colors[idx % len(default_colors)]),
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69 name="%s (area = %.3f)" % (idx, ap),
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70 )
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71 data.append(trace)
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73 layout = go.Layout(
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74 xaxis=dict(title="Recall", linecolor="lightslategray", linewidth=1),
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75 yaxis=dict(title="Precision", linecolor="lightslategray", linewidth=1),
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76 title=dict(
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77 text=title or "Precision-Recall Curve",
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78 x=0.5,
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79 y=0.92,
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80 xanchor="center",
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81 yanchor="top",
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82 ),
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83 font=dict(family="sans-serif", size=11),
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84 # control backgroud colors
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85 plot_bgcolor="rgba(255,255,255,0)",
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86 )
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87 """
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88 legend=dict(
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89 x=0.95,
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90 y=0,
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91 traceorder="normal",
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92 font=dict(
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93 family="sans-serif",
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94 size=9,
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95 color="black"
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96 ),
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97 bgcolor="LightSteelBlue",
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98 bordercolor="Black",
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99 borderwidth=2
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100 ),"""
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101
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102 fig = go.Figure(data=data, layout=layout)
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103
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104 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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105 # to be discovered by `from_work_dir`
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106 os.rename("output.html", "output")
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107
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108
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109 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
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110 """visualize pr-curve using matplotlib and output svg image"""
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111 backend = matplotlib.get_backend()
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112 if "inline" not in backend:
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113 matplotlib.use("SVG")
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114 plt.style.use("seaborn-colorblind")
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115 plt.figure()
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116
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117 for idx in range(df1.shape[1]):
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118 y_true = df1.iloc[:, idx].values
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119 y_score = df2.iloc[:, idx].values
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120
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121 precision, recall, _ = precision_recall_curve(
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122 y_true, y_score, pos_label=pos_label
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123 )
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124 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
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125
35
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126 plt.step(
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127 recall,
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128 precision,
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129 "r-",
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130 color="black",
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131 alpha=0.3,
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132 lw=1,
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133 where="post",
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134 label="%s (area = %.3f)" % (idx, ap),
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135 )
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136
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137 plt.xlim([0.0, 1.0])
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138 plt.ylim([0.0, 1.05])
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139 plt.xlabel("Recall")
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140 plt.ylabel("Precision")
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141 title = title or "Precision-Recall Curve"
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142 plt.title(title)
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143 folder = os.getcwd()
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144 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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145 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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146
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147
35
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148 def visualize_roc_curve_plotly(df1, df2, pos_label, drop_intermediate=True, title=None):
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149 """output roc-curve in html using plotly
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150
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151 df1 : pandas.DataFrame
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152 Containing y_true
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153 df2 : pandas.DataFrame
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154 Containing y_score
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155 pos_label : None
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156 The label of positive class
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157 drop_intermediate : bool
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158 Whether to drop some suboptimal thresholds
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159 title : str
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160 Plot title
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161 """
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162 data = []
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163 for idx in range(df1.shape[1]):
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164 y_true = df1.iloc[:, idx].values
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165 y_score = df2.iloc[:, idx].values
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166
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167 fpr, tpr, _ = roc_curve(
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168 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
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169 )
32
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170 roc_auc = auc(fpr, tpr)
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171
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172 trace = go.Scatter(
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173 x=fpr,
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174 y=tpr,
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175 mode="lines",
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176 marker=dict(color=default_colors[idx % len(default_colors)]),
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177 name="%s (area = %.3f)" % (idx, roc_auc),
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178 )
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179 data.append(trace)
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180
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181 layout = go.Layout(
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182 xaxis=dict(
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183 title="False Positive Rate", linecolor="lightslategray", linewidth=1
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184 ),
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185 yaxis=dict(title="True Positive Rate", linecolor="lightslategray", linewidth=1),
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186 title=dict(
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187 text=title or "Receiver Operating Characteristic (ROC) Curve",
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188 x=0.5,
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189 y=0.92,
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190 xanchor="center",
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191 yanchor="top",
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192 ),
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193 font=dict(family="sans-serif", size=11),
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194 # control backgroud colors
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195 plot_bgcolor="rgba(255,255,255,0)",
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196 )
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197 """
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198 # legend=dict(
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199 # x=0.95,
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200 # y=0,
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201 # traceorder="normal",
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202 # font=dict(
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203 # family="sans-serif",
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204 # size=9,
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205 # color="black"
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206 # ),
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207 # bgcolor="LightSteelBlue",
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208 # bordercolor="Black",
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209 # borderwidth=2
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210 # ),
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211 """
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212
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213 fig = go.Figure(data=data, layout=layout)
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214
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215 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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216 # to be discovered by `from_work_dir`
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217 os.rename("output.html", "output")
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218
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219
36
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220 def visualize_roc_curve_matplotlib(
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221 df1, df2, pos_label, drop_intermediate=True, title=None
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222 ):
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223 """visualize roc-curve using matplotlib and output svg image"""
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224 backend = matplotlib.get_backend()
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225 if "inline" not in backend:
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226 matplotlib.use("SVG")
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227 plt.style.use("seaborn-colorblind")
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228 plt.figure()
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229
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230 for idx in range(df1.shape[1]):
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231 y_true = df1.iloc[:, idx].values
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232 y_score = df2.iloc[:, idx].values
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233
36
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234 fpr, tpr, _ = roc_curve(
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235 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
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236 )
32
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237 roc_auc = auc(fpr, tpr)
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238
35
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239 plt.step(
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240 fpr,
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241 tpr,
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242 "r-",
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243 color="black",
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244 alpha=0.3,
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245 lw=1,
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246 where="post",
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247 label="%s (area = %.3f)" % (idx, roc_auc),
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248 )
32
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249
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250 plt.xlim([0.0, 1.0])
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251 plt.ylim([0.0, 1.05])
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252 plt.xlabel("False Positive Rate")
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253 plt.ylabel("True Positive Rate")
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254 title = title or "Receiver Operating Characteristic (ROC) Curve"
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255 plt.title(title)
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256 folder = os.getcwd()
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257 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
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258 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
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259
28
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260
35
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261 def main(
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262 inputs,
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263 infile_estimator=None,
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264 infile1=None,
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265 infile2=None,
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266 outfile_result=None,
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267 outfile_object=None,
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268 groups=None,
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269 ref_seq=None,
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270 intervals=None,
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271 targets=None,
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272 fasta_path=None,
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273 model_config=None,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
274 ):
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
275 """
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
276 Parameter
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
277 ---------
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
278 inputs : str
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
279 File path to galaxy tool parameter
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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diff changeset
280
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
281 infile_estimator : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
282 File path to estimator
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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283
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
284 infile1 : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
285 File path to dataset containing features or true labels.
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
286
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
287 infile2 : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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288 File path to dataset containing target values or predicted
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
289 probabilities.
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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290
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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291 outfile_result : str, default is None
c077c537cb67 "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 save the results, either cv_results or test result
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
293
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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294 outfile_object : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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295 File path to save searchCV object
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
296
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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297 groups : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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298 File path to dataset containing groups labels
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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299
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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300 ref_seq : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
301 File path to dataset containing genome sequence file
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
302
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
303 intervals : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
304 File path to dataset containing interval file
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
305
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
306 targets : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
307 File path to dataset compressed target bed file
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
308
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
309 fasta_path : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
310 File path to dataset containing fasta file
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
311
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
312 model_config : str, default is None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
313 File path to dataset containing JSON config for neural networks
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
314 """
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
315 warnings.simplefilter("ignore")
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
316
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
317 with open(inputs, "r") as param_handler:
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
318 params = json.load(param_handler)
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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diff changeset
319
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
320 title = params["plotting_selection"]["title"].strip()
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
321 plot_type = params["plotting_selection"]["plot_type"]
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
322 plot_format = params["plotting_selection"]["plot_format"]
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
323
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
324 if plot_type == "feature_importances":
41
ed7d6d7c6e93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
325 estimator = load_model_from_h5(infile_estimator)
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
326
36
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
327 column_option = params["plotting_selection"]["column_selector_options"][
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
328 "selected_column_selector_option"
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
329 ]
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
330 if column_option in [
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
331 "by_index_number",
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
332 "all_but_by_index_number",
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
333 "by_header_name",
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
334 "all_but_by_header_name",
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
335 ]:
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
336 c = params["plotting_selection"]["column_selector_options"]["col1"]
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
337 else:
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
338 c = None
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
339
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
340 _, input_df = read_columns(
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
341 infile1,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
342 c=c,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
343 c_option=column_option,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
344 return_df=True,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
345 sep="\t",
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
346 header="infer",
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
347 parse_dates=True,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
348 )
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
349
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
350 feature_names = input_df.columns.values
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
351
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
352 if isinstance(estimator, Pipeline):
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
353 for st in estimator.steps[:-1]:
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
354 if isinstance(st[-1], SelectorMixin):
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
355 mask = st[-1].get_support()
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
356 feature_names = feature_names[mask]
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
357 estimator = estimator.steps[-1][-1]
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
358
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
359 if hasattr(estimator, "coef_"):
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
360 coefs = estimator.coef_
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
361 else:
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
362 coefs = getattr(estimator, "feature_importances_", None)
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
363 if coefs is None:
36
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
364 raise RuntimeError(
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
365 "The classifier does not expose "
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
366 '"coef_" or "feature_importances_" '
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
367 "attributes"
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
368 )
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
369
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
370 threshold = params["plotting_selection"]["threshold"]
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
371 if threshold is not None:
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
372 mask = (coefs > threshold) | (coefs < -threshold)
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
373 coefs = coefs[mask]
c077c537cb67 "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]
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
375
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
376 # sort
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
377 indices = np.argsort(coefs)[::-1]
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
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378
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
379 trace = go.Bar(x=feature_names[indices], y=coefs[indices])
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
380 layout = go.Layout(title=title or "Feature Importances")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
381 fig = go.Figure(data=[trace], layout=layout)
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
382
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
383 plotly.offline.plot(fig, filename="output.html", auto_open=False)
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
384 # to be discovered by `from_work_dir`
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3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
385 os.rename("output.html", "output")
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
386
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
387 return 0
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
388
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
389 elif plot_type in ("pr_curve", "roc_curve"):
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
390 df1 = pd.read_csv(infile1, sep="\t", header="infer")
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
391 df2 = pd.read_csv(infile2, sep="\t", header="infer").astype(np.float32)
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
392
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
393 minimum = params["plotting_selection"]["report_minimum_n_positives"]
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
394 # filter out columns whose n_positives is beblow the threhold
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
395 if minimum:
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
396 mask = df1.sum(axis=0) >= minimum
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
397 df1 = df1.loc[:, mask]
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
398 df2 = df2.loc[:, mask]
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
399
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
400 pos_label = params["plotting_selection"]["pos_label"].strip() or None
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
401
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
402 if plot_type == "pr_curve":
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
403 if plot_format == "plotly_html":
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
404 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
405 else:
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
406 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
407 else: # 'roc_curve'
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
408 drop_intermediate = params["plotting_selection"]["drop_intermediate"]
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
409 if plot_format == "plotly_html":
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
410 visualize_roc_curve_plotly(
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
411 df1,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
412 df2,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
413 pos_label,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
414 drop_intermediate=drop_intermediate,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
415 title=title,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
416 )
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
417 else:
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
418 visualize_roc_curve_matplotlib(
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
419 df1,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
420 df2,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
421 pos_label,
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
422 drop_intermediate=drop_intermediate,
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
423 title=title,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
424 )
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
425
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
426 return 0
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
427
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
428 elif plot_type == "rfecv_gridscores":
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
429 input_df = pd.read_csv(infile1, sep="\t", header="infer")
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
430 scores = input_df.iloc[:, 0]
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
431 steps = params["plotting_selection"]["steps"].strip()
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
432 steps = safe_eval(steps)
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
433
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
434 data = go.Scatter(
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
435 x=list(range(len(scores))),
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
436 y=scores,
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
437 text=[str(_) for _ in steps] if steps else None,
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
438 mode="lines",
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
439 )
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
440 layout = go.Layout(
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
441 xaxis=dict(title="Number of features selected"),
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
442 yaxis=dict(title="Cross validation score"),
36
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
443 title=dict(
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
444 text=title or None, x=0.5, y=0.92, xanchor="center", yanchor="top"
fc0801adfba1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents: 35
diff changeset
445 ),
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
446 font=dict(family="sans-serif", size=11),
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
447 # control backgroud colors
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
448 plot_bgcolor="rgba(255,255,255,0)",
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
449 )
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
450 """
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
451 # legend=dict(
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
452 # x=0.95,
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
453 # y=0,
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
454 # traceorder="normal",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
455 # font=dict(
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
456 # family="sans-serif",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
457 # size=9,
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
458 # color="black"
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
459 # ),
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
460 # bgcolor="LightSteelBlue",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
461 # bordercolor="Black",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
462 # borderwidth=2
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
463 # ),
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
464 """
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
465
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
466 fig = go.Figure(data=[data], layout=layout)
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
467 plotly.offline.plot(fig, filename="output.html", auto_open=False)
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
468 # to be discovered by `from_work_dir`
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
469 os.rename("output.html", "output")
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
470
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
471 return 0
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
472
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
473 elif plot_type == "learning_curve":
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
474 input_df = pd.read_csv(infile1, sep="\t", header="infer")
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
475 plot_std_err = params["plotting_selection"]["plot_std_err"]
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
476 data1 = go.Scatter(
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
477 x=input_df["train_sizes_abs"],
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
478 y=input_df["mean_train_scores"],
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
479 error_y=dict(array=input_df["std_train_scores"]) if plot_std_err else None,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
480 mode="lines",
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
481 name="Train Scores",
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
482 )
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
483 data2 = go.Scatter(
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
484 x=input_df["train_sizes_abs"],
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
485 y=input_df["mean_test_scores"],
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
486 error_y=dict(array=input_df["std_test_scores"]) if plot_std_err else None,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
487 mode="lines",
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
488 name="Test Scores",
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
489 )
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
490 layout = dict(
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
491 xaxis=dict(title="No. of samples"),
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
492 yaxis=dict(title="Performance Score"),
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
493 # modify these configurations to customize image
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
494 title=dict(
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
495 text=title or "Learning Curve",
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
496 x=0.5,
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
497 y=0.92,
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
498 xanchor="center",
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
499 yanchor="top",
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
500 ),
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
501 font=dict(family="sans-serif", size=11),
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
502 # control backgroud colors
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
503 plot_bgcolor="rgba(255,255,255,0)",
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
504 )
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
505 """
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
506 # legend=dict(
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
507 # x=0.95,
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
508 # y=0,
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
509 # traceorder="normal",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
510 # font=dict(
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
511 # family="sans-serif",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
512 # size=9,
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
513 # color="black"
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
514 # ),
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
515 # bgcolor="LightSteelBlue",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
516 # bordercolor="Black",
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
517 # borderwidth=2
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
518 # ),
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
519 """
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
520
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
521 fig = go.Figure(data=[data1, data2], layout=layout)
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
522 plotly.offline.plot(fig, filename="output.html", auto_open=False)
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
523 # to be discovered by `from_work_dir`
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
524 os.rename("output.html", "output")
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
525
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
526 return 0
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
527
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
528 elif plot_type == "keras_plot_model":
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
529 with open(model_config, "r") as f:
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
530 model_str = f.read()
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
531 model = model_from_json(model_str)
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
532 plot_model(model, to_file="output.png")
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
533 os.rename("output.png", "output")
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
534
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
535 return 0
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
536
32
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
537 # save pdf file to disk
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
538 # fig.write_image("image.pdf", format='pdf')
e801d2034575 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 29
diff changeset
539 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
540
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
541
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
542 if __name__ == "__main__":
28
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
543 aparser = argparse.ArgumentParser()
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
544 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
545 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
546 aparser.add_argument("-X", "--infile1", dest="infile1")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
547 aparser.add_argument("-y", "--infile2", dest="infile2")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
548 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
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549 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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550 aparser.add_argument("-g", "--groups", dest="groups")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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551 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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552 aparser.add_argument("-b", "--intervals", dest="intervals")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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553 aparser.add_argument("-t", "--targets", dest="targets")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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554 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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555 aparser.add_argument("-c", "--model_config", dest="model_config")
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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556 args = aparser.parse_args()
c077c537cb67 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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557
35
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558 main(
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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559 args.inputs,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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560 args.infile_estimator,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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561 args.infile1,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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562 args.infile2,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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563 args.outfile_result,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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564 outfile_object=args.outfile_object,
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565 groups=args.groups,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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566 ref_seq=args.ref_seq,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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567 intervals=args.intervals,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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568 targets=args.targets,
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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569 fasta_path=args.fasta_path,
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570 model_config=args.model_config,
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571 )