Mercurial > repos > bgruening > sklearn_pca

annotate ml_visualization_ex.py @ 0:2d7016b3ae92 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
author bgruening
date Fri, 02 Oct 2020 08:45:21 +0000
parents
children 132805688fa3
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2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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1 import argparse
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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2 import json
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3 import matplotlib
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4 import matplotlib.pyplot as plt
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5 import numpy as np
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6 import os
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7 import pandas as pd
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8 import plotly
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9 import plotly.graph_objs as go
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10 import warnings
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11
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12 from keras.models import model_from_json
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13 from keras.utils import plot_model
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14 from sklearn.feature_selection.base import SelectorMixin
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15 from sklearn.metrics import precision_recall_curve, average_precision_score
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16 from sklearn.metrics import roc_curve, auc, confusion_matrix
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17 from sklearn.pipeline import Pipeline
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18 from galaxy_ml.utils import load_model, read_columns, SafeEval
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19
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21 safe_eval = SafeEval()
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22
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23 # plotly default colors
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24 default_colors = [
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25 '#1f77b4', # muted blue
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26 '#ff7f0e', # safety orange
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27 '#2ca02c', # cooked asparagus green
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28 '#d62728', # brick red
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29 '#9467bd', # muted purple
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30 '#8c564b', # chestnut brown
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31 '#e377c2', # raspberry yogurt pink
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32 '#7f7f7f', # middle gray
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33 '#bcbd22', # curry yellow-green
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34 '#17becf' # blue-teal
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35 ]
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36
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37
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38 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None):
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39 """output pr-curve in html using plotly
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40
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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41 df1 : pandas.DataFrame
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42 Containing y_true
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43 df2 : pandas.DataFrame
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44 Containing y_score
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45 pos_label : None
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46 The label of positive class
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47 title : str
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48 Plot title
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49 """
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50 data = []
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51 for idx in range(df1.shape[1]):
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52 y_true = df1.iloc[:, idx].values
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53 y_score = df2.iloc[:, idx].values
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54
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55 precision, recall, _ = precision_recall_curve(
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56 y_true, y_score, pos_label=pos_label)
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57 ap = average_precision_score(
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58 y_true, y_score, pos_label=pos_label or 1)
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59
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60 trace = go.Scatter(
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61 x=recall,
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62 y=precision,
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63 mode='lines',
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64 marker=dict(
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65 color=default_colors[idx % len(default_colors)]
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66 ),
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67 name='%s (area = %.3f)' % (idx, ap)
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68 )
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69 data.append(trace)
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70
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71 layout = go.Layout(
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72 xaxis=dict(
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73 title='Recall',
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74 linecolor='lightslategray',
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75 linewidth=1
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76 ),
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77 yaxis=dict(
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78 title='Precision',
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79 linecolor='lightslategray',
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80 linewidth=1
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81 ),
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82 title=dict(
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83 text=title or 'Precision-Recall Curve',
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84 x=0.5,
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85 y=0.92,
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86 xanchor='center',
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87 yanchor='top'
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88 ),
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89 font=dict(
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90 family="sans-serif",
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91 size=11
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92 ),
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93 # control backgroud colors
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94 plot_bgcolor='rgba(255,255,255,0)'
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95 )
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96 """
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97 legend=dict(
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98 x=0.95,
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99 y=0,
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100 traceorder="normal",
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101 font=dict(
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102 family="sans-serif",
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103 size=9,
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104 color="black"
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105 ),
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106 bgcolor="LightSteelBlue",
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107 bordercolor="Black",
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108 borderwidth=2
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109 ),"""
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110
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111 fig = go.Figure(data=data, layout=layout)
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112
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113 plotly.offline.plot(fig, filename="output.html", auto_open=False)
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114 # to be discovered by `from_work_dir`
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115 os.rename('output.html', 'output')
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116
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117
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118 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
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119 """visualize pr-curve using matplotlib and output svg image
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120 """
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121 backend = matplotlib.get_backend()
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122 if "inline" not in backend:
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123 matplotlib.use("SVG")
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124 plt.style.use('seaborn-colorblind')
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125 plt.figure()
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126
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127 for idx in range(df1.shape[1]):
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128 y_true = df1.iloc[:, idx].values
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129 y_score = df2.iloc[:, idx].values
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130
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131 precision, recall, _ = precision_recall_curve(
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132 y_true, y_score, pos_label=pos_label)
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133 ap = average_precision_score(
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134 y_true, y_score, pos_label=pos_label or 1)
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135
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136 plt.step(recall, precision, 'r-', color="black", alpha=0.3,
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137 lw=1, where="post", label='%s (area = %.3f)' % (idx, ap))
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138
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139 plt.xlim([0.0, 1.0])
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140 plt.ylim([0.0, 1.05])
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141 plt.xlabel('Recall')
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142 plt.ylabel('Precision')
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143 title = title or 'Precision-Recall Curve'
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144 plt.title(title)
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145 folder = os.getcwd()
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146 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
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147 os.rename(os.path.join(folder, "output.svg"),
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148 os.path.join(folder, "output"))
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149
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150
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151 def visualize_roc_curve_plotly(df1, df2, pos_label,
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152 drop_intermediate=True,
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153 title=None):
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154 """output roc-curve in html using plotly
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155
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156 df1 : pandas.DataFrame
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157 Containing y_true
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158 df2 : pandas.DataFrame
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159 Containing y_score
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160 pos_label : None
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161 The label of positive class
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162 drop_intermediate : bool
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163 Whether to drop some suboptimal thresholds
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164 title : str
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165 Plot title
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166 """
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167 data = []
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168 for idx in range(df1.shape[1]):
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169 y_true = df1.iloc[:, idx].values
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170 y_score = df2.iloc[:, idx].values
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171
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172 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label,
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173 drop_intermediate=drop_intermediate)
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174 roc_auc = auc(fpr, tpr)
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175
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176 trace = go.Scatter(
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177 x=fpr,
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178 y=tpr,
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179 mode='lines',
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180 marker=dict(
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181 color=default_colors[idx % len(default_colors)]
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182 ),
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183 name='%s (area = %.3f)' % (idx, roc_auc)
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184 )
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bgruening
parents:
diff changeset
185 data.append(trace)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
186
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
187 layout = go.Layout(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
188 xaxis=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
189 title='False Positive Rate',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
190 linecolor='lightslategray',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
191 linewidth=1
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
192 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
193 yaxis=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
194 title='True Positive Rate',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
195 linecolor='lightslategray',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
196 linewidth=1
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
197 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
198 title=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
199 text=title or 'Receiver Operating Characteristic (ROC) Curve',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
200 x=0.5,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
201 y=0.92,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
202 xanchor='center',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
203 yanchor='top'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
204 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
205 font=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
206 family="sans-serif",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
207 size=11
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
208 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
209 # control backgroud colors
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
210 plot_bgcolor='rgba(255,255,255,0)'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
211 )
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
212 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
213 # legend=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
214 # x=0.95,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
215 # y=0,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
216 # traceorder="normal",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
217 # font=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
218 # family="sans-serif",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
219 # size=9,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
220 # color="black"
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
221 # ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
222 # bgcolor="LightSteelBlue",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
223 # bordercolor="Black",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
224 # borderwidth=2
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
225 # ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
226 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
227
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
228 fig = go.Figure(data=data, layout=layout)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
229
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
230 plotly.offline.plot(fig, filename="output.html", auto_open=False)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
231 # to be discovered by `from_work_dir`
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
232 os.rename('output.html', 'output')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
233
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
234
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
235 def visualize_roc_curve_matplotlib(df1, df2, pos_label,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
236 drop_intermediate=True,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
237 title=None):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
238 """visualize roc-curve using matplotlib and output svg image
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
239 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
240 backend = matplotlib.get_backend()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
241 if "inline" not in backend:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
242 matplotlib.use("SVG")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
243 plt.style.use('seaborn-colorblind')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
244 plt.figure()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
245
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
246 for idx in range(df1.shape[1]):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
247 y_true = df1.iloc[:, idx].values
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
248 y_score = df2.iloc[:, idx].values
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
249
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
250 fpr, tpr, _ = roc_curve(y_true, y_score, pos_label=pos_label,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
251 drop_intermediate=drop_intermediate)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
252 roc_auc = auc(fpr, tpr)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
253
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
254 plt.step(fpr, tpr, 'r-', color="black", alpha=0.3, lw=1,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
255 where="post", label='%s (area = %.3f)' % (idx, roc_auc))
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
256
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
257 plt.xlim([0.0, 1.0])
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
258 plt.ylim([0.0, 1.05])
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
259 plt.xlabel('False Positive Rate')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
260 plt.ylabel('True Positive Rate')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
261 title = title or 'Receiver Operating Characteristic (ROC) Curve'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
262 plt.title(title)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
263 folder = os.getcwd()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
264 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
265 os.rename(os.path.join(folder, "output.svg"),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
266 os.path.join(folder, "output"))
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
267
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
268
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
269 def get_dataframe(file_path, plot_selection, header_name, column_name):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
270 header = 'infer' if plot_selection[header_name] else None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
271 column_option = plot_selection[column_name]["selected_column_selector_option"]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
272 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
273 col = plot_selection[column_name]["col1"]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
274 else:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
275 col = None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
276 _, input_df = read_columns(file_path, c=col,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
277 c_option=column_option,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
278 return_df=True,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
279 sep='\t', header=header,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
280 parse_dates=True)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
281 return input_df
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
282
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
283
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
284 def main(inputs, infile_estimator=None, infile1=None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
285 infile2=None, outfile_result=None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
286 outfile_object=None, groups=None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
287 ref_seq=None, intervals=None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
288 targets=None, fasta_path=None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
289 model_config=None, true_labels=None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
290 predicted_labels=None, plot_color=None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
291 title=None):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
292 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
293 Parameter
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
294 ---------
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
295 inputs : str
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
296 File path to galaxy tool parameter
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
297
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
298 infile_estimator : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
299 File path to estimator
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
300
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
301 infile1 : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
302 File path to dataset containing features or true labels.
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
303
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
304 infile2 : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
305 File path to dataset containing target values or predicted
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
306 probabilities.
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
307
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
308 outfile_result : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
309 File path to save the results, either cv_results or test result
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
310
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
311 outfile_object : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
312 File path to save searchCV object
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
313
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
314 groups : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
315 File path to dataset containing groups labels
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
316
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
317 ref_seq : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
318 File path to dataset containing genome sequence file
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
319
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
320 intervals : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
321 File path to dataset containing interval file
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
322
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
323 targets : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
324 File path to dataset compressed target bed file
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
325
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
326 fasta_path : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
327 File path to dataset containing fasta file
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
328
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
329 model_config : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
330 File path to dataset containing JSON config for neural networks
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
331
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
332 true_labels : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
333 File path to dataset containing true labels
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
334
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
335 predicted_labels : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
336 File path to dataset containing true predicted labels
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
337
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
338 plot_color : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
339 Color of the confusion matrix heatmap
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
340
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
341 title : str, default is None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
342 Title of the confusion matrix heatmap
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
343 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
344 warnings.simplefilter('ignore')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
345
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
346 with open(inputs, 'r') as param_handler:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
347 params = json.load(param_handler)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
348
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
349 title = params['plotting_selection']['title'].strip()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
350 plot_type = params['plotting_selection']['plot_type']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
351 plot_format = params['plotting_selection']['plot_format']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
352
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
353 if plot_type == 'feature_importances':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
354 with open(infile_estimator, 'rb') as estimator_handler:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
355 estimator = load_model(estimator_handler)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
356
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
357 column_option = (params['plotting_selection']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
358 ['column_selector_options']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
359 ['selected_column_selector_option'])
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
360 if column_option in ['by_index_number', 'all_but_by_index_number',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
361 'by_header_name', 'all_but_by_header_name']:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
362 c = (params['plotting_selection']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
363 ['column_selector_options']['col1'])
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
364 else:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
365 c = None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
366
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
367 _, input_df = read_columns(infile1, c=c,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
368 c_option=column_option,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
369 return_df=True,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
370 sep='\t', header='infer',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
371 parse_dates=True)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
372
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
373 feature_names = input_df.columns.values
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
374
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
375 if isinstance(estimator, Pipeline):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
376 for st in estimator.steps[:-1]:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
377 if isinstance(st[-1], SelectorMixin):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
378 mask = st[-1].get_support()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
379 feature_names = feature_names[mask]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
380 estimator = estimator.steps[-1][-1]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
381
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
382 if hasattr(estimator, 'coef_'):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
383 coefs = estimator.coef_
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
384 else:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
385 coefs = getattr(estimator, 'feature_importances_', None)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
386 if coefs is None:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
387 raise RuntimeError('The classifier does not expose '
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
388 '"coef_" or "feature_importances_" '
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
389 'attributes')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
390
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
391 threshold = params['plotting_selection']['threshold']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
392 if threshold is not None:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
393 mask = (coefs > threshold) | (coefs < -threshold)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
394 coefs = coefs[mask]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
395 feature_names = feature_names[mask]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
396
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
397 # sort
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
398 indices = np.argsort(coefs)[::-1]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
399
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
400 trace = go.Bar(x=feature_names[indices],
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
401 y=coefs[indices])
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
402 layout = go.Layout(title=title or "Feature Importances")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
403 fig = go.Figure(data=[trace], layout=layout)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
404
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
405 plotly.offline.plot(fig, filename="output.html",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
406 auto_open=False)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
407 # to be discovered by `from_work_dir`
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
408 os.rename('output.html', 'output')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
409
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
410 return 0
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
411
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
412 elif plot_type in ('pr_curve', 'roc_curve'):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
413 df1 = pd.read_csv(infile1, sep='\t', header='infer')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
414 df2 = pd.read_csv(infile2, sep='\t', header='infer').astype(np.float32)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
415
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
416 minimum = params['plotting_selection']['report_minimum_n_positives']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
417 # filter out columns whose n_positives is beblow the threhold
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
418 if minimum:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
419 mask = df1.sum(axis=0) >= minimum
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
420 df1 = df1.loc[:, mask]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
421 df2 = df2.loc[:, mask]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
422
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
423 pos_label = params['plotting_selection']['pos_label'].strip() \
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
424 or None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
425
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
426 if plot_type == 'pr_curve':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
427 if plot_format == 'plotly_html':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
428 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
429 else:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
430 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
431 else: # 'roc_curve'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
432 drop_intermediate = (params['plotting_selection']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
433 ['drop_intermediate'])
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
434 if plot_format == 'plotly_html':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
435 visualize_roc_curve_plotly(df1, df2, pos_label,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
436 drop_intermediate=drop_intermediate,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
437 title=title)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
438 else:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
439 visualize_roc_curve_matplotlib(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
440 df1, df2, pos_label,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
441 drop_intermediate=drop_intermediate,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
442 title=title)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
443
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
444 return 0
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
445
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
446 elif plot_type == 'rfecv_gridscores':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
447 input_df = pd.read_csv(infile1, sep='\t', header='infer')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
448 scores = input_df.iloc[:, 0]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
449 steps = params['plotting_selection']['steps'].strip()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
450 steps = safe_eval(steps)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
451
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
452 data = go.Scatter(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
453 x=list(range(len(scores))),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
454 y=scores,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
455 text=[str(_) for _ in steps] if steps else None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
456 mode='lines'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
457 )
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
458 layout = go.Layout(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
459 xaxis=dict(title="Number of features selected"),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
460 yaxis=dict(title="Cross validation score"),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
461 title=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
462 text=title or None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
463 x=0.5,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
464 y=0.92,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
465 xanchor='center',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
466 yanchor='top'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
467 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
468 font=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
469 family="sans-serif",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
470 size=11
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
471 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
472 # control backgroud colors
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
473 plot_bgcolor='rgba(255,255,255,0)'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
474 )
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
475 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
476 # legend=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
477 # x=0.95,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
478 # y=0,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
479 # traceorder="normal",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
480 # font=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
481 # family="sans-serif",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
482 # size=9,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
483 # color="black"
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
484 # ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
485 # bgcolor="LightSteelBlue",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
486 # bordercolor="Black",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
487 # borderwidth=2
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
488 # ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
489 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
490
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
491 fig = go.Figure(data=[data], layout=layout)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
492 plotly.offline.plot(fig, filename="output.html",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
493 auto_open=False)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
494 # to be discovered by `from_work_dir`
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
495 os.rename('output.html', 'output')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
496
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
497 return 0
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
498
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
499 elif plot_type == 'learning_curve':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
500 input_df = pd.read_csv(infile1, sep='\t', header='infer')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
501 plot_std_err = params['plotting_selection']['plot_std_err']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
502 data1 = go.Scatter(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
503 x=input_df['train_sizes_abs'],
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
504 y=input_df['mean_train_scores'],
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
505 error_y=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
506 array=input_df['std_train_scores']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
507 ) if plot_std_err else None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
508 mode='lines',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
509 name="Train Scores",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
510 )
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
511 data2 = go.Scatter(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
512 x=input_df['train_sizes_abs'],
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
513 y=input_df['mean_test_scores'],
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
514 error_y=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
515 array=input_df['std_test_scores']
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
516 ) if plot_std_err else None,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
517 mode='lines',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
518 name="Test Scores",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
519 )
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
520 layout = dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
521 xaxis=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
522 title='No. of samples'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
523 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
524 yaxis=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
525 title='Performance Score'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
526 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
527 # modify these configurations to customize image
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
528 title=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
529 text=title or 'Learning Curve',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
530 x=0.5,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
531 y=0.92,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
532 xanchor='center',
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
533 yanchor='top'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
534 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
535 font=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
536 family="sans-serif",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
537 size=11
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
538 ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
539 # control backgroud colors
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
540 plot_bgcolor='rgba(255,255,255,0)'
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
541 )
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
542 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
543 # legend=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
544 # x=0.95,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
545 # y=0,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
546 # traceorder="normal",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
547 # font=dict(
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
548 # family="sans-serif",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
549 # size=9,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
550 # color="black"
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
551 # ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
552 # bgcolor="LightSteelBlue",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
553 # bordercolor="Black",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
554 # borderwidth=2
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
555 # ),
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
556 """
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
557
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
558 fig = go.Figure(data=[data1, data2], layout=layout)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
559 plotly.offline.plot(fig, filename="output.html",
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
560 auto_open=False)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
561 # to be discovered by `from_work_dir`
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
562 os.rename('output.html', 'output')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
563
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
564 return 0
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
565
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
566 elif plot_type == 'keras_plot_model':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
567 with open(model_config, 'r') as f:
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
568 model_str = f.read()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
569 model = model_from_json(model_str)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
570 plot_model(model, to_file="output.png")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
571 os.rename('output.png', 'output')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
572
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
573 return 0
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
574
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
575 elif plot_type == 'classification_confusion_matrix':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
576 plot_selection = params["plotting_selection"]
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
577 input_true = get_dataframe(true_labels, plot_selection, "header_true", "column_selector_options_true")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
578 header_predicted = 'infer' if plot_selection["header_predicted"] else None
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
579 input_predicted = pd.read_csv(predicted_labels, sep='\t', parse_dates=True, header=header_predicted)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
580 true_classes = input_true.iloc[:, -1].copy()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
581 predicted_classes = input_predicted.iloc[:, -1].copy()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
582 axis_labels = list(set(true_classes))
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
583 c_matrix = confusion_matrix(true_classes, predicted_classes)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
584 fig, ax = plt.subplots(figsize=(7, 7))
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
585 im = plt.imshow(c_matrix, cmap=plot_color)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
586 for i in range(len(c_matrix)):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
587 for j in range(len(c_matrix)):
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
588 ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
589 ax.set_ylabel('True class labels')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
590 ax.set_xlabel('Predicted class labels')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
591 ax.set_title(title)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
592 ax.set_xticks(axis_labels)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
593 ax.set_yticks(axis_labels)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
594 fig.colorbar(im, ax=ax)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
595 fig.tight_layout()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
596 plt.savefig("output.png", dpi=125)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
597 os.rename('output.png', 'output')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
598
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
599 return 0
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
600
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
601 # save pdf file to disk
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
602 # fig.write_image("image.pdf", format='pdf')
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
603 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
604
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
605
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
606 if __name__ == '__main__':
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
607 aparser = argparse.ArgumentParser()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
608 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
609 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
610 aparser.add_argument("-X", "--infile1", dest="infile1")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
611 aparser.add_argument("-y", "--infile2", dest="infile2")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
612 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
613 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
614 aparser.add_argument("-g", "--groups", dest="groups")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
615 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
616 aparser.add_argument("-b", "--intervals", dest="intervals")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
617 aparser.add_argument("-t", "--targets", dest="targets")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
618 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
619 aparser.add_argument("-c", "--model_config", dest="model_config")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
620 aparser.add_argument("-tl", "--true_labels", dest="true_labels")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
621 aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
622 aparser.add_argument("-pc", "--plot_color", dest="plot_color")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
623 aparser.add_argument("-pt", "--title", dest="title")
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
624 args = aparser.parse_args()
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
625
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
626 main(args.inputs, args.infile_estimator, args.infile1, args.infile2,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
627 args.outfile_result, outfile_object=args.outfile_object,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
628 groups=args.groups, ref_seq=args.ref_seq, intervals=args.intervals,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
629 targets=args.targets, fasta_path=args.fasta_path,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
630 model_config=args.model_config, true_labels=args.true_labels,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
631 predicted_labels=args.predicted_labels,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
632 plot_color=args.plot_color,
2d7016b3ae92 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afb24f3c81d625312186750a714d702363012b5"
bgruening
parents:
diff changeset
633 title=args.title)