Mercurial > repos > bgruening > sklearn_build_pipeline
annotate ml_visualization_ex.py @ 29:4c4ec859c31a draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | bgruening |
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date | Sun, 05 Nov 2023 15:54:36 +0000 |
parents | 9160cb4069c2 |
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653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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1 import argparse |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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2 import json |
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664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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3 import os |
664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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4 import warnings |
664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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5 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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6 import matplotlib |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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7 import matplotlib.pyplot as plt |
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653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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8 import numpy as np |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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9 import pandas as pd |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
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10 import plotly |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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11 import plotly.graph_objs as go |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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12 from galaxy_ml.model_persist import load_model_from_h5 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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13 from galaxy_ml.utils import read_columns, SafeEval |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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14 from sklearn.feature_selection._base import SelectorMixin |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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15 from sklearn.metrics import ( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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16 auc, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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17 average_precision_score, |
26
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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18 confusion_matrix, |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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19 precision_recall_curve, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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20 roc_curve, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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21 ) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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22 from sklearn.pipeline import Pipeline |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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23 from tensorflow.keras.models import model_from_json |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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24 from tensorflow.keras.utils import plot_model |
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653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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25 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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26 safe_eval = SafeEval() |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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27 |
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3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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28 # plotly default colors |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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29 default_colors = [ |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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30 "#1f77b4", # muted blue |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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31 "#ff7f0e", # safety orange |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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32 "#2ca02c", # cooked asparagus green |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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33 "#d62728", # brick red |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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34 "#9467bd", # muted purple |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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35 "#8c564b", # chestnut brown |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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36 "#e377c2", # raspberry yogurt pink |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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37 "#7f7f7f", # middle gray |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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38 "#bcbd22", # curry yellow-green |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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39 "#17becf", # blue-teal |
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3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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40 ] |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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41 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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42 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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43 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None): |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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44 """output pr-curve in html using plotly |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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45 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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46 df1 : pandas.DataFrame |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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47 Containing y_true |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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48 df2 : pandas.DataFrame |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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49 Containing y_score |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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50 pos_label : None |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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51 The label of positive class |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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52 title : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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53 Plot title |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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54 """ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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55 data = [] |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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56 for idx in range(df1.shape[1]): |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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57 y_true = df1.iloc[:, idx].values |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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58 y_score = df2.iloc[:, idx].values |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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59 |
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60 precision, recall, _ = precision_recall_curve( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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61 y_true, y_score, pos_label=pos_label |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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62 ) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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63 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1) |
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64 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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65 trace = go.Scatter( |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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66 x=recall, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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67 y=precision, |
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68 mode="lines", |
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69 marker=dict(color=default_colors[idx % len(default_colors)]), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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70 name="%s (area = %.3f)" % (idx, ap), |
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71 ) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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72 data.append(trace) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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73 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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74 layout = go.Layout( |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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75 xaxis=dict(title="Recall", linecolor="lightslategray", linewidth=1), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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76 yaxis=dict(title="Precision", linecolor="lightslategray", linewidth=1), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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77 title=dict( |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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78 text=title or "Precision-Recall Curve", |
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79 x=0.5, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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80 y=0.92, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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81 xanchor="center", |
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82 yanchor="top", |
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83 ), |
19
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84 font=dict(family="sans-serif", size=11), |
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85 # control backgroud colors |
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86 plot_bgcolor="rgba(255,255,255,0)", |
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87 ) |
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88 """ |
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89 legend=dict( |
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90 x=0.95, |
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91 y=0, |
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92 traceorder="normal", |
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93 font=dict( |
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94 family="sans-serif", |
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95 size=9, |
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96 color="black" |
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97 ), |
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98 bgcolor="LightSteelBlue", |
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99 bordercolor="Black", |
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100 borderwidth=2 |
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101 ),""" |
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102 |
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103 fig = go.Figure(data=data, layout=layout) |
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104 |
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105 plotly.offline.plot(fig, filename="output.html", auto_open=False) |
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106 # to be discovered by `from_work_dir` |
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107 os.rename("output.html", "output") |
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108 |
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109 |
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110 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None): |
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111 """visualize pr-curve using matplotlib and output svg image""" |
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112 backend = matplotlib.get_backend() |
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113 if "inline" not in backend: |
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114 matplotlib.use("SVG") |
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115 plt.style.use("seaborn-colorblind") |
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116 plt.figure() |
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117 |
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118 for idx in range(df1.shape[1]): |
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119 y_true = df1.iloc[:, idx].values |
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120 y_score = df2.iloc[:, idx].values |
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121 |
21
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122 precision, recall, _ = precision_recall_curve( |
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123 y_true, y_score, pos_label=pos_label |
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124 ) |
19
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125 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1) |
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126 |
19
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127 plt.step( |
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128 recall, |
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129 precision, |
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130 "r-", |
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131 color="black", |
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132 alpha=0.3, |
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133 lw=1, |
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134 where="post", |
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135 label="%s (area = %.3f)" % (idx, ap), |
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136 ) |
15
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137 |
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138 plt.xlim([0.0, 1.0]) |
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139 plt.ylim([0.0, 1.05]) |
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140 plt.xlabel("Recall") |
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141 plt.ylabel("Precision") |
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142 title = title or "Precision-Recall Curve" |
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143 plt.title(title) |
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144 folder = os.getcwd() |
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145 plt.savefig(os.path.join(folder, "output.svg"), format="svg") |
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146 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output")) |
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147 |
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148 |
19
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149 def visualize_roc_curve_plotly(df1, df2, pos_label, drop_intermediate=True, title=None): |
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150 """output roc-curve in html using plotly |
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151 |
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152 df1 : pandas.DataFrame |
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153 Containing y_true |
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154 df2 : pandas.DataFrame |
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155 Containing y_score |
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156 pos_label : None |
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157 The label of positive class |
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158 drop_intermediate : bool |
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159 Whether to drop some suboptimal thresholds |
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160 title : str |
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161 Plot title |
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162 """ |
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163 data = [] |
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164 for idx in range(df1.shape[1]): |
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165 y_true = df1.iloc[:, idx].values |
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166 y_score = df2.iloc[:, idx].values |
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167 |
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168 fpr, tpr, _ = roc_curve( |
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169 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate |
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170 ) |
15
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171 roc_auc = auc(fpr, tpr) |
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172 |
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173 trace = go.Scatter( |
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174 x=fpr, |
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175 y=tpr, |
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176 mode="lines", |
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177 marker=dict(color=default_colors[idx % len(default_colors)]), |
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178 name="%s (area = %.3f)" % (idx, roc_auc), |
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179 ) |
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180 data.append(trace) |
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181 |
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182 layout = go.Layout( |
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183 xaxis=dict( |
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184 title="False Positive Rate", linecolor="lightslategray", linewidth=1 |
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185 ), |
19
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186 yaxis=dict(title="True Positive Rate", linecolor="lightslategray", linewidth=1), |
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187 title=dict( |
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188 text=title or "Receiver Operating Characteristic (ROC) Curve", |
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189 x=0.5, |
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190 y=0.92, |
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191 xanchor="center", |
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192 yanchor="top", |
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193 ), |
19
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194 font=dict(family="sans-serif", size=11), |
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195 # control backgroud colors |
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196 plot_bgcolor="rgba(255,255,255,0)", |
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197 ) |
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198 """ |
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199 # legend=dict( |
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200 # x=0.95, |
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201 # y=0, |
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202 # traceorder="normal", |
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203 # font=dict( |
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204 # family="sans-serif", |
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205 # size=9, |
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206 # color="black" |
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207 # ), |
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208 # bgcolor="LightSteelBlue", |
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209 # bordercolor="Black", |
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210 # borderwidth=2 |
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211 # ), |
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212 """ |
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213 |
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214 fig = go.Figure(data=data, layout=layout) |
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215 |
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216 plotly.offline.plot(fig, filename="output.html", auto_open=False) |
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217 # to be discovered by `from_work_dir` |
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218 os.rename("output.html", "output") |
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219 |
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220 |
21
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221 def visualize_roc_curve_matplotlib( |
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222 df1, df2, pos_label, drop_intermediate=True, title=None |
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223 ): |
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224 """visualize roc-curve using matplotlib and output svg image""" |
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225 backend = matplotlib.get_backend() |
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226 if "inline" not in backend: |
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227 matplotlib.use("SVG") |
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228 plt.style.use("seaborn-colorblind") |
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229 plt.figure() |
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230 |
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231 for idx in range(df1.shape[1]): |
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232 y_true = df1.iloc[:, idx].values |
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233 y_score = df2.iloc[:, idx].values |
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234 |
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235 fpr, tpr, _ = roc_curve( |
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236 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate |
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237 ) |
15
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238 roc_auc = auc(fpr, tpr) |
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239 |
19
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240 plt.step( |
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241 fpr, |
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242 tpr, |
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243 "r-", |
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244 color="black", |
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245 alpha=0.3, |
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246 lw=1, |
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247 where="post", |
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248 label="%s (area = %.3f)" % (idx, roc_auc), |
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249 ) |
15
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250 |
3f3c6dc38f3e
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251 plt.xlim([0.0, 1.0]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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252 plt.ylim([0.0, 1.05]) |
19
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253 plt.xlabel("False Positive Rate") |
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254 plt.ylabel("True Positive Rate") |
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255 title = title or "Receiver Operating Characteristic (ROC) Curve" |
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256 plt.title(title) |
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257 folder = os.getcwd() |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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258 plt.savefig(os.path.join(folder, "output.svg"), format="svg") |
19
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259 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output")) |
15
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260 |
11
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261 |
26
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262 def get_dataframe(file_path, plot_selection, header_name, column_name): |
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263 header = "infer" if plot_selection[header_name] else None |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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264 column_option = plot_selection[column_name]["selected_column_selector_option"] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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265 if column_option in [ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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266 "by_index_number", |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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267 "all_but_by_index_number", |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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268 "by_header_name", |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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269 "all_but_by_header_name", |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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270 ]: |
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271 col = plot_selection[column_name]["col1"] |
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272 else: |
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273 col = None |
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274 _, input_df = read_columns( |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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275 file_path, |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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276 c=col, |
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277 c_option=column_option, |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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278 return_df=True, |
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279 sep="\t", |
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280 header=header, |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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281 parse_dates=True, |
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282 ) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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283 return input_df |
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284 |
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285 |
19
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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286 def main( |
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287 inputs, |
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288 infile_estimator=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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289 infile1=None, |
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290 infile2=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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291 outfile_result=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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292 outfile_object=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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293 groups=None, |
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294 ref_seq=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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295 intervals=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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296 targets=None, |
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297 fasta_path=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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298 model_config=None, |
26
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299 true_labels=None, |
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300 predicted_labels=None, |
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301 plot_color=None, |
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302 title=None, |
19
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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303 ): |
11
653be9c354ec
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304 """ |
653be9c354ec
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305 Parameter |
653be9c354ec
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306 --------- |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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307 inputs : str |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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308 File path to galaxy tool parameter |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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309 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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310 infile_estimator : str, default is None |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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311 File path to estimator |
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312 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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313 infile1 : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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314 File path to dataset containing features or true labels. |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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315 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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316 infile2 : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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317 File path to dataset containing target values or predicted |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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318 probabilities. |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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319 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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320 outfile_result : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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321 File path to save the results, either cv_results or test result |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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322 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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|
323 outfile_object : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
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324 File path to save searchCV object |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
325 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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|
326 groups : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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|
327 File path to dataset containing groups labels |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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|
328 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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|
329 ref_seq : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
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330 File path to dataset containing genome sequence file |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
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331 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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332 intervals : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
333 File path to dataset containing interval file |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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334 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
335 targets : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
336 File path to dataset compressed target bed file |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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337 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
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338 fasta_path : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
339 File path to dataset containing fasta file |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
340 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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341 model_config : str, default is None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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|
342 File path to dataset containing JSON config for neural networks |
26
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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343 |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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344 true_labels : str, default is None |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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345 File path to dataset containing true labels |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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346 |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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347 predicted_labels : str, default is None |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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348 File path to dataset containing true predicted labels |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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349 |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
changeset
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350 plot_color : str, default is None |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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351 Color of the confusion matrix heatmap |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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|
352 |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
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353 title : str, default is None |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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354 Title of the confusion matrix heatmap |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
355 """ |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
356 warnings.simplefilter("ignore") |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
357 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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358 with open(inputs, "r") as param_handler: |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
359 params = json.load(param_handler) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
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|
360 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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361 title = params["plotting_selection"]["title"].strip() |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
362 plot_type = params["plotting_selection"]["plot_type"] |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
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|
363 plot_format = params["plotting_selection"]["plot_format"] |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
364 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
365 if plot_type == "feature_importances": |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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diff
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|
366 estimator = load_model_from_h5(infile_estimator) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
367 |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
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368 column_option = params["plotting_selection"]["column_selector_options"][ |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
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diff
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|
369 "selected_column_selector_option" |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
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changeset
|
370 ] |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
371 if column_option in [ |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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changeset
|
372 "by_index_number", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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changeset
|
373 "all_but_by_index_number", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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changeset
|
374 "by_header_name", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
375 "all_but_by_header_name", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
376 ]: |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
377 c = params["plotting_selection"]["column_selector_options"]["col1"] |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
378 else: |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
379 c = None |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
380 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
381 _, input_df = read_columns( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
382 infile1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
383 c=c, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
384 c_option=column_option, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
385 return_df=True, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
386 sep="\t", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
387 header="infer", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
388 parse_dates=True, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
389 ) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
390 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
391 feature_names = input_df.columns.values |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
392 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
393 if isinstance(estimator, Pipeline): |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
394 for st in estimator.steps[:-1]: |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
395 if isinstance(st[-1], SelectorMixin): |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
396 mask = st[-1].get_support() |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
397 feature_names = feature_names[mask] |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
398 estimator = estimator.steps[-1][-1] |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
399 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
400 if hasattr(estimator, "coef_"): |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
401 coefs = estimator.coef_ |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
402 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
403 coefs = getattr(estimator, "feature_importances_", None) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
404 if coefs is None: |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
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diff
changeset
|
405 raise RuntimeError( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
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diff
changeset
|
406 "The classifier does not expose " |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
407 '"coef_" or "feature_importances_" ' |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
408 "attributes" |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
409 ) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
410 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
411 threshold = params["plotting_selection"]["threshold"] |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
412 if threshold is not None: |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
413 mask = (coefs > threshold) | (coefs < -threshold) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
414 coefs = coefs[mask] |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
415 feature_names = feature_names[mask] |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
416 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
417 # sort |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
418 indices = np.argsort(coefs)[::-1] |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
419 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
420 trace = go.Bar(x=feature_names[indices], y=coefs[indices]) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
421 layout = go.Layout(title=title or "Feature Importances") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
422 fig = go.Figure(data=[trace], layout=layout) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
423 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
424 plotly.offline.plot(fig, filename="output.html", auto_open=False) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
425 # to be discovered by `from_work_dir` |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
426 os.rename("output.html", "output") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
427 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
428 return 0 |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
429 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
430 elif plot_type in ("pr_curve", "roc_curve"): |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
431 df1 = pd.read_csv(infile1, sep="\t", header="infer") |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
432 df2 = pd.read_csv(infile2, sep="\t", header="infer").astype(np.float32) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
433 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
434 minimum = params["plotting_selection"]["report_minimum_n_positives"] |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
435 # filter out columns whose n_positives is beblow the threhold |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
436 if minimum: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
437 mask = df1.sum(axis=0) >= minimum |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
438 df1 = df1.loc[:, mask] |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
439 df2 = df2.loc[:, mask] |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
440 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
441 pos_label = params["plotting_selection"]["pos_label"].strip() or None |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
442 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
443 if plot_type == "pr_curve": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
444 if plot_format == "plotly_html": |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
445 visualize_pr_curve_plotly(df1, df2, pos_label, title=title) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
446 else: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
447 visualize_pr_curve_matplotlib(df1, df2, pos_label, title) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
448 else: # 'roc_curve' |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
449 drop_intermediate = params["plotting_selection"]["drop_intermediate"] |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
450 if plot_format == "plotly_html": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
451 visualize_roc_curve_plotly( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
452 df1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
453 df2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
454 pos_label, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
455 drop_intermediate=drop_intermediate, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
456 title=title, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
457 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
458 else: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
459 visualize_roc_curve_matplotlib( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
460 df1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
461 df2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
462 pos_label, |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
463 drop_intermediate=drop_intermediate, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
464 title=title, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
465 ) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
466 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
467 return 0 |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
468 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
469 elif plot_type == "rfecv_gridscores": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
470 input_df = pd.read_csv(infile1, sep="\t", header="infer") |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
471 scores = input_df.iloc[:, 0] |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
472 steps = params["plotting_selection"]["steps"].strip() |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
473 steps = safe_eval(steps) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
474 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
475 data = go.Scatter( |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
476 x=list(range(len(scores))), |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
477 y=scores, |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
478 text=[str(_) for _ in steps] if steps else None, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
479 mode="lines", |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
480 ) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
481 layout = go.Layout( |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
482 xaxis=dict(title="Number of features selected"), |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
483 yaxis=dict(title="Cross validation score"), |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
484 title=dict( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
485 text=title or None, x=0.5, y=0.92, xanchor="center", yanchor="top" |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
486 ), |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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487 font=dict(family="sans-serif", size=11), |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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|
488 # control backgroud colors |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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489 plot_bgcolor="rgba(255,255,255,0)", |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
490 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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|
491 """ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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changeset
|
492 # legend=dict( |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
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493 # x=0.95, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
494 # y=0, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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changeset
|
495 # traceorder="normal", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
496 # font=dict( |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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changeset
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497 # family="sans-serif", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
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498 # size=9, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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changeset
|
499 # color="black" |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
500 # ), |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
501 # bgcolor="LightSteelBlue", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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changeset
|
502 # bordercolor="Black", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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changeset
|
503 # borderwidth=2 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
504 # ), |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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|
505 """ |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
506 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
507 fig = go.Figure(data=[data], layout=layout) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
508 plotly.offline.plot(fig, filename="output.html", auto_open=False) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
509 # to be discovered by `from_work_dir` |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
510 os.rename("output.html", "output") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
511 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
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changeset
|
512 return 0 |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
513 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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changeset
|
514 elif plot_type == "learning_curve": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
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|
515 input_df = pd.read_csv(infile1, sep="\t", header="infer") |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
516 plot_std_err = params["plotting_selection"]["plot_std_err"] |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
517 data1 = go.Scatter( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
518 x=input_df["train_sizes_abs"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
519 y=input_df["mean_train_scores"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
520 error_y=dict(array=input_df["std_train_scores"]) if plot_std_err else None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
521 mode="lines", |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
522 name="Train Scores", |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
523 ) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
524 data2 = go.Scatter( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
525 x=input_df["train_sizes_abs"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
526 y=input_df["mean_test_scores"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
527 error_y=dict(array=input_df["std_test_scores"]) if plot_std_err else None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
528 mode="lines", |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
529 name="Test Scores", |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
530 ) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
531 layout = dict( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
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|
532 xaxis=dict(title="No. of samples"), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
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|
533 yaxis=dict(title="Performance Score"), |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
534 # modify these configurations to customize image |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
535 title=dict( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
536 text=title or "Learning Curve", |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
537 x=0.5, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
538 y=0.92, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
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|
539 xanchor="center", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
540 yanchor="top", |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
541 ), |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
542 font=dict(family="sans-serif", size=11), |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
543 # control backgroud colors |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
544 plot_bgcolor="rgba(255,255,255,0)", |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
545 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
546 """ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
547 # legend=dict( |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
548 # x=0.95, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
549 # y=0, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
550 # traceorder="normal", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
551 # font=dict( |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
552 # family="sans-serif", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
553 # size=9, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
554 # color="black" |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
555 # ), |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
556 # bgcolor="LightSteelBlue", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
557 # bordercolor="Black", |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
558 # borderwidth=2 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
559 # ), |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
560 """ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
561 |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
562 fig = go.Figure(data=[data1, data2], layout=layout) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
563 plotly.offline.plot(fig, filename="output.html", auto_open=False) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
564 # to be discovered by `from_work_dir` |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
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|
565 os.rename("output.html", "output") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
566 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
567 return 0 |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
568 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
569 elif plot_type == "keras_plot_model": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
570 with open(model_config, "r") as f: |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
571 model_str = f.read() |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
572 model = model_from_json(model_str) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
573 plot_model(model, to_file="output.png") |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
574 os.rename("output.png", "output") |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
575 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
576 return 0 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
577 |
26
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
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|
578 elif plot_type == "classification_confusion_matrix": |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
579 plot_selection = params["plotting_selection"] |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
changeset
|
580 input_true = get_dataframe( |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
581 true_labels, plot_selection, "header_true", "column_selector_options_true" |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
582 ) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
583 header_predicted = "infer" if plot_selection["header_predicted"] else None |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
584 input_predicted = pd.read_csv( |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
changeset
|
585 predicted_labels, sep="\t", parse_dates=True, header=header_predicted |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
586 ) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
changeset
|
587 true_classes = input_true.iloc[:, -1].copy() |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
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changeset
|
588 predicted_classes = input_predicted.iloc[:, -1].copy() |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
589 axis_labels = list(set(true_classes)) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
changeset
|
590 c_matrix = confusion_matrix(true_classes, predicted_classes) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
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|
591 fig, ax = plt.subplots(figsize=(7, 7)) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
592 im = plt.imshow(c_matrix, cmap=plot_color) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
593 for i in range(len(c_matrix)): |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
594 for j in range(len(c_matrix)): |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
595 ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k") |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
596 ax.set_ylabel("True class labels") |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
597 ax.set_xlabel("Predicted class labels") |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
598 ax.set_title(title) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
599 ax.set_xticks(axis_labels) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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diff
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|
600 ax.set_yticks(axis_labels) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
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changeset
|
601 fig.colorbar(im, ax=ax) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
602 fig.tight_layout() |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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changeset
|
603 plt.savefig("output.png", dpi=125) |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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|
604 os.rename("output.png", "output") |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
605 |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
606 return 0 |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
607 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
608 # save pdf file to disk |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
609 # fig.write_image("image.pdf", format='pdf') |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
12
diff
changeset
|
610 # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2) |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
611 |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
612 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
613 if __name__ == "__main__": |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
614 aparser = argparse.ArgumentParser() |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
615 aparser.add_argument("-i", "--inputs", dest="inputs", required=True) |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
616 aparser.add_argument("-e", "--estimator", dest="infile_estimator") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
617 aparser.add_argument("-X", "--infile1", dest="infile1") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
618 aparser.add_argument("-y", "--infile2", dest="infile2") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
619 aparser.add_argument("-O", "--outfile_result", dest="outfile_result") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
620 aparser.add_argument("-o", "--outfile_object", dest="outfile_object") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
621 aparser.add_argument("-g", "--groups", dest="groups") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
622 aparser.add_argument("-r", "--ref_seq", dest="ref_seq") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
623 aparser.add_argument("-b", "--intervals", dest="intervals") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
624 aparser.add_argument("-t", "--targets", dest="targets") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
625 aparser.add_argument("-f", "--fasta_path", dest="fasta_path") |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
626 aparser.add_argument("-c", "--model_config", dest="model_config") |
26
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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changeset
|
627 aparser.add_argument("-tl", "--true_labels", dest="true_labels") |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
628 aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels") |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
629 aparser.add_argument("-pc", "--plot_color", dest="plot_color") |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
25
diff
changeset
|
630 aparser.add_argument("-pt", "--title", dest="title") |
11
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
631 args = aparser.parse_args() |
653be9c354ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff
changeset
|
632 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
633 main( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
634 args.inputs, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
635 args.infile_estimator, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
636 args.infile1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
637 args.infile2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
638 args.outfile_result, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
639 outfile_object=args.outfile_object, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
640 groups=args.groups, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
641 ref_seq=args.ref_seq, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
642 intervals=args.intervals, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
643 targets=args.targets, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
644 fasta_path=args.fasta_path, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
17
diff
changeset
|
645 model_config=args.model_config, |
26
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
parents:
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646 true_labels=args.true_labels, |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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647 predicted_labels=args.predicted_labels, |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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25
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648 plot_color=args.plot_color, |
9160cb4069c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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649 title=args.title, |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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650 ) |