sklearn_stacking_ensemble_models: ml_visualization

annotate ml_visualization_ex.py @ 14:2fc88dc854ee draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f031d8ddfb73cec24572648666ac44ee47f08aad

author	bgruening
date	Thu, 11 Aug 2022 07:49:08 +0000
parents	0380f10c4e04
children

rev	line source
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	1 import argparse
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	2 import json
10 2d890789ac48 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2" bgruening parents: 9 diff changeset	3 import os
2d890789ac48 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2" bgruening parents: 9 diff changeset	4 import warnings
2d890789ac48 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2" bgruening parents: 9 diff changeset	5
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	6 import matplotlib
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	7 import matplotlib.pyplot as plt
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	8 import numpy as np
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	9 import pandas as pd
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	10 import plotly
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	11 import plotly.graph_objs as go
10 2d890789ac48 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2" bgruening parents: 9 diff changeset	12 from galaxy_ml.utils import load_model, read_columns, SafeEval
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	13 from keras.models import model_from_json
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	14 from keras.utils import plot_model
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	15 from sklearn.feature_selection.base import SelectorMixin
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	16 from sklearn.metrics import (auc, average_precision_score, confusion_matrix,
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	17 precision_recall_curve, roc_curve)
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	18 from sklearn.pipeline import Pipeline
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	19
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	20 safe_eval = SafeEval()
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	21
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	22 # plotly default colors
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	23 default_colors = [
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	24 "#1f77b4", # muted blue
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	25 "#ff7f0e", # safety orange
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	26 "#2ca02c", # cooked asparagus green
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	27 "#d62728", # brick red
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	28 "#9467bd", # muted purple
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	29 "#8c564b", # chestnut brown
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	30 "#e377c2", # raspberry yogurt pink
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	31 "#7f7f7f", # middle gray
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	32 "#bcbd22", # curry yellow-green
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	33 "#17becf", # blue-teal
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	34 ]
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	35
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	36
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	37 def visualize_pr_curve_plotly(df1, df2, pos_label, title=None):
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	38 """output pr-curve in html using plotly
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	39
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	40 df1 : pandas.DataFrame
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	41 Containing y_true
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	42 df2 : pandas.DataFrame
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	43 Containing y_score
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	44 pos_label : None
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	45 The label of positive class
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	46 title : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	47 Plot title
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	48 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	49 data = []
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	50 for idx in range(df1.shape[1]):
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	51 y_true = df1.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	52 y_score = df2.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	53
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	54 precision, recall, _ = precision_recall_curve(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	55 y_true, y_score, pos_label=pos_label
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	56 )
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	57 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	58
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	59 trace = go.Scatter(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	60 x=recall,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	61 y=precision,
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	62 mode="lines",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	63 marker=dict(color=default_colors[idx % len(default_colors)]),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	64 name="%s (area = %.3f)" % (idx, ap),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	65 )
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	66 data.append(trace)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	67
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	68 layout = go.Layout(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	69 xaxis=dict(title="Recall", linecolor="lightslategray", linewidth=1),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	70 yaxis=dict(title="Precision", linecolor="lightslategray", linewidth=1),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	71 title=dict(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	72 text=title or "Precision-Recall Curve",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	73 x=0.5,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	74 y=0.92,
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	75 xanchor="center",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	76 yanchor="top",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	77 ),
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	78 font=dict(family="sans-serif", size=11),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	79 # control backgroud colors
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	80 plot_bgcolor="rgba(255,255,255,0)",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	81 )
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	82 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	83 legend=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	84 x=0.95,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	85 y=0,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	86 traceorder="normal",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	87 font=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	88 family="sans-serif",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	89 size=9,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	90 color="black"
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	91 ),
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	92 bgcolor="LightSteelBlue",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	93 bordercolor="Black",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	94 borderwidth=2
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	95 ),"""
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	96
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	97 fig = go.Figure(data=data, layout=layout)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	98
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	99 plotly.offline.plot(fig, filename="output.html", auto_open=False)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	100 # to be discovered by `from_work_dir`
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	101 os.rename("output.html", "output")
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	102
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	103
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	104 def visualize_pr_curve_matplotlib(df1, df2, pos_label, title=None):
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	105 """visualize pr-curve using matplotlib and output svg image"""
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	106 backend = matplotlib.get_backend()
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	107 if "inline" not in backend:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	108 matplotlib.use("SVG")
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	109 plt.style.use("seaborn-colorblind")
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	110 plt.figure()
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	111
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	112 for idx in range(df1.shape[1]):
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	113 y_true = df1.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	114 y_score = df2.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	115
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	116 precision, recall, _ = precision_recall_curve(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	117 y_true, y_score, pos_label=pos_label
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	118 )
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	119 ap = average_precision_score(y_true, y_score, pos_label=pos_label or 1)
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	120
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	121 plt.step(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	122 recall,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	123 precision,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	124 "r-",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	125 color="black",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	126 alpha=0.3,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	127 lw=1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	128 where="post",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	129 label="%s (area = %.3f)" % (idx, ap),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	130 )
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	131
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	132 plt.xlim([0.0, 1.0])
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	133 plt.ylim([0.0, 1.05])
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	134 plt.xlabel("Recall")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	135 plt.ylabel("Precision")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	136 title = title or "Precision-Recall Curve"
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	137 plt.title(title)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	138 folder = os.getcwd()
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	139 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	140 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	141
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	142
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	143 def visualize_roc_curve_plotly(df1, df2, pos_label, drop_intermediate=True, title=None):
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	144 """output roc-curve in html using plotly
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	145
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	146 df1 : pandas.DataFrame
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	147 Containing y_true
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	148 df2 : pandas.DataFrame
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	149 Containing y_score
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	150 pos_label : None
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	151 The label of positive class
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	152 drop_intermediate : bool
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	153 Whether to drop some suboptimal thresholds
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	154 title : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	155 Plot title
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	156 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	157 data = []
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	158 for idx in range(df1.shape[1]):
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	159 y_true = df1.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	160 y_score = df2.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	161
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	162 fpr, tpr, _ = roc_curve(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	163 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	164 )
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	165 roc_auc = auc(fpr, tpr)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	166
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	167 trace = go.Scatter(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	168 x=fpr,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	169 y=tpr,
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	170 mode="lines",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	171 marker=dict(color=default_colors[idx % len(default_colors)]),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	172 name="%s (area = %.3f)" % (idx, roc_auc),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	173 )
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	174 data.append(trace)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	175
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	176 layout = go.Layout(
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	177 xaxis=dict(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	178 title="False Positive Rate", linecolor="lightslategray", linewidth=1
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	179 ),
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	180 yaxis=dict(title="True Positive Rate", linecolor="lightslategray", linewidth=1),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	181 title=dict(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	182 text=title or "Receiver Operating Characteristic (ROC) Curve",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	183 x=0.5,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	184 y=0.92,
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	185 xanchor="center",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	186 yanchor="top",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	187 ),
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	188 font=dict(family="sans-serif", size=11),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	189 # control backgroud colors
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	190 plot_bgcolor="rgba(255,255,255,0)",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	191 )
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	192 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	193 # legend=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	194 # x=0.95,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	195 # y=0,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	196 # traceorder="normal",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	197 # font=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	198 # family="sans-serif",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	199 # size=9,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	200 # color="black"
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	201 # ),
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	202 # bgcolor="LightSteelBlue",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	203 # bordercolor="Black",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	204 # borderwidth=2
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	205 # ),
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	206 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	207
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	208 fig = go.Figure(data=data, layout=layout)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	209
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	210 plotly.offline.plot(fig, filename="output.html", auto_open=False)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	211 # to be discovered by `from_work_dir`
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	212 os.rename("output.html", "output")
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	213
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	214
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	215 def visualize_roc_curve_matplotlib(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	216 df1, df2, pos_label, drop_intermediate=True, title=None
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	217 ):
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	218 """visualize roc-curve using matplotlib and output svg image"""
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	219 backend = matplotlib.get_backend()
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	220 if "inline" not in backend:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	221 matplotlib.use("SVG")
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	222 plt.style.use("seaborn-colorblind")
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	223 plt.figure()
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	224
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	225 for idx in range(df1.shape[1]):
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	226 y_true = df1.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	227 y_score = df2.iloc[:, idx].values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	228
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	229 fpr, tpr, _ = roc_curve(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	230 y_true, y_score, pos_label=pos_label, drop_intermediate=drop_intermediate
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	231 )
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	232 roc_auc = auc(fpr, tpr)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	233
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	234 plt.step(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	235 fpr,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	236 tpr,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	237 "r-",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	238 color="black",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	239 alpha=0.3,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	240 lw=1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	241 where="post",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	242 label="%s (area = %.3f)" % (idx, roc_auc),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	243 )
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	244
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	245 plt.xlim([0.0, 1.0])
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	246 plt.ylim([0.0, 1.05])
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	247 plt.xlabel("False Positive Rate")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	248 plt.ylabel("True Positive Rate")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	249 title = title or "Receiver Operating Characteristic (ROC) Curve"
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	250 plt.title(title)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	251 folder = os.getcwd()
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	252 plt.savefig(os.path.join(folder, "output.svg"), format="svg")
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	253 os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	254
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	255
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	256 def get_dataframe(file_path, plot_selection, header_name, column_name):
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	257 header = "infer" if plot_selection[header_name] else None
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	258 column_option = plot_selection[column_name]["selected_column_selector_option"]
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	259 if column_option in [
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	260 "by_index_number",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	261 "all_but_by_index_number",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	262 "by_header_name",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	263 "all_but_by_header_name",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	264 ]:
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	265 col = plot_selection[column_name]["col1"]
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	266 else:
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	267 col = None
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	268 _, input_df = read_columns(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	269 file_path,
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	270 c=col,
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	271 c_option=column_option,
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	272 return_df=True,
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	273 sep="\t",
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	274 header=header,
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	275 parse_dates=True,
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	276 )
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	277 return input_df
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	278
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	279
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	280 def main(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	281 inputs,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	282 infile_estimator=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	283 infile1=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	284 infile2=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	285 outfile_result=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	286 outfile_object=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	287 groups=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	288 ref_seq=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	289 intervals=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	290 targets=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	291 fasta_path=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	292 model_config=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	293 true_labels=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	294 predicted_labels=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	295 plot_color=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	296 title=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	297 ):
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	298 """
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	299 Parameter
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	300 ---------
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	301 inputs : str
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	302 File path to galaxy tool parameter
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	303
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	304 infile_estimator : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	305 File path to estimator
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	306
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	307 infile1 : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	308 File path to dataset containing features or true labels.
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	309
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	310 infile2 : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	311 File path to dataset containing target values or predicted
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	312 probabilities.
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	313
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	314 outfile_result : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	315 File path to save the results, either cv_results or test result
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	316
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	317 outfile_object : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	318 File path to save searchCV object
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	319
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	320 groups : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	321 File path to dataset containing groups labels
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	322
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	323 ref_seq : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	324 File path to dataset containing genome sequence file
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	325
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	326 intervals : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	327 File path to dataset containing interval file
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	328
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	329 targets : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	330 File path to dataset compressed target bed file
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	331
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	332 fasta_path : str, default is None
963e449636d3 "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 fasta file
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	334
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	335 model_config : str, default is None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	336 File path to dataset containing JSON config for neural networks
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	337
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	338 true_labels : str, default is None
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	339 File path to dataset containing true labels
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	340
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	341 predicted_labels : str, default is None
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	342 File path to dataset containing true predicted labels
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	343
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	344 plot_color : str, default is None
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	345 Color of the confusion matrix heatmap
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	346
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	347 title : str, default is None
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	348 Title of the confusion matrix heatmap
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	349 """
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	350 warnings.simplefilter("ignore")
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	351
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	352 with open(inputs, "r") as param_handler:
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	353 params = json.load(param_handler)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	354
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	355 title = params["plotting_selection"]["title"].strip()
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	356 plot_type = params["plotting_selection"]["plot_type"]
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	357 plot_format = params["plotting_selection"]["plot_format"]
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	358
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	359 if plot_type == "feature_importances":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	360 with open(infile_estimator, "rb") as estimator_handler:
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	361 estimator = load_model(estimator_handler)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	362
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	363 column_option = params["plotting_selection"]["column_selector_options"][
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	364 "selected_column_selector_option"
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	365 ]
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	366 if column_option in [
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	367 "by_index_number",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	368 "all_but_by_index_number",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	369 "by_header_name",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	370 "all_but_by_header_name",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	371 ]:
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	372 c = params["plotting_selection"]["column_selector_options"]["col1"]
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	373 else:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	374 c = None
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	375
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	376 _, input_df = read_columns(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	377 infile1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	378 c=c,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	379 c_option=column_option,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	380 return_df=True,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	381 sep="\t",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	382 header="infer",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	383 parse_dates=True,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	384 )
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	385
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	386 feature_names = input_df.columns.values
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	387
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	388 if isinstance(estimator, Pipeline):
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	389 for st in estimator.steps[:-1]:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	390 if isinstance(st[-1], SelectorMixin):
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	391 mask = st[-1].get_support()
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	392 feature_names = feature_names[mask]
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	393 estimator = estimator.steps[-1][-1]
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	394
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	395 if hasattr(estimator, "coef_"):
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	396 coefs = estimator.coef_
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	397 else:
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	398 coefs = getattr(estimator, "feature_importances_", None)
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	399 if coefs is None:
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	400 raise RuntimeError(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	401 "The classifier does not expose "
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	402 '"coef_" or "feature_importances_" '
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	403 "attributes"
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	404 )
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	405
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	406 threshold = params["plotting_selection"]["threshold"]
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	407 if threshold is not None:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	408 mask = (coefs > threshold) \| (coefs < -threshold)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	409 coefs = coefs[mask]
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	410 feature_names = feature_names[mask]
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	411
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	412 # sort
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	413 indices = np.argsort(coefs)[::-1]
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	414
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	415 trace = go.Bar(x=feature_names[indices], y=coefs[indices])
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	416 layout = go.Layout(title=title or "Feature Importances")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	417 fig = go.Figure(data=[trace], layout=layout)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	418
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	419 plotly.offline.plot(fig, filename="output.html", auto_open=False)
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	420 # to be discovered by `from_work_dir`
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	421 os.rename("output.html", "output")
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	422
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	423 return 0
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	424
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	425 elif plot_type in ("pr_curve", "roc_curve"):
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	426 df1 = pd.read_csv(infile1, sep="\t", header="infer")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	427 df2 = pd.read_csv(infile2, sep="\t", header="infer").astype(np.float32)
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	428
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	429 minimum = params["plotting_selection"]["report_minimum_n_positives"]
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	430 # filter out columns whose n_positives is beblow the threhold
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	431 if minimum:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	432 mask = df1.sum(axis=0) >= minimum
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	433 df1 = df1.loc[:, mask]
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	434 df2 = df2.loc[:, mask]
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	435
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	436 pos_label = params["plotting_selection"]["pos_label"].strip() or None
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	437
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	438 if plot_type == "pr_curve":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	439 if plot_format == "plotly_html":
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	440 visualize_pr_curve_plotly(df1, df2, pos_label, title=title)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	441 else:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	442 visualize_pr_curve_matplotlib(df1, df2, pos_label, title)
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	443 else: # 'roc_curve'
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	444 drop_intermediate = params["plotting_selection"]["drop_intermediate"]
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	445 if plot_format == "plotly_html":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	446 visualize_roc_curve_plotly(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	447 df1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	448 df2,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	449 pos_label,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	450 drop_intermediate=drop_intermediate,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	451 title=title,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	452 )
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	453 else:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	454 visualize_roc_curve_matplotlib(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	455 df1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	456 df2,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	457 pos_label,
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	458 drop_intermediate=drop_intermediate,
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	459 title=title,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	460 )
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	461
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	462 return 0
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	463
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	464 elif plot_type == "rfecv_gridscores":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	465 input_df = pd.read_csv(infile1, sep="\t", header="infer")
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	466 scores = input_df.iloc[:, 0]
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	467 steps = params["plotting_selection"]["steps"].strip()
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	468 steps = safe_eval(steps)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	469
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	470 data = go.Scatter(
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	471 x=list(range(len(scores))),
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	472 y=scores,
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	473 text=[str(_) for _ in steps] if steps else None,
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	474 mode="lines",
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	475 )
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	476 layout = go.Layout(
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	477 xaxis=dict(title="Number of features selected"),
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	478 yaxis=dict(title="Cross validation score"),
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	479 title=dict(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	480 text=title or None, x=0.5, y=0.92, xanchor="center", yanchor="top"
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	481 ),
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	482 font=dict(family="sans-serif", size=11),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	483 # control backgroud colors
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	484 plot_bgcolor="rgba(255,255,255,0)",
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	485 )
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	486 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	487 # legend=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	488 # x=0.95,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	489 # y=0,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	490 # traceorder="normal",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	491 # font=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	492 # family="sans-serif",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	493 # size=9,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	494 # color="black"
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	495 # ),
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	496 # bgcolor="LightSteelBlue",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	497 # bordercolor="Black",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	498 # borderwidth=2
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	499 # ),
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	500 """
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	501
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	502 fig = go.Figure(data=[data], layout=layout)
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	503 plotly.offline.plot(fig, filename="output.html", auto_open=False)
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	504 # to be discovered by `from_work_dir`
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	505 os.rename("output.html", "output")
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	506
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	507 return 0
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	508
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	509 elif plot_type == "learning_curve":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	510 input_df = pd.read_csv(infile1, sep="\t", header="infer")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	511 plot_std_err = params["plotting_selection"]["plot_std_err"]
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	512 data1 = go.Scatter(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	513 x=input_df["train_sizes_abs"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	514 y=input_df["mean_train_scores"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	515 error_y=dict(array=input_df["std_train_scores"]) if plot_std_err else None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	516 mode="lines",
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	517 name="Train Scores",
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	518 )
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	519 data2 = go.Scatter(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	520 x=input_df["train_sizes_abs"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	521 y=input_df["mean_test_scores"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	522 error_y=dict(array=input_df["std_test_scores"]) if plot_std_err else None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	523 mode="lines",
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	524 name="Test Scores",
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	525 )
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	526 layout = dict(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	527 xaxis=dict(title="No. of samples"),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	528 yaxis=dict(title="Performance Score"),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	529 # modify these configurations to customize image
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	530 title=dict(
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	531 text=title or "Learning Curve",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	532 x=0.5,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	533 y=0.92,
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	534 xanchor="center",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	535 yanchor="top",
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	536 ),
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	537 font=dict(family="sans-serif", size=11),
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	538 # control backgroud colors
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	539 plot_bgcolor="rgba(255,255,255,0)",
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	540 )
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	541 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	542 # legend=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	543 # x=0.95,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	544 # y=0,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	545 # traceorder="normal",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	546 # font=dict(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	547 # family="sans-serif",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	548 # size=9,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	549 # color="black"
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	550 # ),
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	551 # bgcolor="LightSteelBlue",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	552 # bordercolor="Black",
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	553 # borderwidth=2
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	554 # ),
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	555 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	556
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	557 fig = go.Figure(data=[data1, data2], layout=layout)
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	558 plotly.offline.plot(fig, filename="output.html", auto_open=False)
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	559 # to be discovered by `from_work_dir`
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	560 os.rename("output.html", "output")
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	561
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	562 return 0
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	563
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	564 elif plot_type == "keras_plot_model":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	565 with open(model_config, "r") as f:
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	566 model_str = f.read()
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	567 model = model_from_json(model_str)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	568 plot_model(model, to_file="output.png")
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	569 os.rename("output.png", "output")
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	570
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	571 return 0
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	572
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	573 elif plot_type == "classification_confusion_matrix":
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	574 plot_selection = params["plotting_selection"]
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	575 input_true = get_dataframe(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	576 true_labels, plot_selection, "header_true", "column_selector_options_true"
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	577 )
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	578 header_predicted = "infer" if plot_selection["header_predicted"] else None
11 0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	579 input_predicted = pd.read_csv(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	580 predicted_labels, sep="\t", parse_dates=True, header=header_predicted
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717" bgruening parents: 10 diff changeset	581 )
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	582 true_classes = input_true.iloc[:, -1].copy()
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	583 predicted_classes = input_predicted.iloc[:, -1].copy()
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	584 axis_labels = list(set(true_classes))
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	585 c_matrix = confusion_matrix(true_classes, predicted_classes)
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	586 fig, ax = plt.subplots(figsize=(7, 7))
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	587 im = plt.imshow(c_matrix, cmap=plot_color)
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	588 for i in range(len(c_matrix)):
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	589 for j in range(len(c_matrix)):
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	590 ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k")
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	591 ax.set_ylabel("True class labels")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	592 ax.set_xlabel("Predicted class labels")
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	593 ax.set_title(title)
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	594 ax.set_xticks(axis_labels)
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	595 ax.set_yticks(axis_labels)
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	596 fig.colorbar(im, ax=ax)
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	597 fig.tight_layout()
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	598 plt.savefig("output.png", dpi=125)
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	599 os.rename("output.png", "output")
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	600
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	601 return 0
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	602
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	603 # save pdf file to disk
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	604 # fig.write_image("image.pdf", format='pdf')
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 4 diff changeset	605 # fig.write_image("image.pdf", format='pdf', width=3402, height=2262)
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	606
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	607
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	608 if __name__ == "__main__":
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	609 aparser = argparse.ArgumentParser()
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	610 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	611 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	612 aparser.add_argument("-X", "--infile1", dest="infile1")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	613 aparser.add_argument("-y", "--infile2", dest="infile2")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	614 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	615 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	616 aparser.add_argument("-g", "--groups", dest="groups")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	617 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	618 aparser.add_argument("-b", "--intervals", dest="intervals")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	619 aparser.add_argument("-t", "--targets", dest="targets")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	620 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	621 aparser.add_argument("-c", "--model_config", dest="model_config")
8 6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	622 aparser.add_argument("-tl", "--true_labels", dest="true_labels")
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	623 aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels")
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	624 aparser.add_argument("-pc", "--plot_color", dest="plot_color")
6430b9b00d2f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69" bgruening parents: 7 diff changeset	625 aparser.add_argument("-pt", "--title", dest="title")
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	626 args = aparser.parse_args()
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: diff changeset	627
9 b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	628 main(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	629 args.inputs,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	630 args.infile_estimator,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	631 args.infile1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	632 args.infile2,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	633 args.outfile_result,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	634 outfile_object=args.outfile_object,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	635 groups=args.groups,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	636 ref_seq=args.ref_seq,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	637 intervals=args.intervals,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	638 targets=args.targets,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	639 fasta_path=args.fasta_path,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	640 model_config=args.model_config,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	641 true_labels=args.true_labels,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	642 predicted_labels=args.predicted_labels,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	643 plot_color=args.plot_color,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	644 title=args.title,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04" bgruening parents: 8 diff changeset	645 )

Mercurial > repos > bgruening > sklearn_stacking_ensemble_models

annotate ml_visualization_ex.py @ 14:2fc88dc854ee draft default tip