Mercurial > repos > bgruening > plotly_parallel_coordinates_plot
annotate paracords_plot.py @ 1:7b21a9b5922f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 7ba5d8f0e920dccbc82588e4f4a7b9039dc3ea36
author | bgruening |
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date | Wed, 10 Oct 2018 02:29:28 -0400 |
parents | 7b2455348edf |
children | 9958188c6195 |
rev | line source |
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7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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1 import sys |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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2 import argparse |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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3 import plotly |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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4 import plotly.graph_objs as go |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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5 import pandas as pd |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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6 |
1
7b21a9b5922f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 7ba5d8f0e920dccbc82588e4f4a7b9039dc3ea36
bgruening
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7 def main(infile, col_dimensions, categorized, col_color): |
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7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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8 """ |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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9 Produce an interactive paracords plotting html |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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10 Args: |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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11 infile: str, tabular file |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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12 col_dimensions: str, comma separated index numbers. For example: "3,4,5" |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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13 col_color: str, index number |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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14 """ |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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15 df = pd.read_csv(infile, sep='\t', parse_dates=True) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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16 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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17 dimensions = [] |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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18 col_dimensions = [int(x)-1 for x in col_dimensions.split(',')] |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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19 for col in col_dimensions: |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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20 values = df[df.columns[col]] |
1
7b21a9b5922f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 7ba5d8f0e920dccbc82588e4f4a7b9039dc3ea36
bgruening
parents:
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21 if categorized == 'boolfalse' and all(type(e) is int for e in values ): |
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7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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22 dimensions.append( |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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23 dict( values = values, |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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24 tickformat = ",.2r", |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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25 label = df.columns[col]) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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26 ) |
1
7b21a9b5922f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 7ba5d8f0e920dccbc82588e4f4a7b9039dc3ea36
bgruening
parents:
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27 elif categorized == 'boolfalse' and all(type(e) is float for e in values ): |
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7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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28 dimensions.append( |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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29 dict( values = values, |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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30 tickformat = "g", |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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31 label = df.columns[col]) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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32 ) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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33 else: |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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34 unique_values = list(set(values)) |
1
7b21a9b5922f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 7ba5d8f0e920dccbc82588e4f4a7b9039dc3ea36
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35 unique_values.sort() |
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7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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36 dimensions.append( |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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37 dict( range = [0, len(unique_values)-1], |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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38 tickvals = list(range(len(unique_values))), |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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39 ticktext = [str(e) for e in unique_values], |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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40 values = list(map(lambda e: unique_values.index(e), values )), |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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41 label = df.columns[col]) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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42 ) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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43 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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44 col_color = int(col_color) - 1 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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45 colors = df[df.columns[col_color]] |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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46 if all(type(e) is int for e in colors ): |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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47 tickformat = ",.2r" |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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48 elif all(type(e) is float for e in colors ): |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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49 tickformat = "g" |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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50 else: |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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51 sys.exit("Error: the column for coloring must contain all numerical values!") |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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52 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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53 dimensions.append( |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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54 dict( |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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55 values = colors, |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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56 tickformat = tickformat, |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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57 label = df.columns[col_color] |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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58 ) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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59 ) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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60 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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61 line = dict( |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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62 color = colors, |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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63 colorscale = 'Jet', |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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64 showscale = True, |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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65 reversescale = True |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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66 ) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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67 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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68 data = [ |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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69 go.Parcoords( |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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70 line = line, |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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71 dimensions = dimensions |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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72 ) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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73 ] |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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74 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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75 plotly.offline.plot(data, filename = "output.html", auto_open=False) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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76 |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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77 if __name__ == "__main__": |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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78 aparser = argparse.ArgumentParser() |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
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79 aparser.add_argument( "-i", "--input", dest="infile", required=True) |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
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80 aparser.add_argument( "-d", "--col_dimensions", dest="col_dimensions") |
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7b21a9b5922f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 7ba5d8f0e920dccbc82588e4f4a7b9039dc3ea36
bgruening
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81 aparser.add_argument( "-t", "--categorized_datatype", dest="categorized") |
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7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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82 aparser.add_argument( "-c", "--col_color", dest="col_color") |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
diff
changeset
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83 args = aparser.parse_args() |
7b2455348edf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
bgruening
parents:
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changeset
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84 |
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7b21a9b5922f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 7ba5d8f0e920dccbc82588e4f4a7b9039dc3ea36
bgruening
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85 main(args.infile, args.col_dimensions, args.categorized, args.col_color) |