Mercurial > repos > bgruening > plotly_parallel_coordinates_plot
comparison paracords_plot.py @ 0:7b2455348edf draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit 93fcfe0fa6a64246d13e0fb7e35a357985b02465
author | bgruening |
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date | Sun, 23 Sep 2018 07:52:27 -0400 |
parents | |
children | 7b21a9b5922f |
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-1:000000000000 | 0:7b2455348edf |
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1 import sys | |
2 import argparse | |
3 import plotly | |
4 import plotly.graph_objs as go | |
5 import pandas as pd | |
6 | |
7 def main(infile, col_dimensions, col_color): | |
8 """ | |
9 Produce an interactive paracords plotting html | |
10 Args: | |
11 infile: str, tabular file | |
12 col_dimensions: str, comma separated index numbers. For example: "3,4,5" | |
13 col_color: str, index number | |
14 """ | |
15 df = pd.read_csv(infile, sep='\t', parse_dates=True) | |
16 | |
17 dimensions = [] | |
18 col_dimensions = [int(x)-1 for x in col_dimensions.split(',')] | |
19 for col in col_dimensions: | |
20 values = df[df.columns[col]] | |
21 if all(type(e) is int for e in values ): | |
22 dimensions.append( | |
23 dict( values = values, | |
24 tickformat = ",.2r", | |
25 label = df.columns[col]) | |
26 ) | |
27 elif all(type(e) is float for e in values ): | |
28 dimensions.append( | |
29 dict( values = values, | |
30 tickformat = "g", | |
31 label = df.columns[col]) | |
32 ) | |
33 else: | |
34 unique_values = list(set(values)) | |
35 dimensions.append( | |
36 dict( range = [0, len(unique_values)-1], | |
37 tickvals = list(range(len(unique_values))), | |
38 ticktext = [str(e) for e in unique_values], | |
39 values = list(map(lambda e: unique_values.index(e), values )), | |
40 label = df.columns[col]) | |
41 ) | |
42 | |
43 col_color = int(col_color) - 1 | |
44 colors = df[df.columns[col_color]] | |
45 if all(type(e) is int for e in colors ): | |
46 tickformat = ",.2r" | |
47 elif all(type(e) is float for e in colors ): | |
48 tickformat = "g" | |
49 else: | |
50 sys.exit("Error: the column for coloring must contain all numerical values!") | |
51 | |
52 dimensions.append( | |
53 dict( | |
54 values = colors, | |
55 tickformat = tickformat, | |
56 label = df.columns[col_color] | |
57 ) | |
58 ) | |
59 | |
60 line = dict( | |
61 color = colors, | |
62 colorscale = 'Jet', | |
63 showscale = True, | |
64 reversescale = True | |
65 ) | |
66 | |
67 data = [ | |
68 go.Parcoords( | |
69 line = line, | |
70 dimensions = dimensions | |
71 ) | |
72 ] | |
73 | |
74 plotly.offline.plot(data, filename = "output.html", auto_open=False) | |
75 | |
76 if __name__ == "__main__": | |
77 aparser = argparse.ArgumentParser() | |
78 aparser.add_argument( "-i", "--input", dest="infile", required=True) | |
79 aparser.add_argument( "-d", "--col_dimensions", dest="col_dimensions") | |
80 aparser.add_argument( "-c", "--col_color", dest="col_color") | |
81 args = aparser.parse_args() | |
82 | |
83 main(args.infile, args.col_dimensions, args.col_color) |