bin/boxplot.py at master · lpryszcz/bin · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
#!/usr/bin/env python2
desc="""Plot boxplot
"""
epilog="""Author:
l.p.pryszcz+git@gmail.com

Warsaw, 23/12/2015
"""

import argparse, os, sys, random
from datetime import datetime
import matplotlib.pyplot as plt
import matplotlib as mpl
import numpy as np

def plot(handle, out, cols, names, bins, title, xlab, ylab, xlog, ylog, \
              vmax, vmin, vMinSum, collapse, normed, alpha, legendLoc, colors,\
              verbose, dlimit=1):
    """
    """
    if verbose:
        sys.stderr.write( "Parsing data...\n" )
    x = [[] for i in range(len(cols))]
    for l in handle:
        try:
            ldata = l[:-1].split('\t')
            vals = []
            for col in cols:
                if col>=len(ldata) or not ldata[col]:
                    continue
                v=float(ldata[col])
                if vmin<v<vmax:
                    vals.append(v)
            #skip entire line if one value out of bounds
            # or if sum of values below threshold
            if len(vals)!=len(cols) or sum(vals)<vMinSum:
              continue
            for i, v in enumerate(vals):
              x[i].append(v)
        except:
            sys.stderr.write("[Error] Cannot parse line: %s\n" % ",".join(l.split('\t')))
    if verbose:
        sys.stderr.write( " %s values loaded.\n" % len(x) )
    fig = plt.figure()
    #add subplots
    ax = fig.add_subplot(111)
    ax.boxplot(x, labels=names)

    #add title
    ax.set_title(title)
    #add subplots labels
    ax.set_ylabel(ylab)#, fontsize=30)
    #plot legend only if collapsed
    if xlog:
    	ax.set_xscale('log')
    if ylog:
        ax.set_yscale('log', nonposy='clip')

    ax.grid(True)
    #save or show
    if type(out) is file and out.name=='<stdout>':
    	plt.show()
    else:
        fpath = out #handle.name+".png"
        fformat = fpath.split('.')[-1]
        plt.savefig(fpath, dpi=300, format=fformat, orientation='landscape', transparent=False)
        sys.stderr.write("Figure written to: %s\n" % fpath)


def main():

    usage   = "%(prog)s [options] -v"
    parser  = argparse.ArgumentParser( usage=usage,description=desc,epilog=epilog )

    parser.add_argument("-v", "--verbose", default=False, action="store_true", help="verbose")
    parser.add_argument('--version', action='version', version='1.0')
    parser.add_argument("-i", "--input",   default=sys.stdin, type=file,
                        help="input           [stdin]")
    parser.add_argument("-o", "--output",  default=sys.stdout,
                        help="input           [stdout]")
    parser.add_argument("-b", "--bins",    default=100, type=int,
                        help="number of bins  [%(default)s]")
    parser.add_argument("-c", "--col",     default=[1, 2], nargs="+", type=int,
                        help="columns to use  [%(default)s]")
    parser.add_argument("-n", "--names",   default="", nargs="+",
                        help="column names    [%(default)s]")
    parser.add_argument("-t", "--title",   default="Histogram",
                        help="histogram title [%(default)s]")
    parser.add_argument("-x", "--xlab",    default="",
                        help="x-axis label    [%(default)s]")
    parser.add_argument("-y", "--ylab",    default="",
                        help="y-axis label    [%(default)s]")
    parser.add_argument("--ylog", "--log", default=False, action="store_true",
                        help="log Y scale")
    parser.add_argument("--xlog",          default=False, action="store_true",
                        help="log X scale")
    parser.add_argument("--max",           default=float('inf'), type=float,
                        help="max value       [%(default)s]")
    parser.add_argument("--min",           default=float('-inf'), type=float,
                        help="min value       [%(default)s]")
    parser.add_argument("--vMinSum",           default=float('-inf'), type=float,
                        help="min Sum of values [%(default)s]")
    parser.add_argument("--collapse",      default=False, action="store_true",
                        help="collapse into single subplot")
    parser.add_argument("--normed",        default=0, choices=(0, 1), type=int,
                        help="normalise values")
    parser.add_argument("--alpha",         default=0.75, type=float,
                        help="plot alpha      [%(default)s]")
    parser.add_argument("--colors",        nargs="+", default=['b', 'grey', 'r', 'y', 'g'],
                        help="plot alpha      [%(default)s]")
    parser.add_argument("--legendLoc",     default=1, choices=(1, 2, 3, 4), type=int,
                        help="legend location (1=top right, 2=top left, 3=bottom left, 4=bottom right")


    o = parser.parse_args()
    if o.verbose:
        sys.stderr.write( "Options: %s\n" % str(o) )

    plot(o.input, o.output, o.col, o.names, o.bins, o.title, o.xlab, o.ylab, \
              o.xlog, o.ylog, o.max, o.min, o.vMinSum, o.collapse, o.normed, o.alpha, o.legendLoc, \
              o.colors, o.verbose)

if __name__=='__main__':
    t0  = datetime.now()
    main()
    dt  = datetime.now()-t0
    sys.stderr.write( "#Time elapsed: %s\n" % dt )