calib/slurm_scripts/real_tests_plotting.py at master · vpc-ccg/calib · 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
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
#!/usr/bin/env python3
import sys
import os
import plotly
import plotly.graph_objs as go
import math

results_path=sys.argv[1].rstrip('/')
variants_path=sys.argv[2].rstrip('/')
snps_path=sys.argv[3].rstrip('/')

snps = set()
for line in open(variants_path):
    line = line.rstrip().split('\t')
    chrom = line[0]
    pos = int(line[1])
    ref = line[2].upper()
    alt = line[3].upper()
    snps.add(
        (
            chrom,
            pos,
            ref,
            alt
        )
    )
for line in open(snps_path):
    line = line.rstrip().split('\t')
    chrom = line[0]
    pos = int(line[1])
    ref = line[2].upper()
    alt = line[3].upper()
    snps.add(
        (
            chrom,
            pos,
            ref,
            alt
        )
    )


tools=['calib', 'starcode', 'umitools', 'raw']

names=dict(
    calib='Calib',
    rainbow='Rainbow',
    umitools='UMI-tools',
    starcode='starcode-umi',
    raw='No clustering',
)
legend_names=dict(
    calib='Calib',
    rainbow='Rainbow',
    umitools='UMI-tools',
    starcode='starcode-umi',
    raw='No clustering',
)
seq_errs = set()
for tool in tools:
    for f in os.listdir('{}/{}.sinvict/'.format(results_path, tool)):
        seq_errs.add(f.strip('/'))
seq_errs = list(reversed(sorted(seq_errs)))

mutation_calls = dict()
for seq_err in seq_errs:
    mutation_calls[seq_err] = dict()
    for tool in tools:
        sinvict_path = '{}/{}.sinvict/{}/calls_level1.sinvict'.format(results_path, tool, seq_err)
        mutation_calls[seq_err][tool] = dict()
        for line in open(sinvict_path):
            line = line.rstrip().split('\t')
            chrom = line[0]
            pos = int(line[1])
            ref = line[3].upper()
            alt = line[5].upper()
            mutation_calls[seq_err][tool][(chrom,pos,ref,alt,)]=line

colors_1 = [
    '#e41a1c',
    '#377eb8',
    '#4daf4a',
    '#984ea3',
    '#ff7f00',
]

colors_2 = [
    '#f4a3a4',
    '#afcbe3',
    '#b8dfb7',
    '#d6b8dA',
    '#ffcc99',
]
data=list()
height=1200
width=1200
for idx, tool in enumerate(tools):
    all_counts = list()
    validated_counts = list()
    for seq_err in seq_errs:
        mutation_calls_set = set(mutation_calls[seq_err][tool].keys())
        all_counts.append(len(mutation_calls_set))
        validated_counts.append(len(mutation_calls_set.intersection(snps)))
    trace = go.Bar(
        orientation='h',
        y = seq_errs,
        x = validated_counts,
        text = ['{}'.format(count) for count in validated_counts],
        textposition = 'inside',
        name = '{} verified or reported         '.format(names[tool]),
        marker=dict(
            color=colors_1[idx]
        ),
        legendgroup=tool,
    )
    data.append(trace)
    trace = go.Bar(
        orientation='h',
        y = seq_errs,
        x = all_counts,
        text = ['{}'.format(count) for count in all_counts],
        textposition = 'inside',
        name = '{} all calls'.format(names[tool]),
        marker=dict(
            color=colors_2[idx],
        ),
        legendgroup=tool,
    )
    data.append(trace)
layout = go.Layout(
    barmode='group',
    xaxis=dict(
        type='log',
    ),
    yaxis=dict(
        type='category',
    ),
    font=dict(
        size=24,
    ),
    legend=dict(
        traceorder='grouped+reversed',
        #x=0.50,
        #y=0.05,
        tracegroupgap=20,
    ),
)
fig = go.Figure(data=data, layout=layout)
plotly.offline.plot(fig, filename='{}/plots.html'.format(results_path), auto_open=False)