-
Notifications
You must be signed in to change notification settings - Fork 0
/
circos.example.conf
162 lines (140 loc) · 2.62 KB
/
circos.example.conf
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
150
151
152
153
154
155
156
157
158
159
160
161
162
<<include /.mounts/labs/simpsonlab/sw/miniconda3/envs/rdeborja/etc/colors_fonts_patterns.conf>>
<<include /.mounts/labs/simpsonlab/sw/miniconda3/envs/rdeborja/example/etc/ideogram.conf>>
<<include /.mounts/labs/simpsonlab/users/rdeborja/projects/mls/8165/ticks.conf>>
<image>
dir = .
file = <sample>_read_cnv_tx.fixed.png
png = yes
svg = no
radius = 1500p
angle_offset = -90
auto_alpha_colors = yes
auto_alpha_steps = 5
</image>
karyotype = /.mounts/labs/simpsonlab/sw/miniconda3/envs/rdeborja/data/karyotype/karyotype.human.hg38.txt
chromosomes_units = 1000000
chromosomes = -hsX;-hsY
chromosomes_display_default = yes
<plots>
# Data out of bounds should be hidden. Otherwise the
# default is to clip the data to range min/max.
range = hide
# scatter plot for raw values [6,13]
<plot>
type = scatter
file = <sample>.raw.fixed.bed
r0 = 0.91r
r1 = 0.99r
min = 6
max = 13
glyph = circle
glyph_size = 4
color = blue
<axes>
<axis>
color = lblue
thickness = 2
spacing = 0.1r
</axis>
</axes>
<backgrounds>
<background>
color = vlblue_a5
</background>
</backgrounds>
# <rules>
# <rule>
# condition = 1
# glyph_size = eval( 6 + 4*abs(var(value)))
# flow = continue
# </rule>
# <rule>
# condition = var(value) < -2
# stroke_color = black
# stroke_thickness = 2
# </rule>
# </rules>
</plot>
# scatter plot for values [-3,0]
<plot>
type = scatter
#file = 8165.fixed.seg
file = 8165.calls.fixed.bed
r0 = 0.80r
r1 = 0.85r
min = -2
max = 0
glyph = circle
glyph_size = 4
color = red
<axes>
<axis>
color = lred
thickness = 2
spacing = 0.1r
</axis>
</axes>
<backgrounds>
<background>
color = vlred_a5
</background>
</backgrounds>
<rules>
<rule>
condition = 1
glyph_size = eval( 6 + 4*abs(var(value)))
flow = continue
</rule>
<rule>
condition = var(value) < -2
stroke_color = black
stroke_thickness = 2
</rule>
</rules>
</plot>
# scatter plot for values [0,3]
<plot>
type = scatter
file = <sample>.calls.fixed.bed
r0 = 0.85r
r1 = 0.90r
min = 0
max = 2
glyph = circle
glyph_size = 4
color = green
<axes>
<axis>
color = lgreen
thickness = 2
spacing = 0.1r
</axis>
</axes>
<backgrounds>
<background>
color = vlgreen_a5
</background>
</backgrounds>
<rules>
<rule>
condition = 1
glyph_size = eval( 6 + 4*abs(var(value)))
flow = continue
</rule>
<rule>
condition = var(value) > 2
stroke_color = black
stroke_thickness = 2
</rule>
</rules>
</plot>
</plots>
<links>
<link>
file = <sample>.translocation.fixed.link
color = black_a5
radius = 0.78r
thickness = 3.5
</link>
</links>
<<include /.mounts/labs/simpsonlab/sw/miniconda3/envs/rdeborja/etc/housekeeping.conf>>