annotate report_clonality/circos/circos.conf @ 40:106275b54470 draft

Uploaded
author davidvanzessen
date Tue, 30 May 2017 07:26:33 -0400
parents 7b8147b61a34
children 124b7fd92a3e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
1
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
2 # This is the main configuration file for the Circos tableviewer. This file also
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
3 # depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
4 # row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
5 # off by default).
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
6 #
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
7 # In addition to these configuration files, the bin/make-conf script creates
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
8 # colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
9 # cell percentile values). These configuration files are also included via the <<include>> directive.
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
10 #
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
11 # Some elements of the output image are toggled off by default (e.g. row and column highlights,
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
12 # anchor links to segment labels, tick marks).
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
13
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
14 <colors>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
15 <<include DATA_DIR/etc_colors.conf>>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
16 <<include DATA_DIR/colors.conf>>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
17 <<include DATA_DIR/colors_percentile.conf>>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
18 </colors>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
19
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
20 <fonts>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
21 <<include DATA_DIR/fonts.conf>>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
22 </fonts>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
23
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
24 <<include DATA_DIR/ideogram.conf>>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
25 <<include DATA_DIR/ticks.conf>>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
26
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
27 karyotype = DATA_DIR/karyotype.txt
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
28
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
29 <image>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
30 dir = DATA_DIR
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
31 file = circos.png
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
32 24bit = yes
34
7b8147b61a34 Uploaded
davidvanzessen
parents: 33
diff changeset
33 svg = yes
0
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
34 png = yes
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
35 # radius of inscribed circle in image
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
36 radius = 1500p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
37 background = white
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
38 # by default angle=0 is at 3 o'clock position
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
39 angle_offset = -180
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
40 auto_alpha_colors = yes
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
41 auto_alpha_steps = 5
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
42 </image>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
43
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
44 chromosomes_units = 10
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
45 chromosomes_display_default = yes
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
46 chromosomes_order_by_karyotype = yes
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
47
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
48 <highlights>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
49
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
50 show = yes
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
51
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
52 <highlight>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
53 show = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
54 file = DATA_DIR/row.txt
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
55 r0 = 1r+200p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
56 r1 = 1r+220p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
57 stroke_color = black
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
58 stroke_thickness = 2
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
59 </highlight>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
60
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
61 <highlight>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
62 show = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
63 file = DATA_DIR/col.txt
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
64 r0 = 1r+230p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
65 r1 = 1r+250p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
66 stroke_color = black
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
67 stroke_thickness = 2
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
68 </highlight>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
69
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
70 <highlight>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
71 show = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
72 file = DATA_DIR/all.txt
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
73 r0 = 1r+10p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
74 r1 = 1r+35p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
75 stroke_color = black
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
76 stroke_thickness = 2
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
77 </highlight>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
78
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
79 </highlights>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
80
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
81 <plots>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
82
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
83 <plot>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
84 type = text
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
85 file = DATA_DIR/segmentlabel.txt
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
86 label_font = condensedbold
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
87 color = black
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
88 label_size = 30p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
89 r0 = 1r+50p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
90 r1 = 1r+500p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
91 rpadding = 0p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
92 padding = 0p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
93
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
94 show_links = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
95 link_dims = 0p,10p,32p,10p,5p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
96 link_thickness = 3p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
97 link_color = black
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
98
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
99 label_snuggle = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
100 # shift label up to its height in pixels in the angular direction
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
101 max_snuggle_distance = 2r
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
102 snuggle_sampling = 2
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
103 snuggle_tolerance = 0.25r
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
104
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
105 </plot>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
106
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
107 </plots>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
108
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
109 <links>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
110
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
111 <link cellvalues>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
112 ribbon = yes
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
113 flat = yes
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
114 file = DATA_DIR/cells.txt
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
115 bezier_radius = 0.0r
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
116 radius = 0.999r-15p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
117 thickness = 1
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
118 color = grey
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
119 stroke_color = black
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
120 stroke_thickness = 1
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
121 <rules>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
122
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
123 <rule>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
124 importance = 95
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
125 condition = 1
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
126 radius1 = 0.999r+2p
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
127 flow = continue
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
128 </rule>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
129
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
130 </rules>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
131
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
132 </link>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
133
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
134 </links>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
135
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
136 #anglestep = 0.5
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
137 #minslicestep = 10
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
138 #beziersamples = 40
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
139 #debug = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
140 #warnings = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
141 #imagemap = no
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
142
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
143 #units_ok = bupr
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
144 #units_nounit = n
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
145
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
146 <<include DATA_DIR/housekeeping.conf>>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
147