Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/circos/circos.conf @ 0:afe85eb6572e draft

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author davidvanzessen
date Mon, 29 Aug 2016 05:41:20 -0400
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1
2 # This is the main configuration file for the Circos tableviewer. This file also
3 # depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of
4 # row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned
5 # off by default).
6 #
7 # In addition to these configuration files, the bin/make-conf script creates
8 # colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on
9 # cell percentile values). These configuration files are also included via the <<include>> directive.
10 #
11 # Some elements of the output image are toggled off by default (e.g. row and column highlights,
12 # anchor links to segment labels, tick marks).
13
14 <colors>
15 <<include DATA_DIR/etc_colors.conf>>
16 <<include DATA_DIR/colors.conf>>
17 <<include DATA_DIR/colors_percentile.conf>>
18 </colors>
19
20 <fonts>
21 <<include DATA_DIR/fonts.conf>>
22 </fonts>
23
24 <<include DATA_DIR/ideogram.conf>>
25 <<include DATA_DIR/ticks.conf>>
26
27 karyotype = DATA_DIR/karyotype.txt
28
29 <image>
30 dir = DATA_DIR
31 file = circos.png
32 24bit = yes
33 svg = no
34 png = yes
35 pdf = no
36 # radius of inscribed circle in image
37 radius = 1500p
38 background = white
39 # by default angle=0 is at 3 o'clock position
40 angle_offset = -180
41 auto_alpha_colors = yes
42 auto_alpha_steps = 5
43 </image>
44
45 chromosomes_units = 10
46 chromosomes_display_default = yes
47 chromosomes_order_by_karyotype = yes
48
49 <highlights>
50
51 show = yes
52
53 <highlight>
54 show = no
55 file = DATA_DIR/row.txt
56 r0 = 1r+200p
57 r1 = 1r+220p
58 stroke_color = black
59 stroke_thickness = 2
60 </highlight>
61
62 <highlight>
63 show = no
64 file = DATA_DIR/col.txt
65 r0 = 1r+230p
66 r1 = 1r+250p
67 stroke_color = black
68 stroke_thickness = 2
69 </highlight>
70
71 <highlight>
72 show = no
73 file = DATA_DIR/all.txt
74 r0 = 1r+10p
75 r1 = 1r+35p
76 stroke_color = black
77 stroke_thickness = 2
78 </highlight>
79
80 </highlights>
81
82 <plots>
83
84 <plot>
85 type = text
86 file = DATA_DIR/segmentlabel.txt
87 label_font = condensedbold
88 color = black
89 label_size = 30p
90 r0 = 1r+50p
91 r1 = 1r+500p
92 rpadding = 0p
93 padding = 0p
94
95 show_links = no
96 link_dims = 0p,10p,32p,10p,5p
97 link_thickness = 3p
98 link_color = black
99
100 label_snuggle = no
101 # shift label up to its height in pixels in the angular direction
102 max_snuggle_distance = 2r
103 snuggle_sampling = 2
104 snuggle_tolerance = 0.25r
105
106 </plot>
107
108 </plots>
109
110 <links>
111
112 <link cellvalues>
113 ribbon = yes
114 flat = yes
115 file = DATA_DIR/cells.txt
116 bezier_radius = 0.0r
117 radius = 0.999r-15p
118 thickness = 1
119 color = grey
120 stroke_color = black
121 stroke_thickness = 1
122 <rules>
123
124 <rule>
125 importance = 95
126 condition = 1
127 radius1 = 0.999r+2p
128 flow = continue
129 </rule>
130
131 </rules>
132
133 </link>
134
135 </links>
136
137 #anglestep = 0.5
138 #minslicestep = 10
139 #beziersamples = 40
140 #debug = no
141 #warnings = no
142 #imagemap = no
143
144 #units_ok = bupr
145 #units_nounit = n
146
147 <<include DATA_DIR/housekeeping.conf>>
148