Mercurial > repos > s-kaufmann > synteny_mapper

comparison circos-files/synteny-region-default.conf @ 2:67eb55a9debe draft

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author s-kaufmann
date Mon, 10 Feb 2014 09:06:15 -0500
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1:7601ef706058 2:67eb55a9debe
1 # The <ideogram> block defines the position, size, labels and other
2 # properties of the segments on which data are drawn. These segments
3 # are usually chromosomes, but can be any integer axis.
4
5 <ideogram>
6
7 <spacing>
8 # Spacing between ideograms. Suffix "r" denotes a relative value. It
9 # is relative to circle circumference (e.g. space is 0.5% of
10 # circumference).
11 default = 0.005r
12 </spacing>
13
14 # Ideogram position, thickness and fill.
15 #
16 # Radial position within the image of the ideograms. This value is
17 # usually relative ("r" suffix).
18 radius = 0.65r
19
20 # Thickness of ideograms, which can be absolute (e.g. pixels, "p"
21 # suffix) or relative ("r" suffix). When relative, it is a fraction of
22 # image radius.
23 thickness = 30p
24
25 # Ideograms can be drawn as filled, outlined, or both. When filled,
26 # the color will be taken from the last field in the karyotype file,
27 # or set by chromosomes_colors. Color names are discussed in
28 #
29 # http://www.circos.ca/documentation/tutorials/configuration/configuration_files
30 #
31 # When stroke_thickness=0p or if the parameter is missing, the ideogram is
32 # has no outline and the value of stroke_color is not used.
33
34 fill = yes # A
35
36 stroke_color = dgrey # B
37 stroke_thickness = 1p # B
38
39 # Minimum definition for ideogram labels.
40
41 show_label = yes
42 # see etc/fonts.conf for list of font names
43 label_font = bold
44 label_radius = (dims(ideogram,radius_inner)+dims(ideogram,radius_outer)-conf(ideogram,label_size))/2
45 label_with_tag = yes
46
47 label_size = 14
48 label_color = white
49 label_parallel = yes
50
51
52 </ideogram>
53
54
55
56 show_ticks = yes
57 show_tick_labels = yes
58
59 <ticks>
60
61 radius = 1r
62 color = black
63 thickness = 1p
64
65 # the tick label is derived by multiplying the tick position
66 # by 'multiplier' and casting it in 'format':
67 #
68 # sprintf(format,position*multiplier)
69
70 multiplier = 1e-6
71
72 # %d - integer
73 # %f - float
74 # %.1f - float with one decimal
75 # %.2f - float with two decimals
76 #
77 # for other formats, see http://perldoc.perl.org/functions/sprintf.html
78
79 format = %d
80
81 <tick>
82 spacing = 0.1u
83 size = 5p
84 </tick>
85
86 <tick>
87 spacing = 1u
88 size = 10p
89 show_label = yes
90 label_size = 12p
91 label_offset = 10p
92 format = %d
93 </tick>
94
95 </ticks>
96
97 #
98 # These should be present in every Circos configuration file and
99 # overridden as required. To see the content of these files,
100 # look in etc/ in the Circos distribution.
101
102
103
104 # RGB/HSV color definitions, color lists, location of fonts, fill patterns.
105 # Included from Circos distribution.
106 <<include etc/colors_fonts_patterns.conf>>
107
108 # Debugging, I/O an dother system parameters
109 # Included from Circos distribution.
110 <<include etc/housekeeping.conf>>