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comparison circos-files/synteny-region-default.conf~ @ 6:8a4190457eb7 draft

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author s-kaufmann
date Tue, 06 May 2014 04:23:25 -0400
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5:eb0aecd0480c 6:8a4190457eb7
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 <colors>
6 <<include etc/colors.synteny.conf>>
7 <<include etc/colors.mouse.conf>>
8 </colors>
9
10 <ideogram>
11
12 <spacing>
13 # Spacing between ideograms. Suffix "r" denotes a relative value. It
14 # is relative to circle circumference (e.g. space is 0.5% of
15 # circumference).
16 default = 0.005r
17 </spacing>
18
19 # Ideogram position, thickness and fill.
20 #
21 # Radial position within the image of the ideograms. This value is
22 # usually relative ("r" suffix).
23 radius = 0.65r
24
25 # Thickness of ideograms, which can be absolute (e.g. pixels, "p"
26 # suffix) or relative ("r" suffix). When relative, it is a fraction of
27 # image radius.
28 thickness = 30p
29
30 # Ideograms can be drawn as filled, outlined, or both. When filled,
31 # the color will be taken from the last field in the karyotype file,
32 # or set by chromosomes_colors. Color names are discussed in
33 #
34 # http://www.circos.ca/documentation/tutorials/configuration/configuration_files
35 #
36 # When stroke_thickness=0p or if the parameter is missing, the ideogram is
37 # has no outline and the value of stroke_color is not used.
38
39 fill = yes # A
40
41 stroke_color = dgrey # B
42 stroke_thickness = 1p # B
43
44 # Minimum definition for ideogram labels.
45
46 show_label = yes
47 # see etc/fonts.conf for list of font names
48 label_font = bold
49 label_radius = (dims(ideogram,radius_inner)+dims(ideogram,radius_outer)-conf(ideogram,label_size))/2
50 label_with_tag = yes
51
52 label_size = 14
53 label_color = white
54 label_parallel = yes
55
56
57 </ideogram>
58
59
60
61 show_ticks = yes
62 show_tick_labels = yes
63
64 <ticks>
65
66 radius = 1r
67 color = black
68 thickness = 1p
69
70 # the tick label is derived by multiplying the tick position
71 # by 'multiplier' and casting it in 'format':
72 #
73 # sprintf(format,position*multiplier)
74
75 multiplier = 1e-6
76
77 # %d - integer
78 # %f - float
79 # %.1f - float with one decimal
80 # %.2f - float with two decimals
81 #
82 # for other formats, see http://perldoc.perl.org/functions/sprintf.html
83
84 format = %d
85
86 <tick>
87 spacing = 0.1u
88 size = 5p
89 </tick>
90
91 <tick>
92 spacing = 1u
93 size = 10p
94 show_label = yes
95 label_size = 12p
96 label_offset = 10p
97 format = %d
98 </tick>
99
100 </ticks>
101
102 #
103 # These should be present in every Circos configuration file and
104 # overridden as required. To see the content of these files,
105 # look in etc/ in the Circos distribution.
106
107
108
109 # RGB/HSV color definitions, color lists, location of fonts, fill patterns.
110 # Included from Circos distribution.
111 <<include etc/colors_fonts_patterns.conf>>
112
113 # Debugging, I/O an dother system parameters
114 # Included from Circos distribution.
115 <<include etc/housekeeping.conf>>