Mercurial > repos > s-kaufmann > synteny_mapper

comparison circos.conf @ 2:67eb55a9debe draft

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author s-kaufmann
date Mon, 10 Feb 2014 09:06:15 -0500
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children d8da7251bacf
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1:7601ef706058 2:67eb55a9debe
1 <image>
2 png = yes
3 dir = /home/users/kaufmann/Software/galaxy-dist/database/job_working_directory/000/230/dataset_329_files
4 file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_329.dat.png
5 radius = 750p
6 background=white
7 image_map_use = yes
8 image_map_name = circosmap
9 angle_offset = -90
10 auto_alpha_colors = yes
11 auto_alpha_steps = 5
12 </image>
13 karyotype = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_322.dat.karyotype
14 chromosomes_units = 1000000
15 chromosomes_display_default = no
16 <colors>
17 <<include /home/users/kaufmann/Software/shed-tools/testtoolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/036a03435919/synteny_mapper/circos-files/colors.synteny.conf>>
18 <<include /home/users/kaufmann/Software/shed-tools/testtoolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/036a03435919/synteny_mapper/circos-files/colors.mouse.conf>>
19 </colors>
20 chromosomes = hs44542;mm44542
21 chromosomes_reverse = mm44542
22 <highlights>
23 z = 5
24 <highlight>
25 file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.gene-track
26 r0 = 0.9r
27 r1 = 0.99r
28 stroke_thickness = 1
29 stroke_color = black
30 </highlight>
31 </highlights>
32 <plots>
33 <plot>
34 type=text
35 color=black
36 file=/home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.gene-track-labels
37 r0=0.99r
38 r1=1.5r
39 label_size=9
40 label_font=condensed
41 show_links=yes
42 link_dims = 0p,90p,20p,10p,20p
43 link_thickness=1
44 link_color=black
45 padding =0p
46 rpadding = 0p
47 </plot>
48
49 </plots>
50 <links>
51 <link>
52 file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.links
53 radius = 0.88r
54 bezier_radius = 0r
55 color = link_a4
56 stroke_thickness = 1
57 z = 10
58 ribbon = yes
59 <rules>
60 <rule>
61 condition = var(size1) < 10 || var(size2) < 10
62 stroke_thickness = 5
63 flow = continue
64 </rule>
65 <rule>
66 condition = 1
67 z = eval(scalar min(var(size1),var(size2)))
68 flow = continue
69 </rule>
70 <rule>
71 condition = 1
72 stroke_color = link
73 flow = continue
74 </rule>
75 <rule>
76 condition = 1
77 color = link_a4
78 </rule>
79 </rules>
80 </link>
81 <link>
82 file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.jumped
83 radius = 0.88r
84 bezier_radius = 0r
85 color = link_jumped_a4
86 stroke_thickness = 1
87 z = 10
88 ribbon = yes
89 <rules>
90 <rule>
91 condition = var(size1) < 10 || var(size2) < 10
92 stroke_thickness = 5
93 flow = continue
94 </rule>
95 <rule>
96 condition = 1
97 z = eval(scalar min(var(size1),var(size2)))
98 flow = continue
99 </rule>
100 <rule>
101 condition = 1
102 stroke_color = link_jumped
103 flow = continue
104 </rule>
105 <rule>
106 condition = 1
107 color = link_jumped_a4
108 </rule>
109 </rules>
110 </link>
111 </links>
112 <<include /home/users/kaufmann/Software/shed-tools/testtoolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/036a03435919/synteny_mapper/circos-files/synteny-region-default.conf>>