8 — Recipes

12. Inverted Links

circos.conf

<<include etc/colors_fonts_patterns.conf>>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype = data/karyotype/karyotype.human.txt

<image>
<<include etc/image.conf>>
</image>

chromosomes_units           = 1000000
chromosomes_display_default = no
chromosomes                 = hs1:0-120;hs2:100-)

<links>

<link>

file          = data/8/ribbon.txt
ribbon        = yes
flat          = yes
radius        = 0.95r
bezier_radius = 0r
crest         = 0.2
color         = lgrey

<rules>
<rule>
# you can also test whether only one end is
# reversed using var(inv)
condition  = var(rev1) && ! var(rev2)
color      = red
</rule>
<rule>
condition  = var(rev2) && ! var(rev1)
color      = orange
</rule>
<rule>
condition  = var(rev1) && var(rev2) 
color      = blue
</rule>

</rules>
</link>

</links>

<<include etc/housekeeping.conf>>

circos.segdup.conf

<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype = data/8/karyotype.human.colorbychr.txt

<image>
dir = .
file  = circos.png
24bit = yes
png = yes
svg = yes
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
#angle_orientation = counterclockwise

auto_alpha_colors = yes
auto_alpha_steps  = 5
</image>

chromosomes_units           = 1000000

chromosomes_display_default = no
chromosomes = hs1;hs2
#chromosomes                 = hs1:0-120;hs2:100-)

<highlights>
<highlight>
file        = data/8/chr.highlight.txt
r0 = 0.99r
r1 = 0.995r
</highlight>
</highlights>

<links>
<link linkexample>

file          = data/8/segdup.01.txt
radius        = 0.95r
flat          = yes
ribbon        = yes
bezier_radius = 0r
crest         = 0.2
color         = blue

<rules>
<rule>
importance = 100
condition  = _REV2_ == 1
color      = lorange
</rule>

</rules>
</link>
</links>
anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

units_ok = bupr
units_nounit = n

#debug_group = ticks

bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 3

ideogram.conf

<ideogram>

<spacing>
default = 0.005r
break   = 0.5r

axis_break_at_edge = yes
axis_break         = yes
axis_break_style   = 2

<break_style 1>
stroke_color = black
fill_color   = blue
thickness    = 0.25r
stroke_thickness = 2
</break>

<break_style 2>
stroke_color     = black
stroke_thickness = 2
thickness        = 1.5r
</break>

</spacing>

<<include ideogram.position.conf>>
<<include ideogram.label.conf>>
<<include bands.conf>>

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = dims(image,radius) - 50p
label_size       = 36
label_parallel   = yes
label_case       = lower
label_format     = eval(sprintf("chr%s",var(label)))

ideogram.position.conf

radius           = 0.85r
thickness        = 30p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf

show_ticks          = yes
show_tick_labels    = yes

<ticks>
tick_separation      = 3p
label_separation     = 5p
radius               = dims(ideogram,radius_outer)+50p
multiplier           = 1e-6
color          = black
size           = 20p
thickness      = 4p
label_offset   = 5p
format         = %d

<tick>
spacing        = 1u
show_label     = yes
label_size     = 16p
</tick>

<tick>
spacing        = 5u
show_label     = yes
label_size     = 18p
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
</tick>

<tick>
spacing        = 20u
show_label     = yes
label_size     = 24p
</tick>

</ticks>