Circos > Documentation > Tutorials > Recipes > Transparent Links
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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.

8 — Recipes

9. Transparent Links

circos.conf


luminance = lum80
#luminance = ""

<<include colors_fonts_patterns.conf>>

<colors>
# r,g,b,a color definition
#
# a = 0 fully opaque
# a = 1 fully transparent
blackweak = 0,0,0,0.75
</colors>

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

karyotype   = data/karyotype/karyotype.human.txt

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

chromosomes_units  = 1000000

# change the color of each chromosome to lum80 + chr_name
# where the lum80 prefix references a predefined color
# with normalized luminance
chromosomes_color = /./=conf(luminance)var(chr)

# restrict image to hs1-hs9
#chromosomes        = /hs[1-9]$/
#chromosomes_display_default = no

<links>

<link>

file   = data/8/chrall-random.txt
ribbon = yes
flat   = yes # untwist all ribbons
radius = 0.98r
color  = blackweak
bezier_radius    = 0r
stroke_color     = vdgrey_a4
stroke_thickness = 2

<rules>

<rule>
condition = 1
# derive the color name from the chromosome name
# lum80 + chr_name + _a2
#
# lum70*, lum80* and lum90* colors are normalized
# to a given luminance and are predefined at etc/colors.ucsc.conf
#
# _a2 adds transparency (2/6 = 33%) where the denominator
# is derived from auto_alpha_steps+1=6
color     = eval(lc sprintf("%s%s_a4",'conf(luminance)',var(chr1),4))
z         = eval(average(var(size1),var(size2)))
</rule>

</rules>

</link>

</links>

<<include etc/housekeeping.conf>>
data_out_of_range* = trim


ideogram.conf


<ideogram>

<spacing>

default = 10u

</spacing>

# thickness (px) of chromosome ideogram
thickness        = 50p
stroke_thickness = 2
# ideogram border color
stroke_color     = black
fill             = yes
# the default chromosome color is set here and any value
# defined in the karyotype file overrides it
fill_color       = black

# fractional radius position of chromosome ideogram within image
radius         = 0.85r
show_label     = yes
label_with_tag = yes
label_font     = light
label_radius   = dims(ideogram,radius) + 0.075r
label_size     = 60p
label_parallel = yes
label_case     = upper

# cytogenetic bands
band_stroke_thickness = 2

# show_bands determines whether the outline of cytogenetic bands
# will be seen
show_bands            = no
# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
fill_bands            = no

</ideogram>



randomlinks.conf


karyotype = /home/martink/work/circos/dev/data/karyotype.human.txt

################################################################
# 50 links on chr1 only

#chr_rx = hs1$
#size = 10e6,5e6
#ruleset = links1

<rules links1>
rule = . . 50 0
</rules>

################################################################
# links between all chromosomes

nointra = yes
size    = 20e6,10e6
ruleset = links2

<rules links2>
rule = . . 1 1 0.2
rule = hs12 . 2 1 0.5
rule = hs5 . 2 1 0.5
</rules>


ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>
radius               = dims(ideogram,radius_outer)
multiplier           = 1e-6

<tick>
spacing        = 10u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 20p
label_offset   = 5p
format         = %d
</tick>

</ticks>