Circos > Documentation > Tutorials > Recipes > Transparency Background
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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

5. Image Transparency and Background

circos.conf


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

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

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

karyotype = data/8/karyotype.microbe.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
# specify a color or image
# to make the background transparent, use "transparent"
background     = data/8/background.png
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000
chromosomes_display_default = yes

<highlights>

<highlight>
file = data/8/microbe.highlights.1.txt
r0 = 0.95r
r1 = 0.98r
</highlight>

<highlight>
file = data/8/microbe.highlights.13.txt
r0 = 0.91r
r1 = 0.94r
</highlight>

<highlight>
file = data/8/microbe.highlights.14.txt
r0 = 0.86r
r1 = 0.90r
</highlight>

<highlight>
file = data/8/microbe.highlights.2.txt
r0 = 0.82r
r1 = 0.85r
</highlight>

<highlight>
file = data/8/microbe.highlights.4.txt
r0 = 0.53r
r1 = 0.54r
</highlight>
<highlight>
file = data/8/microbe.highlights.5.txt
r0 = 0.51r
r1 = 0.52r
</highlight>

<highlight>
file = data/8/microbe.highlights.6.txt
r0 = 0.46r
r1 = 0.47r
</highlight>
<highlight>
file = data/8/microbe.highlights.7.txt
r0 = 0.48r
r1 = 0.49r
</highlight>

<highlight>
file = data/8/microbe.highlights.8.txt
r0 = 0.41r
r1 = 0.42r
</highlight>
<highlight>
file = data/8/microbe.highlights.9.txt
r0 = 0.43r
r1 = 0.44r
</highlight>
<highlight>
file = data/8/microbe.highlights.10.txt
r0 = 0.19r
r1 = 0.20r
</highlight>
<highlight>
file = data/8/microbe.highlights.19.txt
r0 = 0.21r
r1 = 0.22r
</highlight>
<highlight>
file = data/8/microbe.highlights.20.txt
r0 = 0.23r
r1 = 0.24r
</highlight>
<highlight>
file = data/8/microbe.highlights.21.txt
r0 = 0.25r
r1 = 0.265r
</highlight>
<highlight>
file = data/8/microbe.highlights.22.txt
r0 = 0.275r
r1 = 0.29r
</highlight>
<highlight>
file = data/8/microbe.highlights.23.txt
r0 = 0.30r
r1 = 0.32r
</highlight>
<highlight>
file = data/8/microbe.highlights.24.txt
r0 = 0.33r
r1 = 0.355r
</highlight>
<highlight>
file = data/8/microbe.highlights.25.txt
r0 = 0.365r
r1 = 0.395r
</highlight>
<highlight>
file = data/8/microbe.highlights.11.txt
r0 = 0.17r
r1 = 0.18r
</highlight>
<highlight>
file = data/8/microbe.highlights.12.txt
r0 = 0.15r
r1 = 0.16r
</highlight>

<highlight>
file = data/8/microbe.highlights.15.txt
r0 = 0.72r
r1 = 0.78r
</highlight>

<highlight>
file = data/8/microbe.highlights.16.txt
r0 = 0.56r
r1 = 0.60r
</highlight>

<highlight>
file = data/8/microbe.highlights.17.txt
r0 = 0.615r
r1 = 0.635r
</highlight>

<highlight>
file = data/8/microbe.highlights.18.txt
r0 = 0.65r
r1 = 0.69r
</highlight>
<highlight>
file = data/8/microbe.highlights.26.txt
r0 = 0.65r
r1 = 0.69r
</highlight>

<highlight>
file = data/8/microbe.separator.txt
r0 = 0.80r
r1 = 0.805r
fill_color = vvlgrey
</highlight>
<highlight>
file = data/8/microbe.separator.txt
r0 = 0.70r
r1 = 0.705r
fill_color = vvlgrey
</highlight>
<highlight>
file = data/8/microbe.separator.txt
r0 = 0.55r
r1 = 0.555r
fill_color = vvlgrey
</highlight>
<highlight>
file = data/8/microbe.separator.txt
r0 = 0.50r
r1 = 0.505r
fill_color = vvlgrey
</highlight>
<highlight>
file = data/8/microbe.separator.txt
r0 = 0.45r
r1 = 0.455r
fill_color = vvlgrey
</highlight>
<highlight>
file = data/8/microbe.separator.txt
r0 = 0.40r
r1 = 0.405r
fill_color = vvlgrey
</highlight>
</highlights>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n



ideogram.conf


<ideogram>

<spacing>

default = 0u
break   = 0u

#<pairwise a;b>
#spacing = 5u
#</pairwise>

#<pairwise b;c>
#spacing = 10u
#</pairwise>

#<pairwise c;d>
#spacing = 20u
#</pairwise>

</spacing>

# thickness (px) of chromosome ideogram
thickness        = 20p
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     = no
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.05r
label_size     = 36

# cytogenetic bands
band_stroke_thickness = 2

# show_bands determines whether the outline of cytogenetic bands
# will be seen
show_bands            = yes
# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
fill_bands            = yes

</ideogram>



ticks.conf


show_ticks          = yes
show_tick_labels    = yes

show_grid = no
grid_start         = dims(ideogram,radius_inner)-0.5r
grid_end           = dims(ideogram,radius_inner)

<ticks>
skip_first_label     = yes
skip_last_label      = no
radius               = dims(ideogram,radius_outer)
tick_separation      = 2p
min_label_distance_to_edge = 0p
label_separation = 5p
label_offset     = 2p
label_size = 8p
multiplier = 0.001
color = black

<tick>
spacing        = 1u
size           = 3p
thickness      = 2p
color          = black
show_label     = no
label_size     = 12p
label_offset   = 0p
format         = %.2f
grid           = no
grid_color     = lblue
grid_thickness = 1p
</tick>
<tick>
spacing        = 5u
size           = 5p
thickness      = 1p
color          = black
show_label     = yes
label_size     = 16p
label_offset   = 0p
format         = %s
grid           = yes
grid_color     = lgrey
grid_thickness = 1p
</tick>
<tick>
spacing        = 10u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 16p
label_offset   = 0p
format         = %s
grid           = yes
grid_color     = grey
grid_thickness = 1p
</tick>
<tick>
spacing        = 100u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
suffix = " kb"
label_size     = 36p
label_offset   = 5p
format         = %s
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
</tick>
</ticks>