Circos > Documentation > Tutorials > Recipes > Pattern Fills
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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

15. Pattern Fills

circos.conf


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

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

<patterns>
<<include etc/pattern.conf>>
</patterns>

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

karyotype = data/karyotype/karyotype.human.hg18.txt

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

<highlights>
<highlight>
file        = data/3/chr.highlights.txt
r0 = 0.99r
r1 = 0.995r
</highlight>
</highlights>

<links>
<link linkexample>

file   = data/8/15/tmp.1
ribbon = yes
flat   = yes
radius        = 0.95r
bezier_radius = 0r
crest         = 0.2

color      = black

<rules>
<rule>
importance = 100
condition  = rand() < 0.5
pattern    = eval((qw(hline vline checker dot))[rand(4)])
color      = eval((qw(red orange yellow green blue purple))[rand(6)])
z          = 10
</rule>
</rules>
</link>

</links>

<<include etc/housekeeping.conf>>



ideogram.conf


<ideogram>

<spacing>

default = 10u

</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     = yes
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.05r
label_size     = 36
label_parallel = no

# 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

band_transparency     = 0

</ideogram>



ticks.conf


show_ticks          = yes
show_tick_labels    = yes

grid_start         = dims(ideogram,radius_inner)-0.5r
grid_end           = dims(ideogram,radius_outer)+100

<ticks>
skip_first_label     = no
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 = 1e-6
color = black

<tick>
spacing        = 5u
size           = 5p
thickness      = 2p
color          = black
show_label     = no
label_size     = 8p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = grey
grid_thickness = 1p
</tick>
<tick>
spacing        = 10u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 12p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
</tick>
</ticks>