Circos > Documentation > Tutorials > Quick Start > Axes And Backgrounds
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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.

1 — Quick Start

6. Axes & Backgrounds

circos.conf


# 1.6 AXES AND BACKGROUNDS

karyotype = data/karyotype/karyotype.human.txt
chromosomes_units = 1000000

chromosomes_display_default = no
chromosomes                 = /hs[1234]$/
chromosomes_radius          = hs4:0.9r

<colors>
chr1* = red
chr2* = orange
chr3* = green
chr4* = blue
</colors>

chromosomes_reverse = /hs[234]/
chromosomes_scale   = hs1=0.5r,/hs[234]/=0.5rn

<plots>

<plot>

type = histogram
file = data/5/segdup.hs1234.hist.txt
r1   = 0.88r
r0   = 0.81r

fill_color = vdgrey
extend_bin = no

<rules>
<<include rule.exclude.hs1.conf>>
</rules>

# A track's background can be colored. Using y0/y1 ranges you can
# generate a striped track with focus on specific data ranges.

<<include backgrounds.conf>>

</plot>

<plot>
type = histogram
file = data/5/segdup.hs1234.stacked.txt
r1   = 0.99r
r0   = 0.92r

fill_color  = hs1,hs2,hs3,hs4
orientation = in
extend_bin  = no

<rules>
<<include rule.exclude.hs1.conf>>
</rules>

# Like backgrounds, axes are defined in groups. 
#
# spacing   - absolute or relative spacing of the axis
# position  - fixed position (or positions) for axes
# position_skip - fixed position (or positions) to skip when drawing axis lines
# y0        - absolute or relative start of axis lines
# y1        - absolute or relative start of axis lines
# color     - color of axis lines
# thickness - thickness of axis lines

<<include axes.conf>>

</plot>

</plots>

<links>

<link>
file          = data/5/segdup.txt
radius        = 0.8r
bezier_radius = 0r
color         = black_a4
thickness     = 2

<rules>
<<include rules.link.conf>>
</rules>

</link>

</links>

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

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

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


axes.conf

<axes>
# Show axes only on ideograms that have data for this track
show = data

thickness = 1
color     = lgrey
<axis>
spacing   = 0.1r
</axis>
<axis>
spacing   = 0.2r
color     = grey
</axis>
<axis>
position  = 0.5r
color     = red
</axis>
<axis>
position  = 0.85r
color     = green
thickness = 2
</axis>

</axes>


backgrounds.conf

<backgrounds>
# Show the backgrounds only for ideograms that have data
show  = data
<background>
color = vvlgrey
</background>
<background>
color = vlgrey
y0    = 0.2r
y1    = 0.5r
</background>
<background>
color = lgrey
y0    = 0.5r
y1    = 0.8r
</background>
<background>
color = grey
y0    = 0.8r
</background>

</backgrounds>


ideogram.conf


<ideogram>

<spacing>
default = 0.005r
</spacing>

# Ideogram position, fill and outline
radius           = 0.90r
thickness        = 20p
fill             = yes
stroke_color     = dgrey
stroke_thickness = 2p

# Minimum definition for ideogram labels.

show_label       = yes
# see etc/fonts.conf for list of font names
label_font       = default 
label_radius     = 1.075r  # if ideogram radius is constant, and you'd like labels close to image edge, 
                           # use the dims() function to access the size of the image
                           # label_radius  = dims(image,radius) - 60p
label_size       = 30
label_parallel   = yes

</ideogram>



rule.exclude.hs1.conf

<rule>
condition = on(hs1)
show      = no
</rule>


rules.link.conf

<rule>
condition     = var(intrachr)
show          = no
</rule>
<rule>
condition     = 1
color         = eval(var(chr2))
flow          = continue
</rule>
<rule>
condition     = from(hs1)
radius1       = 0.99r
</rule>
<rule>
condition     = to(hs1)
radius2       = 0.99r
</rule>


ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>
radius           = 1r
color            = black
thickness        = 2p

# the tick label is derived by multiplying the tick position
# by 'multiplier' and casting it in 'format':
#
# sprintf(format,position*multiplier)
#

multiplier       = 1e-6

# %d   - integer
# %f   - float
# %.1f - float with one decimal
# %.2f - float with two decimals
#
# for other formats, see http://perldoc.perl.org/functions/sprintf.html

format           = %d

<tick>
spacing        = 5u
size           = 10p
</tick>

<tick>
spacing        = 25u
size           = 15p
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
</tick>

</ticks>