Circos > Documentation > Tutorials > Highlights > Parameters
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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.

3 — Highlights

2. Highlight Parameters - Part I - Embedded in Data File

circos.conf


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

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

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

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units           = 1000000

chromosomes        = hs1
chromosomes_breaks = -hs1:120-145;-hs1:180-200

chromosomes_display_default = no

<highlights>

z = 0
fill_color = green

<highlight>
file       = data/3/genes.formatted.txt
r0         = 0.7r
r1         = 0.7r + 200p
</highlight>

</highlights>

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

units_ok = bupr
units_nounit = n

ideogram.conf


<ideogram>

<spacing>

default = 3u
break   = 1u

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 = 3
thickness        = 1.5r
</break>

</spacing>

# thickness (px) of chromosome ideogram
thickness        = 100p
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     = condensedbold
label_radius   = dims(ideogram,radius) + 0.05r
label_size     = 48

# 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          = yes
grid_start         = 0.5r
grid_end           = 1.0r

<ticks>
skip_first_label     = no
skip_last_label      = no
radius               = dims(ideogram,radius_outer)
tick_separation      = 2p
min_label_distance_to_edge = 10p
label_separation = 5p
label_offset     = 2p
label_size = 8p
multiplier = 1e-6
color = black

<tick>
spacing        = 1u
size           = 6p
thickness      = 1p
color          = black
show_label     = no
label_size     = 16p
label_offset   = 0p
format         = %.2f
grid           = yes
grid_color     = grey
grid_thickness = 1p
</tick>
<tick>
spacing        = 5u
size           = 10p
thickness      = 1p
color          = black
show_label     = yes
label_size     = 16p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = grey
grid_thickness = 2p
</tick>
<tick>
spacing        = 10u
size           = 16p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 16p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = vdgrey
grid_thickness = 2p
</tick>
</ticks>