Circos > Documentation > Tutorials > Links > Basic 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.

5 — Links and Relationships

1. Drawing Basic Links

circos.conf


<<include colors_fonts_patterns.conf>>

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

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

karyotype   = data/karyotype/karyotype.human.txt

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3
chromosomes_display_default = no

# If you adjust the radius of the ideograms, links incident
# on these ideograms will inherit the new radius.
#chromosomes_radius = hs2:0.9r;hs3:0.8r

# Links (bezier curves or straight lines) are defined in <links> blocks.
# Each link data set is defined within a <link> block. 
#
# As with highlights, parameters defined
# in the root of <links> affect all data sets and are considered
# global settings. Individual parameters value can be refined by
# values defined within <link> blocks, or additionally on each
# data line within the input file.

<links>

<link>
file          = data/5/segdup.txt
radius        = 0.95r
color         = black_a4

# Curves look best when this value is small (e.g. 0.1r or 0r)
bezier_radius = 0.1r
thickness     = 1

# These parameters have default values. To unset them
# use 'undef'
#crest                = undef
#bezier_radius_purity = undef

# Limit how many links to read from file and draw
record_limit  = 2000

</link>

</links>

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

# If you want to turn off all track default values, 
# uncomment the line below. This overrides the
# value of the parameter imported from etc/housekeeping.conf

#track_defaults* = undef
# The defaults for links are
#
# ribbon           = no
# color            = black
# thickness        = 1
# radius           = 0.40r
# bezier_radius    = 0r
# crest                = 0.5
# bezier_radius_purity = 0.75
#
# See etc/tracks/link.conf in Circos distribution

bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 0

ideogram.conf


<ideogram>

<spacing>
default = 0.01r
break   = 0.5r
</spacing>

<<include ideogram.position.conf>>
<<include ideogram.label.conf>>
<<include bands.conf>>

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = dims(ideogram,radius) + 0.075r
label_with_tag   = yes
label_size       = 36
label_parallel   = yes
label_case       = lower
label_format     = eval(sprintf("chr%s",var(label)))

ideogram.position.conf

radius           = 0.90r
thickness        = 100p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>

radius           = dims(ideogram,radius_outer)
orientation      = out
label_multiplier = 1e-6
color            = black
size             = 20p
thickness        = 3p
label_offset     = 5p

<tick>
spacing        = 1u
show_label     = no
</tick>

<tick>
spacing        = 5u
show_label     = yes
label_size     = 20p
format         = %d
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 24p
format         = %d
</tick>

</ticks>