Circos > Documentation > Tutorials > Links > Rules1
Loading
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

4. Link Rules - Part I

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;hs4
chromosomes_display_default = no

<links>

radius    = 0.975r
crest     = 0.5
thickness = 2
color     = black
bezier_radius        = 0r
bezier_radius_purity = 0.5

<link>

file       = data/5/segdup.txt

<rules>
<rule>
condition  = var(intrachr)
show       = no
</rule>
<rule>
condition  = between(hs1,hs2)
color      = green
z          = 10
flow       = continue
</rule>
<rule>
condition  = between(hs2,hs3)
color      = blue
thickness  = 4
z          = 15
</rule>
</rules>

</link>

</links>

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


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>