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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

14. Directed Links

circos.conf


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

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

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

karyotype = karyotype.human.hg18.txt

<image>
dir   = .
file  = links-directed.png
24bit = yes
radius         = 1500p
background     = white
angle_offset   = -90
auto_alpha_colors = yes
auto_alpha_steps  = 5
</image>

chromosomes_units           = 1e6
chromosomes_display_default = yes
chromosomes = hs3:101-121
chromosomes_scale = hs3:50

<plots>
<plot>
type = scatter
glyph = triangle
glyph_size = 24p
file = linkends.txt
min = 0
max = 1
r0 = 0.99r
r1 = 0.99r
fill_color=black
<rules>
<rule>
importance = 100
condition  = 1
fill_color = eval("chr".substr(_CHR_,2))
</rule>
</rules>
</plot>
</plots>

<links>
<link testlinks>
file          = links.txt
thickness     = 2
bezier_radius = 0r
radius        = 0.995r
crest         = 0.25
color         = black_a2
</link>
</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 120
debug           = no
warnings        = no
imagemap        = no

units_ok = bupr
units_nounit = n

#debug_group = ticks


ideogram.conf


<ideogram>

<spacing>

default = 5u

</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     = no
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.10r
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            = no
# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
fill_bands            = no

band_transparency     = 1

</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      = 5p
min_label_distance_to_edge = 0p
label_separation = 5p
label_offset     = 5p
label_size = 8p
multiplier = 1e-6
color = black

<tick>
spacing        = 5u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 24p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = grey
grid_thickness = 1p
</tick>
<tick>
#chromosomes_display_default=no
#chromosomes    = hs3
spacing        = 1u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 24p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = grey
grid_thickness = 1p
</tick>
<tick>
spacing        = 25u
size           = 12p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 24p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
</tick>
</ticks>