Circos > Documentation > Tutorials > Image Maps > Ticks
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.

10 — Image Maps

3. Clickable Tick Marks

circos.conf


<<include colors_fonts_patterns.conf>>

<<include ideogram.conf>>

<ideogram>
band_url* = undef
</ideogram>

<<include ticks.conf>>

karyotype   = data/karyotype/karyotype.human.txt

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

################################################################
# Here are the new image map parameters

image_map_use      = yes

image_map_missing_parameter = removeurl

#image_map_name     = circos
#image_map_file     = circos-tutorial.html
#image_map_protocol = http
#image_map_xshift = 0
#image_map_yshift = 0

# original image is 3000 x 3000, resized for web at 800 x 800

image_map_xfactor = 0.266667
image_map_yfactor = 0.266667
image_map_overlay                  = yes
#image_map_overlay_fill_color      = lred_a5
image_map_overlay_stroke_color     = red
image_map_overlay_stroke_thickness = 2

</image>

chromosomes_units           = 1000000
#chromosomes                 = hs1:0-50
chromosomes_display_default = yes

<<include etc/housekeeping.conf>>

bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 3

ideogram.conf


<ideogram>

<spacing>
default = 0.005r
break   = 0.5r
</spacing>

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

#ideogram_url = http://www.google.com
#ideogram_url = http://www.google.com/search?q=[chr]
#ideogram_url = script?type=ideogram&start=[start]&end=[end]&length=[chrlength]&chr=[chr]&tag=[tag]&label=[label]&idx=[idx]&display_idx=[display_idx]&scale=[scale]
#ideogram_url = script?chr=[chr]
band_url = script?start=[start]&end=[end]&label=[label]

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = dims(image,radius) - 70p
label_size       = 48
label_parallel   = yes
label_case       = upper

ideogram.position.conf

radius           = 0.85r
thickness        = 100p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf


show_ticks       = yes
show_tick_labels = yes

show_grid  = no

<ticks>

radius         = dims(ideogram,radius_outer)
label_offset   = 10p
multiplier     = 1e-6
color          = black

<tick>

spacing        = 25u
size           = 10p
thickness      = 3p
color          = black
show_label     = yes
label_size     = 30p
label_offset   = 0p
format         = %d
grid           = yes
grid_color     = grey
grid_thickness = 2p

url              = script?type=tick&chr=chr[label]&start=[start]&end=[end]
map_size         = 100p

#map_radius_inner = 0.5r
#map_radius_outer = 1.2r

</tick>

<tick>

show = no

spacing        = 5u
spacing_type   = relative
rspacing       = 0.25
size           = 10p
radius         = 0.9r
thickness      = 3p
color          = black
show_label     = yes
label_size     = 30p
label_relative = yes
label_offset   = 0p
format         = %.0f
rmultiplier    = 100
suffix         = %
grid           = yes
grid_color     = grey
grid_thickness = 2p

url              = script?type=tick&chr=chr[label]&start=[start]&end=[end]
map_size         = -100p

#map_radius_inner = 0.5r
#map_radius_outer = 1.2r

</tick>

</ticks>