Circos > Documentation > Tutorials > Image Maps > Highlights Data
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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.

10 — Image Maps

4. Clickable Highlights and Data

circos.conf


<<include colors_fonts_patterns.conf>>

<<include ideogram.conf>>
<<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_strict   = removeparam

#image_map_name     = circos
#image_map_file     = circos.html
#image_map_protocol = http
#image_map_xshift   = 0
#image_map_yshift   = 0
#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 = no

<highlights>

z          = 0
fill_color = green
url        = script?type=highlight&start=[start]&end=[end]&chr=[chr]

# url is specified by the global url setting
# in the <highlights> block, above

<highlight>
file             = data/10/highlights.1.txt
r0               = 1.15r
r1               = 1.075r
fill_color       = blue
stroke_color     = dblue
stroke_thickness = 2
</highlight>

# url is specified within the <highlight> block, and
# it overrides the global url setting in the outer
# <highlights> block

<highlight>
file       = data/10/highlights.2.txt
r0         = 0.925r
r1         = 0.975r
url        = script?type=highlight&id=[id]&color=[fill_color]&r0=[r0]&r1=[r1]
</highlight>

# url is included with each data point, e.g.
# hs1 46486003 46541625 url=script?value=0.0401409

<highlight>
file       = data/10/highlights.3.txt
z          = 5
fill_color = red
ideogram   = yes
</highlight>

</highlights>

<plots>

<plot>
type = tile
file = data/10/tiles.2.txt
r0   = 0.81r
r1   = 0.92r
layers = 8
margin = 0.05u
layers_overflow = hide
orientation = out
thickness = 12
padding = 3
color = black
url = script?type=tile&id=[id]
</plot>

<plot>
type  = text
color = black
file  = data/10/text.2.txt
r0    = 0.6r
r1    = 0.8r

label_size = 18p
label_font = default

show_links     = yes
link_dims      = 0p,3p,5p,3p,3p
link_thickness = 2p
link_color     = red

padding        = 0p
rpadding       = 0p

label_snuggle         = yes
max_snuggle_distance  = 1r
snuggle_tolerance     = 0.25r
snuggle_sampling      = 5

url = script?type=label&id=[id]&text=[value]

<rules>
<rule>
importance = 10
condition  = var(value) =~ /M/
url        = M
</rule>
</rules>
</plot>

<plot>
type  = scatter
fill_color = black
glyph = square
glyph_size = 8p
file  = data/10/plotdata.1.txt
r0    = 0.55r
r1    = 0.6r
min   = -.1
max   = 1.1

<backgrounds>
<background>
color = vvlgrey
</background>
</backgrounds>

url = script?type=scatter-square&value=[value]&start=[start]&end=[end]
</plot>

<plot>
type  = scatter
fill_color = green
glyph = circle
glyph_size = 8p
file  = data/10/plotdata.3.txt
r0    = 0.55r
r1    = 0.6r
min   = -.1
max   = 1.1
url = script?type=scatter-circle&value=[value]&start=[start]&end=[end]
</plot>

<plot>
type  = histogram
fill_under = yes
fill_color = black
color = red
thickness = 2
file  = data/10/plotdata.1.txt
r0    = 0.5r
r1    = 0.55r
min   = 0
max   = 1

<backgrounds>
<background>
color = vlgrey
</background>
</backgrounds>

url = script?type=label&value=[value]

</plot>

<plot>
type  = heatmap
color = spectral-5-div
file  = data/10/plotdata.2.txt
r0    = 0.475r
r1    = 0.5r
min   = 0
max   = 1
url   = script?type=label&value=[value]&color=[color]
</plot>

<plot>
type  = highlight
fill_color = green
file  = data/10/plotdata.4.txt
r0    = 0.425r
r1    = 0.45r
url = script?type=highlight&start=[start]&end=[end]
</plot>
</plots>

<links>
<link>
file   = data/10/ribbon.1.txt
ribbon = yes
flat   = yes
color  = grey_a2
radius = 0.4r
bezier_radius = 0r
url    = script?type=ribbon&start1=[start1]&end1=[end1]&start2=[start2]&end2=[end2]&size1=[size1]&size2=[size2]
</link>
</links>

<<include etc/housekeeping.conf>>


ideogram.conf


<ideogram>

<spacing>

default = 1u

</spacing>

# thickness (px) of chromosome ideogram
thickness        = 100p
stroke_thickness = 2p
# 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         = 0.8r
show_label     = yes
label_with_tag = yes
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.2r
label_size     = 48p
label_parallel = yes
label_case     = upper

ideogram_url = script?type=ideogram&chr=[chr]

# cytogenetic bands
band_stroke_thickness = 2p

# 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

band_url = script?type=band&start=[start]&end=[end]&label=[label]

</ideogram>



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        = 1u
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&start=[start]&end=[end]
map_size         = 100p

#map_radius_inner = 0.5r
#map_radius_outer = 1.2r

</tick>

</ticks>