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>