Circos > Documentation > Tutorials > Image Maps > Ideograms
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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

1. Image Maps - Introduction and Clickable Ideograms

circos.conf


<<include colors_fonts_patterns.conf>>

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

karyotype   = data/karyotype/karyotype.human.txt

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

################################################################
# Image map

image_map_use      = yes

# If a url uses a variable field, such as [id], and
# the corresponding parameter (e.g. id) is not defined,
# then 
# - if image_map_missing_parameter=exit, Circos will exit with an error
# - if image_map_missing_parameter=removeparam (or not defined), the
#      undefined parameter string will be removed
# - if image_map_missing_parameter=removeurl, url will not be used 
#      for that data point or data set

#image_map_missing_parameter = exit

# This is the name of the map, which will appear in the
# <map name="NAME"> tag of the map. If not defined, the
# name of the image will be used.

#image_map_name     = circosmap

# The image map will be written to this file. If this
# value is not defined, then the filename will be used
# with an html extension. If the file specified here
# does not have a directory component, the output
# directory defined by the dir parameter (see above)
# will be prefixed (i.e. the map and image will be
# created in the same directory).

#image_map_file     = map.html

# If urls are not preceeded by a protocol, then this
# protocol will be automatically added to each url. This is
# not strictly necessary, since your browser will assume 
# that http is used. However, if you need https or some other
# protocol, this is the field to adjust.

#image_map_protocol = http

# These values, when defined, will be added to each
# x,y coordinate of the map element boundary. These offsets
# are useful if the Circos image will be composited with
# another image, or cropped, or manipulated in any manner
# that shifts its original (0,0) (upper left) corner. You
# can define one or both values, and they can be negative.

#image_map_xshift = 0
#image_map_yshift = 0

# These factors will be used to multiply the x,y coordinates for each
# map element boundary. These parameters are useful if you are going
# to resize the image later. For example, if you create a 3000 x 3000
# pixel image (radius=1500px), but publish a 800 x 800 pixel image,
# set both factors to 800/3000 = 2.666667. Unless you are stretching
# the image (don't do it!) both factors should have the same value

#image_map_xfactor = 0.266667
#image_map_yfactor = 0.266667

# For debugging purposes, you can overlay the image map elements on
# top of the PNG image (not SVG). Each element in the overlay can have
# a fill color and stroke color. Note that if you add any x/y shift or
# multiplicative factors (above) then the overlay will reflect those
# factors.

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

<ticks>
tick_separation      = 3p
label_separation     = 5p
radius               = dims(ideogram,radius_outer)
multiplier           = 1e-6
color          = black
size           = 20p
thickness      = 4p
label_offset   = 5p
format         = %d

<tick>
spacing        = 1u
show_label     = yes
label_size     = 16p
</tick>

<tick>
spacing        = 5u
show_label     = yes
label_size     = 18p
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
</tick>

<tick>
spacing        = 20u
show_label     = yes
label_size     = 24p
</tick>

</ticks>