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.

11 — Image Maps

2. Image Maps - Clickable Cytogenetic Bands

Chromosomes can have cytogenetic bands associated with them in the karyotype file. These bands serve to define distinct regions on the chromosome. Typically, the bands are used to orient large-scale structures (>5Mb) on the chromosome and act as visual markers. You can use these bands for any purpose, however.

To associate a url with each band, use the band_url parameter in the <ideogram> block. 

<ideogram>
band_url = script?start=[end]&end=[end]&label=[label]
...

parameters for bands

Bands have the following parameters available automatically in their URL

  • chr - chromosome of band
  • parent - internal field
  • name - name of the band
  • start - base position of band start
  • end - base position of band end
  • size - size of band
  • color - color of band
  • label - the label of the band (this can be different than the name)

Like for ideograms, you can include an id parameter in the band definition and use it subsequently in the URL. So, in the karyotype file you might have 

...
band hs1 p31.2 p31.2 68700000 69500000 gneg
band hs1 p31.1 p31.1 69500000 84700000 gpos100 id=treasure_here
band hs1 p22.3 p22.3 84700000 88100000 gneg
...

and then use a URL like 

band_url = script?id=[id]

If you have image_map_missing_parameter=removeparam, then all bands without a defined id parameter will have a URL like 

script?id=

with the exception of chr1p31.1 which will have 

script?id=treasure_here

But, if you define image_map_missing_parameter=removeurl, then only bands with the id parameter defined will have a URL - other bands will not have an entry in the image map.

managing overlapping links - ideograms and bands

Bands are drawn on top of ideograms and therefore band image map elements locally override ideogram map elements. This is accomplished by placing the band image map element before the ideogram element in the map file. Both elements are there, but W3 specification for client-side image maps specifies that "If two or more defined regions overlap, the region-defining element that appears earliest in the document takes precedence (i.e., responds to user input)".

The second image in this tutorial demonstrates the result of defining both an ideogram and a band url 

ideogram_url = script?chr=[chr]
band_url     = script?start=[start]&end=[end]&label=[label]

You'll notice that in the region of the ideogram band links are active in the image map. However, since the ideogram image map also includes the label of the ideogram, you can still access the link of the ideogram through the label.

In the case of bands without a URL, the ideogram link would be accesible within the area of the band.