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.
To create links that access regions of an ideogram, define a
parameter within a <tick> mark block.
<tick> spacing = 25u size = 10p ... url = script?type=tick&start=[start]&end=[end] </tick>
With this setting, the area in the image map associated with the
tick will be a slice that extends from the base of the tick (usually
outer ideogram radius), to the end of the tick (defined by the tick
size). Since this may be too small, you can use the
to extend the area to any value.
<tick> spacing = 25u size = 10p ... url = script?type=tick&start=[start]&end=[end] map_size = 100p </tick>
The first image in this tutorial shows the image map with a
map_size=100p. This value may take on a negative value, in
which case the link area will be extended inward from the base of the
tick. This is shown in the second example image.
You can precisely control the radial extent of the tick mark link
area by using
<tick> spacing = 25u size = 10p ... url = script?type=tick&start=[start]&end=[end] map_radius_inner = 0.5r map_radius_outer = 1.2r </tick>
You can define any number of tick map layers. The fourth image in this example shows two tick mark layers: one layer of absolute ticks spaced every 25Mb and one layer of relative ticks spaced every 1/4 of an ideogram. Each layer is at a different radius and has its own set of links.
If you have multiple tick definitions at the same radius (e.g. one tick definition for 25Mb ticks, one for 5Mb ticks and one for 1Mb ticks, for example), I suggest that you attach a url parameter to only one of them. Although you can create overlapping image map elements for each tick spacing, this is likely to confuse the user.