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.
9 — Recipes
11. Heat Map Links
You can color links by an associated value to create a heatmap effect.
Heatmaps were discussed in 2d Tracks—Heatmap tutorial.
assigning value to links
At this time there is no way to associate a value with a link in the same way. However, you can subvert one of the link parameters to do so. For example, use a value parameter.
hs12 117427133 132349534 hs2 94056542 114056542 value=2 hs22 33232924 49691432 hs4 88399610 108399610 value=5
coloring links by value
Now that each link has a value, it's time to use it to set its color. Rules are used for this.
To reference the link's value, use var(value).
The first rule maps the "url" value onto a list of colors. In this example, the "url" value is in the range [0,4]. To map the value to a color, you will need to use an eval() block and write a Perl one-liner to sample a list. If the list contains entries that do not have a space (e.g. single word colors), you can use the qw() operator which turns words into a list.
qw(red orange green blue purple)
Perl's syntax to sample an element of a list is
( ...list here...)[i]
Combining these
(qw(red orange green blue purple))[i]
In this case the value of i is the value parameter, reference by var(value).
<rules> <rule> # always trigger this rule condition = 1 # use the link's value to sample from a list of colors color = eval((qw(red orange green blue purple))[ var(value) ]) # continue parsing other rules flow = continue </rule> <rule> # always trigger this rule condition = 1 # add _a3 to the color of the ribbon, giving it 50% transparency (3/6) color = eval(sprintf("%s_a3",var(color))) </rule> </rules>