8 — Recipes

11. Heat Map Links

You can color links by an associated value to create a heatmap effect.

Heatmaps were discussed in Tutorial 6.5. They were a combination of a highlight (had a start and end value) and a scatter plot (had an associated value). The heatmap track colors were defined as a comma-separated list, which was selected based on the value of the heatmap element.

giving links a value

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, if you're not using z-depth, use the z parameter. Below, I use z to associate a value of 2 with link_4 and 5 with link_5.

link_4 hs12 117427133 132349534 color=chr12,z=2
link_4 hs2 94056542 114056542 color=chr12,z=2
link_5 hs22 33232924 49691432 color=chr22,z=5
link_5 hs4 88399610 108399610 color=chr22,z=5

Alternatively, you can use the "url" parameter to achieve the same result.

link_4 hs12 117427133 132349534 color=chr12,url=2
link_4 hs2 94056542 114056542 color=chr12,url=2
link_5 hs22 33232924 49691432 color=chr22,url=5
link_5 hs4 88399610 108399610 color=chr22,url=5

At the moment, this is a cludge — in future versions a "value" parameter will be supported.

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 links value (e.g. if the "url") parameter was used, the parsable string _URL{N}_ is used, where N=1 for "url" parmameter of the start of the link and N=2 for the end of the link. Since in this case both ends have the same value, I use _URL1_ arbitrarily.

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...)[INDEX]

Combining these

(qw(red orange green blue purple))[INDEX]

In this case the INDEX is the "url" value, referenced by _URL1_.

To use Perl code in a rule, you need to pass it through eval(), so that Circos knows to interpret it correctly. Below are the two rules that (1) map the value to a color and (2) add transparency to the color.

<rules>

<rule>
importance = 100
# always trigger this rule
condition  = 1
# use the link's id value to sample from a list of colors
color = eval((qw(red orange green blue purple))[ _URL1_ ])
# continue parsing other rules
flow = continue
</rule>

<rule>
importance = 90
# 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',_COLOR_))
</rule>

</rules>