8 — Recipes

12. Inverted Links

In this tutorial, I will show how to write rules that format inverted links.

A link is considered inverted if the orientation of its two ends is inverted with respect to one another. For example, given a link defined by the two ends chrA:start1-end1 and chrB:start2-end2, the link is inverted if

start1 < end1 && start2 > end2

or

start1 > end1 && start2 < end2

The interpretation of the case

start1 > end1 && start2 > end2

depends on your application.

link geometry

Recall that links are defined by specifing the position and orientation of their ends. When links are drawn as ribbons, the relative orientation of the link's ends affects whether the ribbon has a twist (see Link—Twists tutorial).

In that tutorial, you saw that you can make a link ribbon flat (i.e. without a twist), regardless of the orientation of the link, by setting

flat = yes

in the link block. By adding the twist parameter to the link, the ribbon could be made to twist even if flat=yes was set.

hs1 100 200 hs2 100 200
# this link's ribbon will be twisted, even if flat=yes is set
hs3 100 200 hs4 100 200 twist=1

Adding the inverted parameter to one of the link's ends in the data file swaps its start and end coordinates. This parameter is useful if you want to keep start < end for all your links, but still store information about the orientation.

hs1 100 200 hs2 100 200
# when a link end has inverted*=1, its start/end coordinates
# are reversed. For the start of the link use inverted1 and
# for the end inverted2.
hs3 100 200 hs4 100 200 inverted1=1

The difference between the twist and inverted parameters is that twist is meant to affect how a link's ribbon is drawn and inverted is meant to actually alter how a link is defined.

Keep in mind that the orientation of the link's ideograms has an effect on the link's twist. Link ribbons, by default, have their corners drawn in the order start1 -> end1 -> end2 -> start2, which results in a twist for a link with start < end for both ends when the ideograms are oriented in the same direction.

testing for inversion

To test whether a link is inverted, use the var(rev1) and var(rev2) keywords in a rule. Each of these strings evaluate to 1 if the start and end of the link are inverted, respectively.

For example, this rule will color orange all links which have their ends inverted.

<rule>
condition  = var(rev2)
color      = orange
</rule>

You can test one or both ends for inversion, though if both ends of a link are inverted the link itself could be consider as not inverted. It is up to you how to interpret this case.

<rule>
condition  = var(rev1) && var(rev2)
color      = red
</rule>

<rule>
condition  = var(rev1)
color      = green
</rule>

<rule>
condition  = var(rev2)
color      = orange
</rule>

defining inverted links

To indicate that a link is inverted, you can either reverse the coordinates of one of its ends, or assign it the inverted parameter.

# this is a normal link
chr1 100 200 chr2 100 200

# this is an inverted link - its first end is inverted
chr1 200 100 chr2 100 200

# this is an inverted link - its first end is inverted using the 'inverted' flag
chr1 100 200 chr2 100 200 inverted1=1

# this is an inverted link - its second end is inverted
chr1 100 200 chr2 200 100

# this is an inverted link - its second end is inverted using the 'inverted' flag
chr1 100 200 chr2 100 200 inverted2=1

How you choose to store information about inversion is up to you. Unless you are using the link input file in other analysis that requires strictly that start<=end, I suggest you use explicit coordinate inversion.