Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
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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
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.
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
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
inverted parameters is
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.
To test whether a link is inverted, use the
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>
To indicate that a link is inverted, you can either reverse the coordinates of one of its ends, or assign it the
# 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