8 — Recipes

7. Variable Radius Link Ends

Using entries in the link data file, or rules, you can independently manipulate the radial position of each end of a link. One application of this is to move link ends out of the way of another data track.

This is done by setting radius1 and radius2 values, which are the radial positions of the link ends associated with the first and second data point, respectively.

The first way to achieve this is to associate a radius value with one or both of the ends.

hs1 486 76975 hs15 100263879 100338121 radius1=0.5r
hs1 342608 393885 hs15 100218755 100268630 radius2=0.5r
hs1 576306 626811 hs15 100218755 100268630 radius=0.75r

Link ends for which radius is not defined will use the radius value defined in the <link> or <links> blcok.

The second way to adjust radius values is to use a rule and set radius1 and radius2 variables.

<rules>

# if a rule is triggered, continue testing with other rules
flow       = continue

# remap the color of the link to the first chromosome
<rule>
condition  = 1
color      = eval(sprintf("%s_a4",var(chr1)))
</rule>

# Alter radial position of one or both ends of a link, depending
# on its position. The function on(RX) tests whether a link
# is on a chromosome matching the regular expression RX.

# to/from hs1
<rule>
# the trailing $ (end of string anchor) is required so that 
# chromosome names like hs10, hs11, hs12, etc don't match
condition  = on(hs1$)
radius     = 0.85r
</rule>

# to hs10, hs11 or hs12
<rule>
condition  = to(hs1[012])
radius2    = 0.75r
</rule>

# from hs10, hs11, hs12
<rule>
condition  = from(hs1[012])
radius1    = 0.75r
</rule>

# from hs14 and has start beyond 100mb
<rule>
condition  = from(hs14) && var(start1) > 100mb
radius1    = 1r+50p
z          = 5
thickness  = 3
color      = blue
</rule>

# to hs5 and has end within 50mb of position 100mb
<rule>
condition  = to(hs5) && abs(var(start2) - 100mb) < 50mb
radius2    = 1r+50p
z          = 5
thickness  = 3
color      = red
</rule>

</rules>