8 — Recipes

9. Transparent Links

This tutorial shows how you can improve the layout of your links using color transparency. The data for this tutorial was created using tools/randomlinks. This script generates random links between chromosomes based on your karyotype file and a flexible configuration which controls how many links to create, how large their spans should be, and so on. The configuration file, randomlinks.conf, can be found in this tutorial's directory.

using z-depth

If you have many ribbon links that overlap, one way to bring important (e.g. large) links to the foreground is to use z-depth.

This rule will set the z-depth for each link independently, as a function of its size. Larger links (i.e. those with large start/end spans) will have a high z-depth and therefore be shown on top.

<rules>
<rule>
condition  = 1
z          = eval( scalar min(var(size1),var(size2) ) )
</rule>
</rules>

The problem of link occlusion still remains - if you have a lot of links you won't be able to see them all.

defining transparent colors

To define a transparent color, add a fourth value to its RGB triplet. This value will be the transparency and it is a number between 0 (opaque) and 127 (fully transparent). For example, in addition to the default colors, I add a transparent black

<<include colors_fonts_patterns.conf>>
<colors>
blackweak = 0,0,0,100
</colors>

The transparency is 100/127, which gives blackweak an RGB value of 200,200,200 when drawn on white. When links are assigned this color,

<link>
ribbon = yes
color  = blackweak
...
</link>

the ribbons are drawn with transparency.

The blackweak color is black with 79% transparency. The alpha blending in GD results in multiplication of overlapping RGB colors. Thus, for every overlapping ribbon the RGB values are scaled from 200,200,200 by 79% (two overlapping ribbons result in 157,157,157, three in 123,123,123, and so on).

automatic definition of colors with transparency

By default, Circos defines 5 levels of transparency for each color you define.

Each color (e.g. pure red, pred=255,0,0) will yield 5 new color definitions pred_a1, pred_a2, pred_a3, pred_a4, and pred_a5 with each _aN color having a transparency N/(5+1). Thus pred_a1 will have a 17% transparency, pred_a2 33%, pred_a3 50%, pred_a4 67% and pred_a5 83%.

Note that pred_a0 is not defined (you already have it in pred) and pred_a5 is not 100% transparent.

With the automatic allocation of these colors, you can immediately use them

<link>
ribbon = yes
color  = black_a5 # black with 83% transparency
...
</link>

You can change the number of transparency steps using auto_alpha_steps in the <image> block.

<image>
<<include etc/image.conf>>
# overwrite auto_alpha_steps from default value included in etc/image.conf
auto_alpha_steps* = 10
</image>

adding transparency with rules

You can easily make elements that use opaque colors (e.g. red) to use transparent versions (e.g. red_a5) by writing rules to rewrite the color value.

For this example, I generated random links across all chromosomes in the human genome. Each link is conventionally colored by its starting chromosome.

hs7 127586339 141410899 hsY 30737607 31414129 color=chr7

but uses an opaque color. By writing the rule below, each color name has the transparency suffix (_aN) attached and becomes transparent.

<rule>
condition  = 1
color      = eval( var(color) ."_a4")
</rule>

With this rule, all links color names are modified (e.g. chr7 to chr7_a4) and shown at 67% transparency (default value of auto_alpha_steps=5).

transparency in bitmaps vs svg

Transparency in SVG is experimental. It works, but it is basic. For example, independent transparency for outlines is not yet available.