Re: [circos] Circos plot links with different bezier radius/crest/bezier_radius_purity

[Martin Krzywinski]

You don't need to have multiple files. You can create <rule> blocks to change how links are drawn based on position, existing formatting or other link properties.

The way you've defined your <rule> blocks, however, doesn't match what you want to do. Your <rule> blocks apply the color and stroke_color "grey" to specific links, but change nothing else.

I've attached an example in which different <rule> blocks are used to change the geometry: bezier_radius and crest. 

For your conditions, you want to use

condition = between(chr1A,chr1B)

to apply to links between these two chromosomes.

Links for which <rule> block's condition(s) is/are true will be affected by the block. Otherwise, the data point is not affected but it is still drawn.

The bezier_radius_purity is influenced by the distance between link ends. See

http://www.circos.ca/documentation/tutorials/links/geometry/images

It's a useful parameter if you have a large variety of links and want to visually separate them.

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Fri, Apr 7, 2017 at 2:54 AM, Dani <or.d...@gmail.com> wrote:

Hello, 

I have 3 pairs of links and to make it clear and avoid overlaps I want to adjust the bezier radius, crest or bezier radius purity.
I have created 2 different link.conf files,

<links>
<link>
file                 = data/links.tab
radius               = 0.93r
crest                = 0.1
color                = grey
ribbon               = yes
flat                 = yes
stroke_color         = grey
stroke_thickness     = 0.1
bezier_radius        = 0
bezier_radius_purity = 0.5
<rules>
<rule>
condition            = var(chr1) eq "chr1A"
condition            = var(chr2) eq "chr1B"
color                = grey
stroke_color         = grey
</rule>
<rule>
etc

And the links below I want to be higher than the previous one,

<links>
<link chain>
file                 = data/_links.tab
radius               = 0.93r
crest                = 0.3
color                = grey
ribbon               = yes
flat                 = yes
stroke_color         = grey
stroke_thickness     = 0.1
bezier_radius        = 0
bezier_radius_purity = 0.7
<rules>
condition            = var(chr1) eq "chr2A"
condition            = var(chr2) eq "chr2B"
color                = grey
stroke_color         = grey
</rule>
<rule>
etc

This doesn't work, all links are the same, doI have to include the bezier radius or purity under the condition?
Many thanks!

--
You received this message because you are subscribed to the Google Groups "Circos" group.
To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsub...@googlegroups.com.
To post to this group, send email to circos-data-visualization@googlegroups.com.
Visit this group at https://groups.google.com/group/circos-data-visualization.
For more options, visit https://groups.google.com/d/optout.