Question: Circos: how to draw ribbons?
0
gravatar for tmms
2.6 years ago by
tmms0
tmms0 wrote:

Hello

Does anyone has experience with circos?

I want to draw a figure like this, but I am struggling to draw it. I have two bacterial genomes and they are represented in one circle (every half is one genome). I also have the coordinates of the regios that I want to connect with ribbons like in the figure. They were "calculated" using a different program. I can not find how to input these coordinates in circos. Does anyone already tried this?

Thanks in advance.

circos assembly • 944 views
ADD COMMENTlink modified 2.6 years ago by theobroma221.1k • written 2.6 years ago by tmms0

Have you been working with circos previosly? If so, how your circos.conf file looks like? In general your link data file should have this structure:

genom1 region1_start region1_end genom2 region2_start region2_end

e.g.

hs1 100 200 hs2 250 300
hs1 400 550 hs3 500 750
hs2 600 700 hs3 1100 1125

and so on.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by ahaswer150

Thank you for the reply. I already figured out what I did wrong.

I used the wrong names for the links. They should have the same name as the chromosomes defined in the karyotype. I also did not make a seperate linkfile. As soon as I did that, I just had to add "<<include path="" to="" linkfile="" links.conf="">>" in conf-file. Afterwards everything worked perfectly.

ADD REPLYlink written 2.6 years ago by tmms0
0
gravatar for theobroma22
2.6 years ago by
theobroma221.1k
theobroma221.1k wrote:

You can use the RCircos.Ribbon.Plot() function in the RCircos package.

ADD COMMENTlink written 2.6 years ago by theobroma221.1k
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