Create a circos plot based on 23andMe raw data

Question

[Dennis]

Dear community,

I got 2 data sets of raw 23andMe SNP data (.txt files) and I would like to create a circos plot with connected genes (like here). I don't really care about the meaning, or what the connection of genes is based on (in the example above it's the KEGG database), I much rather aim for a beautiful image (it's an data/art project).

I have circos installed, I converted the raw data to VCF (if needed) but I'm clueless on how to draw lines between ideograms in circos.

Any ideas are much appreciated! Thanks guys,

Dennis

Answer 1

[cschu181]

To generate links you need to have your data in a tabular format (I think tab-delimited or space-delimited works). The columns are as follows.

Assuming you want to connect a region on chromosome A with a region on chromosome B and this table is in a file named linkdata.txt.

1. ID of chromosome A
2. start position on chromosome A
3. end position on chromosome A
4. ID of chromosome B
5. start position on chromosome B
6. end position on chromosome B

I think you can also have a 7th column with attributes for the link, such as colour etc.

Edit: Strike the previous sentence. If I understand correctly, colours and other attritbutes are set for a group of links in the <link> section described below.

Then in your circos configuration file you need to have a section named <links>, in which you reference the data file:

<links>    
<link>
file          = linkdata.txt
radius        = 1r
bezier_radius = 0r
color         = black_a4
thickness     = 2
</link>    
</links>

For more ideas, have a look at the official circos documentation for links.