Compare CAZym repertories

[Elodie Drula]

Hi,

I am trying to use your really useful tool "Circos".

I would like to to exactly this kind of pictures: http://circos.ca/intro/published_images/img/circos-oomycetes.png

But I don't know how to superpose many circle. Plus this data is not genomic.

I am currently reading your circos-course, in the session 1 you teach how to generate the first circle but in the session 2 you jump directly to the generation of an histogram.

In this particular case, the second circle is not a histogram.
How can I said/generate this kind of picture please ?

Thanks in advance for your help !

[Martin Krzywinski]

Here's how you would create an image like this.

You'd set up a single axis that corresponded to the length of your heatmap. The length would be arbitrary, e.g. 1000 and the karyotype file might be

chr - axis axis 0 1000 black

Now that you have your axis, you would define each concentric heatmap as a file with colored segments associated with values

axis 0 50 0.5

axis 51 70 0.75

axis 71 125 1.2

...

The length and value of each bin would depend on your data.

Then you'd create a heatmap track for each 

<plots>

<plot>

type = heatmap

file = data.1.txt

r1 = 0.95r

r0 = 0.90r

color = blues-9-seq # or create your own color scheme

</plot>

# more tracks here

</plots>

The way you would make the track concentric is to adjust the start/end radius positions of each track (r0, r1).

<plots>

<plot>

...

file = data.1.txt

r1 = 0.95r

r0 = 0.90r

...
</plot>

<plot>

...

file = data.2.txt

r1 = 0.90r

r0 = 0.85r

...
</plot>

<plot>

...

file = data.3.txt

r1 = 0.85r

r0 = 0.80r

...
</plot>

...

</plots>

It's possible to automate this, but if you've never used Circos or are not an advanced user it's easier to just explicitly define each track.

This tutorial does something similar, except that it uses the chromosomes in the human genome as the axis.

http://www.circos.ca/documentation/tutorials/recipes/nature_cover_encode/images

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

--
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.

[Elodie Drula]

Thanks so much for your answer.
Your example is a good start for me.

Perfect !

[Elodie Drula]

OK, my next problem are the labelling for my axis.
In your example with the chromosomes, name are added automatically  (session 1, example 1).
My pastebin : https://pastebin.com/KAy2UtBd
I would like to add tag for the name of my species (example here : http://circos.ca/intro/published_images/img/circos-oomycetes.png ===> Pap or Par)
and tag for my CAZym family (example : PL1 or PL3 ...)

Thanks !

Le jeudi 29 juin 2017 22:28:23 UTC+2, Elodie Drula a écrit :

Hi,

I am trying to use your really useful tool "Circos".

I would like to to exactly this kind of pictures: http://circos.cahttps://pastebin.com/KAy2UtBd/intro/published_images/img/circos-oomycetes.png

But I don't know how to superpose many circle. Plus this data is not genomic.

I am currently reading your circos-course, in the session 1 you teach how to generate the first circle but in the session 2 you jump directly to the generation of an histogram.

In this particular case, the second circle is not a histogram.
How can I said/generate this kind of picture please ?

[Martin]

Circos doesn't support positioning of text freely on the image, unfortunately. 

There is a way to hack this but it's a little ugly and if it's a one-off image, it much easier to add these kinds of labels by hand.