Circos png margins

[Minita Shah]

Hi,

I am trying to fit multiple concentric circles representing copy-number information from many samples in a circos plot. What is the best way to increase the margin of the png image so that it doesn't cut off the outer circles? Would I have to decrease the radius to fit all of them? Attached image shows the problem I am facing.

Thanks,

Minita

[Martin Krzywinski]

In the <ideogram> block (usually in ideogram.conf), reduce the value of the radius parameter, which defines the position of the ideogram segments to something like

radius = 0.7r

This will move the ideograms to 70% of the radius of the inscribed circle and give you more room to place tracks outside the ideograms.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Minita Shah]

So i tried that and I was wondering if that was the only way to go about it? I do want to use the inner part of the circle for structural variants (so links) so I do want some minimum space. Is there no way to change the background size restrictions?

On Friday, February 19, 2016 at 12:45:46 PM UTC-5, Martin wrote:

In the <ideogram> block (usually in ideogram.conf), reduce the value of the radius parameter, which defines the position of the ideogram segments to something like

radius = 0.7r

This will move the ideograms to 70% of the radius of the inscribed circle and give you more room to place tracks outside the ideograms.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Fri, Feb 19, 2016 at 7:07 AM, Minita Shah <shah....@gmail.com> wrote:

Hi,

I am trying to fit multiple concentric circles representing copy-number information from many samples in a circos plot. What is the best way to increase the margin of the png image so that it doesn't cut off the outer circles? Would I have to decrease the radius to fit all of them? Attached image shows the problem I am facing.

Thanks,

Minita

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[Martin Krzywinski]

The way Circos works is that you first set the size of the background image in <image> radius parameter and then set the relative size of the ideogram circle, using <ideogram> radius parameter.

When creating a bitmap, there's no way to "grow" the background canvas to accommodate the tracks, as they stack, and then allow for some amount of margin. If the tracks don't fit on the bitmap, they're cropped.

However, if you create an SVG file, you can achieve this by reading the SVG into e.g. Illustrator and then resizing the canvas. 

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Mon, Feb 22, 2016 at 8:03 AM, Minita Shah <shah....@gmail.com> wrote:

So i tried that and I was wondering if that was the only way to go about it? I do want to use the inner part of the circle for structural variants (so links) so I do want some minimum space. Is there no way to change the background size restrictions?

On Friday, February 19, 2016 at 12:45:46 PM UTC-5, Martin wrote:

In the <ideogram> block (usually in ideogram.conf), reduce the value of the radius parameter, which defines the position of the ideogram segments to something like

radius = 0.7r

This will move the ideograms to 70% of the radius of the inscribed circle and give you more room to place tracks outside the ideograms.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Fri, Feb 19, 2016 at 7:07 AM, Minita Shah <shah....@gmail.com> wrote:

Hi,

I am trying to fit multiple concentric circles representing copy-number information from many samples in a circos plot. What is the best way to increase the margin of the png image so that it doesn't cut off the outer circles? Would I have to decrease the radius to fit all of them? Attached image shows the problem I am facing.

Thanks,

Minita

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[Minita Shah]

Ok, thanks Martin. I will give it a try.

On Wednesday, February 24, 2016 at 7:57:31 PM UTC-5, Martin wrote:

The way Circos works is that you first set the size of the background image in <image> radius parameter and then set the relative size of the ideogram circle, using <ideogram> radius parameter.

When creating a bitmap, there's no way to "grow" the background canvas to accommodate the tracks, as they stack, and then allow for some amount of margin. If the tracks don't fit on the bitmap, they're cropped.

However, if you create an SVG file, you can achieve this by reading the SVG into e.g. Illustrator and then resizing the canvas. 

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Mon, Feb 22, 2016 at 8:03 AM, Minita Shah <shah....@gmail.com> wrote:

So i tried that and I was wondering if that was the only way to go about it? I do want to use the inner part of the circle for structural variants (so links) so I do want some minimum space. Is there no way to change the background size restrictions?

On Friday, February 19, 2016 at 12:45:46 PM UTC-5, Martin wrote:

In the <ideogram> block (usually in ideogram.conf), reduce the value of the radius parameter, which defines the position of the ideogram segments to something like

radius = 0.7r

This will move the ideograms to 70% of the radius of the inscribed circle and give you more room to place tracks outside the ideograms.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Fri, Feb 19, 2016 at 7:07 AM, Minita Shah <shah....@gmail.com> wrote:

Hi,

I am trying to fit multiple concentric circles representing copy-number information from many samples in a circos plot. What is the best way to increase the margin of the png image so that it doesn't cut off the outer circles? Would I have to decrease the radius to fit all of them? Attached image shows the problem I am facing.

Thanks,

Minita

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[Bhuwan Khatri]

Hi Minita,

Can you please share your circos.conf script? I am very new to circos and I am trying to draw circos image for my CNV data. I will appreciate your help. Thank u.