Re: [circos] Regarding heatmap of multiple rings

[Martin Krzywinski]

Hi Shalu,

The heat map tutorial gives an example of how to stack heat map tracks

http://www.circos.ca/documentation/tutorials/2d_tracks/heat_maps/images

You would have 5 <plot> blocks of type=heatmap, each having a different file, r0, r1 and (optionally) color scheme.

To add a space between the first/last ideogram to add a legend to each track, use the <pairwise> tag

http://www.circos.ca/documentation/tutorials/ideograms/spacing_breaks/

The data format for heat maps is described here

http://www.circos.ca/documentation/tutorials/configuration/data_files/

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Sat, May 18, 2013 at 2:40 AM, shalu jhanwar <shalu.j...@gmail.com> wrote:

I also want to use circos to represent differentially methylated genes same as shown in the attachment. I am new to this. I am following on-line tutorials, but I have
couple of questions regarding an image, I am interested in:

I want to generate heatmap using circos (same as in the figure, I attached for your kind perusal). Please let me know:
- How can I generate multiple rings of 5 genomes with different radius as shown in the figure? (I know how can I represent 5 different genomes in a single ring, but I don't what I need to mention in the configuration file in order to represent it in the multiple rings?)

- What should be the format of my input data file in order to draw heatmap? All the 5 genome data should be in the same file?

Thanks.

Shalu

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[shalu jhanwar]

Hi Martin,

I haev tried to generate the heatmap as suggested by you. I have couple of questions:
i) The quality of PNG image is not good, even after incresing the size. So I looked for the SVG. When I opened it in illustrator, made some modifications and tried to save in pdf, then it didn't save any of the rings in the output pdf and gave me warning "that it contains  some features which is not supported by the illustrator. Same happened with photoshop and inkscape". Please let me know how can I make/export high quality image?  I am attaching the circos.conf and circos.png file for your kind perusal.
ii) I want to zoom one aera of the image to show people to have a closer look. How can I do this in the heat map?

Please reply me at your earliest.

[Martin Krzywinski]

Please include *all* relevant files - data and conf.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[shalu jhanwar]

Hi Martin,

Please find all the input files data on the drive, conf file and the desired picture too, I generated using circos and illustrator:

https://drive.google.com/folderview?id=0Bysm9NFhsVbtLVZ5eldoZS1aVUk&usp=sharing

Please click on "Download anyway" to obtain all the files.
Also please let me know in case of any inconvinience.
I want a portion of the picture to zoom as well to show the minute difference. I tried this but I am unable to do this.

I would highly appreciate your quick reply.

Many thanks in advance!

Shalu




Please download all the files

[shalu jhanwar]

Hi Martin,

Many thanks for your kind reply. The quality is really awesome. Please explain me the following:

i) Regarding spectral-11-div colour scheme, what would be my scale (for e.g. as I showed static in the input files such that 0-30 green, 30-50 yellow etc) Here how could I be able to decide scale from 0-100?

ii) Regarding rules.txt, I am unable to understand rule "# elements with larger z value will be drawn top # here, set z to be -size, so that large regions drawn below small regions". Please explain me a bit.

iii) Can I draw legends also within the figure using circos (please see the image which I shared with you as the image size is big so I am unable to attach here) ? I did it using illustrator but it is not accurate?

iv) I want to zoom an area of the plot for e.g. chr1 such that as shown here in your tutorial (http://circos.ca/documentation/tutorials/scaling/zooming/images). Could you please explain how can I do this in my case?

Many thanks.

Shalu

[Martin Krzywinski]

i. 

You can obtain the color legend -- range of values and associated colors -- using -debug_group legend

To restrict the values to a given range, set min and max in the <plot>

http://www.circos.ca/documentation/tutorials/2d_tracks/heat_maps/

ii.

Elements are drawn in order of their z value. So elements that have a larger z value are drawn on top of those with a smaller z value.

iii.

No. You need to make a legend in Illustrator. Use the legend text dump (i) to guide you.

iv.

Ideogram scaling is described in this tutorial

http://www.circos.ca/documentation/tutorials/scaling/

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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