How to plot methylation pattern as heatmap through circos

[himanshu kumar]

I am working on DNA methylation , and I want to plot the circos image that can show the methylation pattern like hyper or hypo methylated on the basis of their methylation values. Sample data and other files have been attached.

Data Description:

having three files like mCG, mCHG, mCHH.

First column Cc0 to Cc11 ( id notation according to chromosome number)

Second column methylated position

Third column methylation value.

I want to show it on the basis of color contrast like more hyper should be darker and less hyper should be lighter in the same color.

Likewise for more hypo should be darker in color and less one should be lighter in same color.

I am not able to make desired image, please suggest the required changes.

Thank You.

[Martin Krzywinski]

Your data files are not formatted correctly.

First, the format is

chr start end value

Second, your start positions doesn't seem to be compatible with the size of chromosomes in your karyotype file. 

For example, Cc01 has a size of about 17.6 Mb in karyotype.pigeon.txt but in your data file the maximum start position is 1452. What are the units of 1452? 

You're want your data lines to be something like

Cc01 16000000 16000000 25

if your start and end position for methylation is the same.

Then, use

<plot>
type  = heatmap

...

color = blues-5-seq

# this will make the minimum size of each data point to be 0.1 * chromosome_units, or 100kb

# and make the data points visible

minsize = 0.1u

</plot>

Don't use a type=highlight plot -- this kind of plot won't map values onto color.

M

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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