how to generate a violin plot based on ChIP-seq data

[crazyhottommy]

Dear all,

I want to generate a violin plot like fig1 B here http://www.sciencedirect.com/science...92867411015170

Given a ChIP-seq data set (raw bam file), I can do a MACS peak call and identify the peaks
( Intervals around several hundred bp)

I then group the peaks into two or more groups based on certain criteria.
how can I plot the peak intensity (# of raw counts for each peak Interval? )
in these two groups in a violin plot?

I know a little bit R and python.

Thanks so much!

[kopi-o]

For R, there is the vioplot package and violinplot() from the usingR package. There are other alternatives as well.

[crazyhottommy]

For R, there is the vioplot package and violinplot() from the usingR package. There are other alternatives as well.

thanks, I did a little bit google and can generate the violin graph, the problem is that my data is skewed.

in a default box-plot generated by R, I have a lot of outliers for the upper bound. I can set the argument outline=FALSE to get rid of them.

How can I do it in a violin plot then?

Thanks again.