R package or tool to draw peaks on chromosomes (like in UCSC)

Question

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Hi,

I uploaded peaks into the UCSC genome browser and I can see all of the peaks on the full chromosome. Now I'd like to draw the entire genome, with each chromosome showing the peaks throughout to get a good visual idea of the peaks distribution on the chromosomes. I am looking fir a tool that does this, has anyone any ideas? I assume there must be an option in R to do this.

My peaks are in bed format.

I am not very proficient in R, so any help would be greatly appreciated.

Answer 1

[bernatgel]

You can also give karyoploteR a try.

It has functions to plot peaks, reads densities and many other either in a whole genome view, in a subset of chromosomes or in a local region view.

There's a karyoploteR tutorial page with examples of this kind of plots. For example:

Answer 2

[jared.andrews07]

ChIPseeker has a simple function to do this (covplot).

[blur]

looks great, thanks!