genomics graphs in R

Question

[mimarcelape]

I'm trying to do graphs likes this in R for genomics analysis.

https://github.com/griffithlab/pmbio.org/blob/master/assets/lectures/PMBIO_Module05_Somatic.pdf

Graphs like circos plot, Copy number variants (CNVs) plot, Structural variants (SVs) plot.

[Ram]

OK, and what? What's your question?

Answer 1

[bhumm]

I agree with @Ram - this 'question' is not defined and unfocused. I assume you are asking for resources.

For circos plots, I would recommend circular as it is very well documented. Another option is BioCircos.

To plot CNVs (amongst many other things) you can use ggcoverage.

For structural variants, I would recommend the command line tool samplot.

Finally, for CNVs and SVs you could always visualize using IGV, but I suppose that is a little less elegant.