Plots for DNA methylation data

Question

[sarahawan92]

Hi Everyone,

I have conducted DNA methylation analysis using the Limma and Minfi packages. However, I am struggling to generate plots for my methylation data. I am specifically interested in generating basic plots such as volcano plots, heatmaps, GO analysis plots, and bar plots. Should I consider using the 'ggplot2' package or are there other packages that I should consider? Please provide me with your advice. Thank you in advance.

Answer 1

[Basti]

Yes you can use ggplot2 to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a general code for volcanoplots, heatmaps etc to your own data. There are also some good tutorials available on this forum that will help you to create such plots (if you used methylation array) : Methylation Analysis Tutorial in R - Part 1