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How to create a dotplot like this for GSEA analysis from DNA methylation data (ChAMP.GSEA) in R?

enter image description here

I've tried with DOSE package and others, but they don't support this type of data

methylation gsea

This seems like a simple ggplot with a 4 variable (GeneRatio, p.adjust, Count and something like "disease") data.frame. Are you having difficulties collecting the data or creating the plot?

create the plot. I have the OR and adjPvalue for each TOP10 Gene Pathways. I can't find any tutorial for this plot type specificaly.

You don't need a tutorial. Google is your friend. ggplot is all about adding layers to your plot, so start with a simple dot plot and change one thing at a time until you get to what you want.

2 answers

Check out the R graph gallery, a nice resource for various plot types, in your case you're looking for "bubble" plots. But very simply for your data you could do:

library(ggplot2)

df <- data.frame(
  paths = paste0("path",1:3),
  ratio = runif(3),
  count = rnorm(3,200,50),
  p.adjust = runif(3)
)

ggplot(df, aes(x = ratio, y = paths, color = p.adjust, size = count)) + 
  geom_point(stat = 'identity') + 
  xlab("ratio") + ylab("path") + ggtitle("your data") + 
  theme_bw()

that particular figure was likely created by enrichplot, see http://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html#dot-plot

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