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

Question

[andrechristianes]

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

[Ram]

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?

[andrechristianes]

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.

[Ram]

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.

Answer 1

[Papyrus]

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()

[andrechristianes]

Thank you! I got it!

Answer 2

[cmdcolin]

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