Thank you! I got it!
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I've tried with DOSE package and others, but they don't support this type of data
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()
Thank you! I got it!
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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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.