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add cut off lines to volcano plot

Dear all

I got the volcano plot of deseq2 output with this code :

 with(res, plot(log2FoldChange, -log10(pvalue), pch=20, main="Volcano plot", xlim=c(-8,8)))
with(subset(res, padj<0.1 ), points(log2FoldChange, -log10(pvalue), pch=20, col="red"))
with(subset(res, abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="orange"))
 with(subset(res, padj<0.1 & abs(log2FoldChange)>1), points(log2FoldChange, -log10(pvalue), pch=20, col="green"))
library(calibrate)
with(subset(res, padj<0.1 & abs(log2FoldChange)>1), textxy(log2FoldChange, -log10(pvalue), labs=Geneid, cex=.8))

but I want add the cut off lines (padj and log2FoldChange) to the plot, any help for the code?

Thanks

volcano plot
• 2,834 views • link
written by Sam Sam

refer to abline function in R.

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written by cpad0112 cpad0112

Hello Sam!

We believe that this post does not fit the main topic of this site.

Basic R question. Please search the web and especially Stack Exchange.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

I respectfully disagree - where there are other ways to learn about the abline() function, this looks like a perfectly appropriate question for Biostars.

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written by Charles Warden Charles Warden

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