Question: add cut off lines to volcano plot
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gravatar for Sam
2.1 years ago by
Sam140
Sam140 wrote:

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 • 960 views
ADD COMMENTlink written 2.1 years ago by Sam140

refer to abline function in R.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by cpad011215k

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!

ADD REPLYlink written 2.1 years ago by ATpoint46k
1

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

ADD REPLYlink written 2.1 years ago by Charles Warden8.0k
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