Question: add cut off lines to volcano plot

0

Sam •

**140**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

refer to abline function in R.

15kHello 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.

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46kI respectfully disagree - where there are other ways to learn about the

`abline()`

function, this looks like a perfectly appropriate question for Biostars.8.0k