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.

14kHello Sam!

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

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41kI respectfully disagree - where there are other ways to learn about the

`abline()`

function, this looks like a perfectly appropriate question for Biostars.7.9k