Question: Add gene names for significant genes in volcano plot (CummeRbund)
gravatar for pat.longjump
2.5 years ago by
pat.longjump0 wrote:

Hi all,

I generated a volcano plot with CummeRbund. Now I want to label the significant genes with the gene names. How can this be done?


rna-seq cummerbund R • 1.5k views
ADD COMMENTlink written 2.5 years ago by pat.longjump0

Could you please also post.. 1) head of your data 2) code used so far

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by badribio240

Just the basic command

csVolcano(genes(object = cuff_data), x = 'Sample1', y = 'Sample2', alpha=0.05, showSignificant=TRUE)

ADD REPLYlink written 2.4 years ago by pat.longjump0

This is the basic code:

csVolcano(object, x, y, alpha=0.05, showSignificant=TRUE,features=FALSE, xlimits = c(-20, 20), ... )

So, why is yours different? Why do you use

csVolcano(genes(cuff_data, ...

Also, perhaps include features=false if you didn't set the feature-level data?

ADD REPLYlink written 2.4 years ago by theobroma221.1k

Did you already try using basic R plotting functions like arrows and text?

ADD REPLYlink written 2.5 years ago by theobroma221.1k
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