EnhancedVolcano with gene names

Question

[mannoulag1]

Hi, I used EnhancedVolcano to obtain a nice volcano plot but I need the gene names in the figure not the gene ID, tt is the result of toptable, Thank you

tt<-topTable(fit2, adjust="fdr", number=Inf)
EnhancedVolcano(tt,lab = rownames(tt),x = "logFC",
y = "adj.P.Val",pCutoff = 0.05,FCcutoff = 2,transcriptPointSize = 1.5,
ylab = bquote(~-Log[10]~adjusted~italic(P)), legend=c("NS","Log2 FC","Adjusted p-value","Adjusted p-value & Log2 FC"),
 transcriptLabSize = 3.0, title= ".........")

Answer 1

[Kevin Blighe]

Hi, I developed EnhancedVolcano. What are your gene IDs, currently? Can you paste them? You may need to convert them via biomaRt.

[mannoulag1]

Hi Kevin, yes thank you very much for providing EnhancedVolcano, I am very interested to use it :) I succeeded to obtain the gene symbols from biomart, so I have ensemble_gene_id and the symbols but how can I use this in lab attribute? thank you

[Kevin Blighe]

Good work, dude!

[mannoulag1]

how can I use this in lab attribute? thank you

[Kevin Blighe]

Ah, you edited your comment. I thought that you had the new labels already. Have you produced a lookup table from biomaRt?

I perform matching between biomaRt output and Affymetrix IDs, here: C: Annotate Affymetrix probesets to Gene symbols

Perhaps you can follow that in order to matching your Ensembl IDs to HGNC IDs.

[mannoulag1]

perfect !!! Thank you kevin