Is it a good idea to plot a volcano plot starting at position x =1
I was wandering if it makes sense to start a volcano plot (x=log2FoldChange) starting at position one, so basically discarding all values below 1 and above -1 leaving only values outside this interval. Can you comment on this?
Hi, I would advise against this. I understand that you want to highlight the most interesting gens by leaving out those whose expression is unaffected. However, people are used to see “classic” volcanoplot and would be rightfully confused if some genes where left out. It also has the advantage to provide context to the visualization – most genes are unaffected, but a few are strongly up- or down–regulated.
A possible solution that allows to keep all genes in the visualization while highlighting the differentially expressed genes would be to use different colors. For instance light-transparent grey for not differentially expressed genes (including those between -1 and 1 log2foldchange) and blue for the others, like this: