Can EnhancedVolcano label genes that aren't significant or meet fold change cut off? Can we select? I tried to but it comes up as a geneid on the x-axis with vertical bar. Just wondering. 4.8 seems to suggest no.
How does EnhancedVolcano determine which genes to label? Is there a way to label more to the ones selected automatically? I guess following 4.8, you can selectLab but they have to be present already in lab. What happens if you selectLab genes that interfere with ones automatically selected by EnhancedVolcano, do they get bumped or removed? Can we remove select labels we don't want? It seems no matter how genes are labeled, it picks the same ones to label.
The default is Log2FC=2, so means minimum 4 fold change? or total 2, so 2 fold change, log2 = ratio 1?
Should I use lfcShrink(res) to get volcano plot or is just res fine? The vignette seems to suggest lfcShrink but pdf manual example has just res. Not sure what the proper or standard way for volcano plots from RNA-seq data run through DESeq2 is and how people normally publish them.
This package does look great. I'm pretty beginner at this and this is pretty user-friendly with nice vignette.