how to draw the volcano plot for DEGs in a different way

Question

[luckyday1661]

Dear guys,

May I know if there is some sample code to use to draw the plot like below?

I have DEGs results from limma, does it need to re run use DESeq2 to use plotMA to get this?

Thank you very much!

Answer 1

[CTLong]

From you Limma DEG results, you could use glimmaMA to generate a MA plot as demonstrated in this vignette (https://bioconductor.org/packages/devel/bioc/vignettes/Glimma/inst/doc/limma_edger.html).

Alternatively, given the DEG matrix, you could also useggplot2 with geom_point to draw the MA plot. Set the aesthetics so that the Y-axis corresponds log2FC and X axis as average log2 expression. Color the points based on if it is upregulated or downregulated (according to your threshold). The code will look something like this:

ggplot(LimmaResult, aes(x=averageExp, y=log2FC)) +
  geom_point(aes(color = Significance))

[luckyday1661]

Thank you very much! This is super helpful! Appreciate!