How to customize the MA Plot (DESeq2) with some gene to be labelled

Question

[bioinforesearchquestions]

Hi,

I am working on the MA plot.

I would like,

1) To color the upregulated genes with red

2) To color the downregulated genes with blue

3) Add labels to some of the genes

I tried one of the package ggpur (ggmaplot),

  maplot = ggmaplot(contrast_results, fdr = 0.05, fc = 1, size = 1,palette = c("#B31B21", "#1465AC", "darkgray"),genenames = as.vector(contrast_results$name),legend="top", top = 15,font.label = c("bold", 10),label.rectangle = TRUE, font.legend = c("bold",12),font.main = "bold")

In general the resolution is bad and the dots are too small and even the legend for the color is too small.

Anybody worked on this package before or any other suggestions are welcomed to accomplish the above three things.

[Ram]

I think these tasks would be better done in a Volcano plot than an MA plot. Kevin's EnhancedVolcano can help you there.

Also, there seem to be sizing, fdr and fold-change parameters in your current command. Have you tried tweaking them?

[bioinforesearchquestions]

I already did the coloring based on FDR, LFC on the volcano plot. Thanks, for sharing a useful link for the Volcano plot. It looks promising and I will try tweaking the Volcano plot using this resource.

But my friend wants it to be on the MA plot :(

[Ram]

Have a conversation with them on why they want it on an MA plot and why not on a Volcano plot. For all we know, they don't know how a Volcano plot would look like.

[russhh]

If it's a gg-prefixed package, you may be able to modify the theming / axis labels using standard ggplot operations. eg, maplot + theme(axis.text=element_text(size=12)) + annotate(..... pick out specific points ...). I prefer MA plots to volcanos, because you can typically see biases in expression pattern.

[bioinforesearchquestions]

Sure, I will try this Russhh. Thanks for the reference. Also I figured out to increase the legend of the figure and the resolution of the image.