MA plots for DE results

[mschilli87]

Description of feature

I noticed that all DE examples use Volcano plots to summarise/visualize the results.

I prefer MA plots as I consider Volcano plots to over-emphasize the importance of p-values. In combination with the fact that they do not provide any information about the expression (range) of the genes, I find they often highlight lowly expressed differential genes that are hard to validate experimentally while 'hiding' genes that I would consider 'low hanging' fruit for follow-up experiments (i.e. well expressed and differential).

Browsing the API documentation I could not find any functionality in pertpy to create MA plots. Since both, edgeR and DEseq2 provide such functions (at least in R), and they are widely used in the field (in my experience at least), I found that very surprising.

Was this a design decision or just a lack of bandwidth to implement? Could you point me to some references that made you prioritize Volcano plots over MA plots so I can re-evaluate my stance? And would you be open to adding MA plots to pertpy? If not, why not?

If there is interest, I could try to find the time to implement it and provide a PR.
I'll likely end up generating some version for my own use anyway, and I think it would be the right thing to do to make the extra effort to upstrean this, if possible.

[Zethson]

See my answer in the other issue about the state of DE in pertpy.

I have nothing against MA plots in pertpy and would appreciate it if you implemented them. Thank you!