Volcano plot has non-intuitive defaults and confusing text - Githubissues

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Volcano plot has non-intuitive defaults and confusing text #106

Closed alexvpickering closed 4 months ago

alexvpickering commented 5 months ago

Why is the default threshold -log10(x) = 4? Points:

No one knows intuitively the correspondence between x and 4 above.
What the user wants to set is x (the actual FDR threshold), not 4.
It is not a raw "p-value" ( Equivalent to p < 1.000e-4) but an adjusted p-value or FDR (reflected on the axis but not in the text).
the default should be FDR or adjusted p-value of 0.05 (standard)
the user should be able to directly specify the FDR, not the -log10(FDR)

rant over