volcano plot with fixed ylim (scales) cannot be "freed up" with scales="free" about prolfqua HOT 5 CLOSED

@jjGG

I did run the examples in the prolfqua package ContrastsPlotter documentation:

cp$volcano(scales = "fixed")

cp$volcano(scales = "free")

Please try to reproduce an possible error using any of the example datasets provided with prolfqua.

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@jjGG

I did limit the p.values to a minimum of 0.0001 ...
Now, there is a parameter minscorein the volcano function, which you can set to whatever you want.

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@wolski - super cool. Thanks for tghe fix!

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Hei Witold,

Leider funktioniert bei mir (prolfqua 1.1.5) der minscore parameter nicht. Eine Idee?

v3 <- plotter$volcano(minscore=c(1E-10))
Error in plotter$volcano(minscore = c(1e-10)) : 
  unused argument (minscore = c(1e-10))

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Super - Danke Witold.

Hat funktioniert. RTFM!
minscore =/ min_score

plotter <- contr$get_Plotter()
v2 <- plotter$volcano()
gridExtra::grid.arrange(v1$FDR,v2$FDR, ncol = 1)

# relax ylim
v3 <- plotter$volcano(min_score=1E-10)

gridExtra::grid.arrange(v2$FDR,v3$FDR, ncol = 1)

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