volcano plot with fixed ylim (scales) cannot be "freed up" with scales="free"

[jjGG]

Hoi Witold,

As you may have seen in the comments, one user SH realized that the volcanos are by default fixed on ylim. Relaxing this with the scales parameter does not work .

-> in all these volcanos, the y-axis always has the same fixed length. pl$volcano(scales = c("fixed")) pl$volcano_plotly(scales = "free") pl$volcano(scales = "free") pl$volcano(scales = "free_y")

Gruess & bis am Dienstag j

[wolski]

@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.

[wolski]

@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.

[jjGG]

@wolski - super cool. Thanks for tghe fix!

[jjGG]

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))

[jjGG]

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)