[BioC] Axes in Volcano Plots

[Wolfgang Huber]

Dear Thomas,

> The current "standard of care" in presenting a volcano plot
> involves labeling the Y axis
> 
> -log10(p value)
> 
> I have found that audiences find this axis hard to deal with,
> and prefer seeing the axes labeled with things like
> 1e-02 to mean p = .01, rather than "5" to mean P = .00001.
> 
> One can get this effect buy using R's  plot option
> 
> log = "y"
> 
> if you avoid transforming the p values into -log10 p values first.
> 
> The problem is that now the volcano appears upside down, with the
> apex of the volcano at the origin and "volcanic eruption" exploding
> downward into quadrants 3 and 4, instead of erupting up.
> 
> One can't simply multiply the the p values by -1, either, since then R
> attempts to take the log of negative numbers (of course).

How about plotting 1/p with log="y"?

> The only solution I can think of is to label the y axis by hand...

Also fine. What's wrong with that?

Best wishes
      Wolfgang

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Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber