[BioC] Axes in Volcano Plots

Thomas Hampton Thomas.H.Hampton at Dartmouth.edu
Wed May 13 16:10:42 CEST 2009

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).

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

Any ideas?



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