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? Thanks, Tom

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