Formatting p-value cut-off line in a volcano plot in R

[Adam52]

I am using the following function in R to develop a simple volcano plot:

EnhancedVolcano(all_genes, x = "logFC", y = "adjust.p.value", lab = all_genes$Gene.ID,
                pCutoff =  10e-2, FCcutoff = 1)

I would like my horizontal pCutoff line to appear to represent p = 0.05, which on a log scale for this figure would appear as 1.3 on the y-axis. However, changing "10e-2" to say "10e-2.5" generates an error :

Error: unexpected numeric constant in: "EnhancedVolcano(all_genes, x =
"logFC", y = "adjust.p.value", lab = all_genes$Gene.ID,
pCutoff = 10e-2.5"

Any suggestions on how I can get a horizontal p-value cut-off line at exactly 1.3 (currently appears at 1.2)?

Here is some reproducible data:

structure(list(X = 1:14, Gene.ID = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N"), logFC = c(1.5, 0.17212922, 0.145542174, 0.304348578, 0.124636936, 0.247841044, 0.160818268, 0.123741518, 0.148530876, 0.148960225, 0.114135472, -0.147118359, 0.095549291, 0.138521594), AveExpr = c(5.426424957, 4.289728233, 4.901134193, 4.742864705, 5.447030699, 4.539641767, 4.650750102, 5.901020922, 5.365944907, 5.818788787, 4.837214384, 7.017656548, 4.531897822, 5.192294452), t = c(6.15098624, 5.452898247, 4.979246654, 4.949519834, 4.818043279, 4.73403717, 4.701937811, 4.522692175, 4.518518374, 4.281900066, 4.247981727, -4.194421592, 4.10350597, 4.088357671), p.value = c(1.27e-09, 6.8e-08, 7.99e-07, 9.26e-07, 1.77e-06, 2.65e-06, 3.09e-06, 7.13e-06, 7.27e-06, 2.1e-05, 2.44e-05, 3.07e-05, 4.53e-05, 4.83e-05), adjust.p.value = c(1.64e-05, 0.000438854, 0.002987004, 0.002987004, 0.004558267, 0.005687325, 0.005687325, 0.010422933, 0.010422933, 0.027128901, 0.028601707, 0.033061438, 0.04452146, 0.04452146), B = c(11.2786109, 7.664706936, 5.439886439, 5.306497286, 4.725465519, 4.361868581, 4.224515919, 3.473656504, 3.45649938, 2.508304771, 2.376338878, 2.169980059, 1.825392322, 1.76867543)), class = "data.frame", row.names = c(NA, -14L))

[AlexisW]

I'm confused about what value you want to use as a cutoff.

A common value is 1e-2 which is a shorthand for 1*10^(-2), i.e. the value 0.01. If you used this value as cutoff, it would appear on the Y axis as -log10(1e-2) = -log10(10^-2) = 2

In your example, you used 10e-2 i.e. 10*10^-2, the value 0.1, which on the Y-axis appears as 1 (and not 1.2).

[advanced: You can double check by re=plotting the line yourself, since EnhancedVolcano() returns a ggplot object, you can add a line on the Y-axis scale that ignores the p-value scale:

EnhancedVolcano(all_genes, x = "logFC", y = "adjust.p.value", lab = all_genes$Gene.ID,
                pCutoff =  .1, FCcutoff = 1) +
  geom_hline(aes(yintercept=1), color='red')

If you are not familiar with {ggplot2}, this paragraph probably looks meaningless to you, you can ignore it]

So in your case, if you are interested in, say, any p-value where -log10(p) > 2.5, this means p < 10^(-2.5) = 0.003162278, so you can use:

EnhancedVolcano(all_genes, x = "logFC", y = "adjust.p.value", lab = all_genes$Gene.ID,
                pCutoff =  10^(-2.5), FCcutoff = 1)

Or for the common 0.05 you can give it explicitly (and EnhancedVolcano will do the conversion to -log10(0.05) = 1.3`):

EnhancedVolcano(all_genes, x = "logFC", y = "adjust.p.value", lab = all_genes$Gene.ID,
                pCutoff =  0.05, FCcutoff = 1)

To be explicit, the notations 0.01, 1e-2, and 10^-2 are completely equivalent ways to represent the same number, for R it doesn't make any difference which one you use, they are available for your convenience. The e notation, also called "scientific notation", only seems to work for integers, just use one of the other two.