How to make a Power Spectral Density Plot in R
From further research I've discovered that the frequency is given by the index of the FFT multiplied by the sampling rate and divided by the size of the array. And the amplitude is the magnitude of the complex number.

So the full code for such a plot would be as follows

# X is some set of Wait times between spikes, below is just an example
X &lt;- c(56, 3, 4, 119, 3, 4, 121, 3, 3, 121, 3, 4, 120, 3, 4, 4, 115)
acf &lt;- acf(X,type="covariance")
ft &lt;- fft(acf$acf)
freq &lt;- (1:nrow(ft))*1000/nrow(ft) #In my case we sample by ms so 1000 hz
A &lt;- (Re(ft)^2 + Im(ft)^2)^.5 #amplitude is magnitude
PSD &lt;- cbind.data.frame(freq,A)
ggplot(PSD, aes(x=freq,y=A)) + geom_line()