The only way to get the alpha levels is to determine what they will be with `p.adjust()`, since they will depend on the distribution of your unadjusted p values. The general steps you should follow will be:

1. Add a column of adjusted p-values to your dataframe (`mydata$padj = p.adjust(mydata, method="BH")`, which is the same as FDR and saves a character).
2. Use `which` and `max` to determine your two alpha threshold (e.g., `max(mydata$pvalue[mydata$padj < 0.05])`

Then you can adjust your plots however you like (presumably with some horizontal lines at the various alphas). Whether you take the smallest non-significant value or the largest significant value is up to you, just describe what "dots on the line" represent.