If you have actual alpha, color, ..., values then you should use ..identity()
scales. This will tell ggplot()
to assign alpha values as they are in your data frame and not to scale them.
ggplot(data=D, aes(x=x, y=y, alpha=alpha)) +
geom_bar(stat="identity", fill="blue") +
facet_grid(group ~. ) +
scale_alpha_identity()