How do you specifically order ggplot2 x axis instead of alphabetical order?

It is a little difficult to answer your specific question without a full, reproducible example. However something like this should work:

#Turn your 'treatment' column into a character vector
data$Treatment <- as.character(data$Treatment)
#Then turn it back into a factor with the levels in the correct order
data$Treatment <- factor(data$Treatment, levels=unique(data$Treatment))

In this example, the order of the factor will be the same as in the data.csv file.

If you prefer a different order, you can order them by hand:

data$Treatment <- factor(data$Treatment, levels=c("Y", "X", "Z"))

However this is dangerous if you have a lot of levels: if you get any of them wrong, that will cause problems.