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

Question

I'm trying to make a heatmap using ggplot2 using the geom_tiles function here is my code below:

p<-ggplot(data,aes(Treatment,organisms))+geom_tile(aes(fill=S))+
  scale_fill_gradient(low = "black",high = "red") + 
  scale_x_discrete(expand = c(0, 0)) + 
  scale_y_discrete(expand = c(0, 0)) + 
  theme(legend.position = "right", 
    axis.ticks = element_blank(), 
    axis.text.x = element_text(size = base_size, angle = 90, hjust = 0, colour = "black"),
    axis.text.y = element_text(size = base_size, hjust = 1, colour = "black")).

data is my data.csv file
my X axis is types of Treatment
my Y axis is types of organisms

I'm not too familiar with commands and programming and I'm relatively new at this. I just want to be able to specify the order of the labels on the x axis. In this case, I'm trying to specify the order of "Treatment". By default, it orders alphabetically. How do I override this/keep the data in the same order as in my original csv file?

I've tried this command

scale_x_discrete(limits=c("Y","X","Z"))

where x, y and z are my treatment condition order. It however doesn't work very well, and give me missing heat boxes.

Answer 1

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.

Answer 2

One can also simply factorise within the aes() call directly. I am not sure why setting the limits doesn't work for you - I assume you get NA's because you might have typos in your level vector.

The below is certainly not much different than user Drew Steen's answer, but with the important difference of not changing the original data frame.

library(ggplot2)
## this vector might be useful for other plots/analyses
level_order <- c('virginica', 'versicolor', 'setosa') 

p <- ggplot(iris)
p + geom_bar(aes(x = factor(Species, level = level_order)))

## or directly in the aes() call without a pre-created vector:
p + geom_bar(aes(x = factor(Species, level = c('virginica', 'versicolor', 'setosa')))) 
## plot identical to the above - not shown

## or use your vector as limits in scale_x_discrete
p + geom_bar(aes(x = Species)) + 
  scale_x_discrete(limits = level_order) 

^{Created on 2022-11-20 with reprex v2.0.2}