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.

score 143 · Accepted Answer · edited Jul 02 '18 at 01:49

143

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.

edited Jul 02 '18 at 01:49

Gregor Thomas

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answered Oct 08 '12 at 13:53

Drew Steen

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Have to wonder why this is even necessary. Why are the axes reordered by ggplot in the first place? Seems dangerous if someone isn't aware this is going to happen. – Dirk Calloway Mar 25 '14 at 10:27
1

I just ran into this problem myself making a [heatmap with qplot](http://martinsbioblogg.wordpress.com/2013/03/21/using-r-correlation-heatmap-with-ggplot2/) and automatically applied variable names. Should it be reported? – bright-star Mar 25 '14 at 10:29
10

@DirkCalloway, this behavior makes sense if you think about how factors work in R. A factor is a vector of integers, each of which is associated with a character 'label'. When you create a factor by reading a column of character values in a text file (e.g. `.csv`), R assigns the integer values in alphabetical order rather than in the order they appear in the file. You can argue whether that makes sense, but `ggplot2` then does the logical thing, which is to display the factor levels in order of their integer values. Your complaint is with `read.table`, not `ggplot2`. – Drew Steen Mar 25 '14 at 14:06

tjebo · Answer 2 · 2020-10-25T10:12:29.963

The accepted answer offers a solution which requires changing of the underlying data frame. This is not necessary. One can also simply factorise within the aes() call directly or create a vector for that instead.

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

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

ggplot(iris, aes(x = factor(Species, level = level_order), y = Petal.Width)) + geom_col()

or

level_order <- factor(iris$Species, level = c('virginica', 'versicolor', 'setosa'))

ggplot(iris, aes(x = level_order, y = Petal.Width)) + geom_col()

or
directly in the aes() call without a pre-created vector:

ggplot(iris, aes(x = factor(Species, level = c('virginica', 'versicolor', 'setosa')), y = Petal.Width)) + geom_col()

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

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