Adding Standard Error to a Bar Plot with ggplot in R

Overview of the Problem and Solution

In this article, we will explore how to add standard error to a bar plot created using ggplot in R. We will start by understanding what each part of the code does, before explaining the correct way to incorporate standard error into our plot.

Step 1: Data Preparation

We begin with creating a sample dataset.

library(reshape2)

Dataset <- c("MO", "IP", "MP","CC")
GPP <- c(1, 3, 4,3)
NPP <-c(4,3,5,2)
df <- data.frame(Dataset,GPP,NPP)
df.m <- reshape2::melt(df)

In this code, we first create a simple dataset with the variables “Dataset”, “GPP” and “NPP”. We then use reshape2::melt() to convert our dataframe into a long format.

Step 2: Creating the Bar Plot

We can now create our bar plot using ggplot.

ggplot(df.m, aes(Dataset, value, fill = variable)) + 
  geom_bar(stat="identity", position = "dodge")

Here, we specify that we want a bar plot (geom_bar()) where the value column represents the height of each bar and the variable column specifies which bars belong to which group.

Step 3: Calculating Standard Error

We now calculate the standard error.

my_se <- df.m %>% 
  group_by(Dataset) %>% 
  summarise(n=n(),
            sd=sd(value),
            se=sd/sqrt(n))

In this code, we first group our dataframe by Dataset and then perform a summary of each column. We calculate the mean (n) number of observations in each group, the standard deviation (sd) of the values for each group, and then calculate the standard error (se) as the standard deviation divided by the square root of the number of observations.

Step 4: Joining Standard Error to Data

We now join our dataframe with the calculated standard errors.

df.m %>% 
  left_join(my_se) %>%
  ggplot(aes(x = Dataset, y = value, fill = variable)) + 
  geom_bar(stat="identity", position = "dodge")+
  geom_errorbar(aes(x=Dataset, ymin=value-se, ymax=value+se), width=0.4, position = position_dodge(.9))

Here, we use left_join() to join our dataframe with the standard error data on Dataset. We then specify that we want a bar plot (geom_bar()) where the value column represents the height of each bar and the variable column specifies which bars belong to which group. Finally, we add an geom_errorbar() layer to display the standard error.

Common Mistakes

There are several common mistakes to watch out for when adding standard error to a bar plot with ggplot:

• Using the wrong variable in the ymin and ymax arguments of geom_errorbar.
• Specifying an invalid value for values argument in scale_fill_manual.
• Not using position_dodge to position the bars correctly.

Conclusion

Adding standard error to a bar plot created with ggplot in R can be achieved by calculating it separately, joining it with your data and then adding it as an additional layer to your graph. Be careful of common mistakes that can affect the appearance of your plot.

Last modified on 2024-02-23