How can i adjust the errorbars on the stacked barplot?

tidyverse
, ,
1

Hello everyone...
I am a master student stuck in a problem for half a day...

I am making a bar plot with the error bars.
I have 2 values which are NOx and NH4_N.
And there are 5 IDs which are S, S_BC, S_EM, S_BC_auEM, and S_EM_BC.

For the bar plot, I want to include NOx and NH4 data in one bar to indicate the Total N uptake. However, the inclusion of the bar worked quite well, but the error bar problem could not be solved.
like the are not stacked or looks so weird like here.

Rplot
Rplot1073×830 90.6 KB

The code is the following...

####Trial
### Uptaken N - Pu2
# Calculate mean and standard error for Uptook_Nox and Uptook_NH4_N by ID

summary_stats_pu2 <- data_1_sub_tray_Pu2 %>%
  group_by(ID) %>%
  summarise(mean_Nox = mean(Uptook_Nox),
            mean_NH4 = mean(Uptook_NH4_N),
            se_Nox = sd(Uptook_Nox) / sqrt(n()),
            se_NH4 = sd(Uptook_NH4_N) / sqrt(n()))

# Reshape data for plotting
plot_data_pu2 <- summary_stats_pu2 %>%
  pivot_longer(cols = c(mean_Nox, mean_NH4), names_to = "Nutrient", values_to = "Mean") %>%
  mutate(Error = ifelse(Nutrient == "mean_Nox", se_Nox, se_NH4),
         Nutrient = factor(Nutrient, levels = c("mean_NH4", "mean_Nox")))  # Ensure NH4 is on top

# Plotting stacked bar chart with error bars
ggplot(plot_data_pu2, aes(x = ID, y = Mean, fill = Nutrient)) +
  geom_bar(stat = "identity", position = position_stack(reverse = TRUE), width = 0.7) +
  geom_errorbar(aes(ymin = Mean - Error, ymax = Mean + Error), 
                position = position_stack(reverse = TRUE, vjust = 0.5), width = 0.5,  # Adjust position and width
                size = 0.5, color = "black") +  # Adjust error bar aesthetics
  labs(x = "ID", y = "Uptake", fill = "Nutrient",
       title = "Uptaken NOx and NH4_N of each treatment at PU2") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  scale_fill_manual(values = c("mean_NH4" = "#7CFC00", "mean_Nox" = "skyblue")) +  # Custom fill colors
  guides(fill = guide_legend(reverse = TRUE))  # Reverse legend order to match stack order

What should I change to make the error bar proper?
Your idea will be highly appreciated... thank you in advance!

2

position stack() will expand the error bars to 100% of height. position_dodge() does work But there is no need to stack the error bars f you calculate the cumulative means grouped by ID, like this:

library(tidyverse)

data_1_sub_tray_Pu2 <- data.frame(
  ID = sample(c("S", "S_BC", "S_BC_auEM", "S_EM", "S_EM_BC"), 100, replace = TRUE),
  Uptook_Nox = runif(100, 0, 1),
  Uptook_NH4_N = runif(100, 0, 1)
)
  
summary_stats_pu2 <- data_1_sub_tray_Pu2 %>%
  group_by(ID) %>%
  summarise(mean_Nox = mean(Uptook_Nox),
            mean_NH4 = mean(Uptook_NH4_N),
            se_Nox = sd(Uptook_Nox) / sqrt(n()),
            se_NH4 = sd(Uptook_NH4_N) / sqrt(n()))

plot_data_pu2 <- summary_stats_pu2 %>%
  pivot_longer(cols = c(mean_Nox, mean_NH4), names_to = "Nutrient", values_to = "Mean") %>%
  mutate(Error = ifelse(Nutrient == "mean_Nox", se_Nox, se_NH4),
         Nutrient = factor(Nutrient, levels = c("mean_NH4", "mean_Nox"))) %>% 
  arrange(ID, rev(Nutrient)) %>% 
  mutate(.by = ID, MeanCum = cumsum(Mean)) 

ggplot(plot_data_pu2, aes(x = ID, y = Mean, fill = Nutrient)) +
  geom_bar(stat = "identity", position = position_stack(), width = 0.7) +
  geom_errorbar(aes(ymin = MeanCum - Error, ymax = MeanCum + Error),
                width = 0.5, # Adjust position and width
                size = 0.5, color = "black") +
  labs(x = "ID", 
       y = "Uptake", 
       fill = "Nutrient",
       title = "Uptaken NOx and NH4_N of each treatment at PU2"
       ) +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  scale_fill_manual(values = c("mean_NH4" = "#7CFC00", "mean_Nox" = "skyblue")) + 
  guides(fill = guide_legend(reverse = TRUE))
1 Like
3

Hi @Sunah ,

Thank you for sharing the code you used — would you mind sharing the data as well so that it's easier for folks here to help? You can do that by first running:

dput(head(data_1_sub_tray_Pu2, 100))

and sharing the output here in a code block.