Figure with error bar and significant markers based on ggplot2

Create the data set

library(ggplot2)
df <- data.frame(treatment = factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3)), response = c(2, 5, 4, 6, 9, 7, 3, 5, 8),group = factor(c(1, 2, 3, 1, 2, 3, 1, 2, 3)),se = c(0.4, 0.2, 0.4, 0.5, 0.3, 0.2, 0.4, 0.6, 0.7))

head(df)

##   treatment response group  se
## 1         1        2     1 0.4
## 2         1        5     2 0.2
## 3         1        4     3 0.4
## 4         2        6     1 0.5
## 5         2        9     2 0.3
## 6         2        7     3 0.2

use geom_errorbar() to draw the histogram

# position should consistent with geom_bar(), because the default setting is 0.9, so we should set the value as 0.9 for geom_errorbar.
ggplot(data=df, aes(x = treatment, y = response, fill = group)) +
  geom_bar(stat = "identity", position = "dodge") +
  geom_errorbar(aes(ymax = response +se, ymin = response-se), position = position_dodge(0.9), width = 0.15) +
  scale_fill_brewer(palette = "Set1")

add significant mark, compared with group 1

label <- c("", "*", "**", "", "**", "*", "", "", "*") 

ggplot(data = df, aes(x = treatment, y = response, fill = group)) + 
geom_bar(stat = "identity", position = "dodge") + 
geom_errorbar(aes(ymax = response + se, ymin = response -  se), 
position = position_dodge(0.9), width = 0.15) + 
geom_text(aes(y = response +  1.5 * se, label = label, group = group), 
position = position_dodge(0.9), size = 5, fontface = "bold") + 
scale_fill_brewer(palette = "Set1")

arrange a set of figure

library(ggpubr)
# 将四幅图放置于一个页面中
p <- ggplot(data = df, aes(x = treatment, y = response, fill = group)) + 
geom_bar(stat = "identity", position = "dodge") + 
geom_errorbar(aes(ymax = response + se, ymin = response -  se), 
position = position_dodge(0.9), width = 0.15) + 
scale_fill_brewer(palette = "Set1")
p1 <- p + ggtitle("add title")
p2 <- p + ggtitle("add title") + xlab("treatment") + ylab("response")
p3 <- ggplot(data = df, aes(x = treatment, y = response, fill = group)) + 
geom_bar(stat = "identity", position = "dodge") + 
geom_errorbar(aes(ymax = response + se, ymin = response -  se), 
position = position_dodge(0.9), width = 0.15) + 
geom_text(aes(y = response +  1.5 * se, label = label, group = group), 
position = position_dodge(0.9), size = 5, fontface = "bold") + 
scale_fill_brewer(palette = "Set1")
ggarrange(p, p1, p2, p3)

Last modified on 2018-07-19