Data Visualization using GGPlot2

Loading required R package

Load the ggplot2 package and set the default theme to theme_classic() with the legend at the top of the plot:

library(ggplot2)
theme_set(
  theme_classic() +
    theme(legend.position = "top")
  )

Data preparation

• Prepare the data: ToothGrowth data set.

df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)

##    len supp dose
## 1  4.2   VC  0.5
## 2 11.5   VC  0.5
## 3  7.3   VC  0.5

• Compute summary statistics for the variable len organized into groups by the variable dose:

library(dplyr)
df.summary <- df %>%
  group_by(dose) %>%
  summarise(
    sd = sd(len, na.rm = TRUE),
    len = mean(len)
  )
df.summary

## # A tibble: 3 x 3
##   dose     sd   len
##   <fct> <dbl> <dbl>
## 1 0.5    4.50  10.6
## 2 1      4.42  19.7
## 3 2      3.77  26.1

Key R functions and error plot types

Key functions to create error plots using the summary statistics data:

• geom_crossbar() for hollow bar with middle indicated by horizontal line
• geom_errorbar() for error bars
• geom_errorbarh() for horizontal error bars
• geom_linerange() for drawing an interval represented by a vertical line
• geom_pointrange() for creating an interval represented by a vertical line, with a point in the middle.

Start by initializing ggplot with the summary statistics data:

• Specify x and y as usually
• Specify ymin = len-sd and ymax = len+sd to add lower and upper error bars. If you want only to add upper error bars but not the lower ones, use ymin = len (instead of len-sd) and ymax = len+sd.

# Initialize ggplot with data
f <- ggplot(
  df.summary, 
  aes(x = dose, y = len, ymin = len-sd, ymax = len+sd)
  )

Possible error plots:

Basic error bars

Create simple error plots:

# Vertical line with point in the middle
f + geom_pointrange()

# Standard error bars
f + geom_errorbar(width = 0.2) +
  geom_point(size = 1.5)

Create horizontal error bars. Put dose on y axis and len on x-axis. Specify xmin and xmax.

# Horizontal error bars with mean points
# Change the color by groups
ggplot(df.summary, aes(x = len, y = dose, xmin = len-sd, xmax = len+sd)) +
  geom_point() +
  geom_errorbarh(height=.2)

• Add jitter points (representing individual points), dot plots and violin plots. For this, you should initialize ggplot with original data (df) and specify the df.summary data in the error plot function, here geom_pointrange().

# Combine with jitter points
ggplot(df, aes(dose, len)) +
  geom_jitter(position = position_jitter(0.2), color = "darkgray") + 
  geom_pointrange(aes(ymin = len-sd, ymax = len+sd),data = df.summary)

# Combine with violin plots
ggplot(df, aes(dose, len)) +
  geom_violin(color = "darkgray", trim = FALSE) + 
  geom_pointrange(aes(ymin = len-sd, ymax = len+sd), data = df.summary)

• Create basic bar/line plots of mean +/- error. So we need only the df.summary data. :
  1. Add lower and upper error bars for the line plot: ymin = len-sd and ymax = len+sd.
  2. Add only upper error bars for the bar plot: ymin = len (instead of len-sd) and ymax = len+sd.

# (1) Line plot
ggplot(df.summary, aes(dose, len)) +
  geom_line(aes(group = 1)) +
  geom_errorbar( aes(ymin = len-sd, ymax = len+sd),width = 0.2) +
  geom_point(size = 2)

# (2) Bar plot
ggplot(df.summary, aes(dose, len)) +
  geom_col(fill = "lightgray", color = "black") +
  geom_errorbar(aes(ymin = len, ymax = len+sd), width = 0.2) 

For line plot, you might want to treat x-axis as numeric:

df.sum2 <- df.summary
df.sum2$dose <- as.numeric(df.sum2$dose)
ggplot(df.sum2, aes(dose, len)) +
  geom_line() +
  geom_errorbar( aes(ymin = len-sd, ymax = len+sd),width = 0.2) +
  geom_point(size = 2)

• Bar plots and line plots + jitter points. We need the original df data for the jitter points and the df.summary data for the other geom layers.
  1. For the line plot: First, add jitter points, then add lines + error bars + mean points on top of the jitter points.
  2. For the bar plot: First, add the bar plot, then add jitter points + error bars on top of the bars.

# (1) Create a line plot of means + 
# individual jitter points + error bars 
ggplot(df, aes(dose, len)) +
  geom_jitter( position = position_jitter(0.2), color = "darkgray") + 
  geom_line(aes(group = 1), data = df.summary) +
  geom_errorbar(
    aes(ymin = len-sd, ymax = len+sd),
    data = df.summary, width = 0.2) +
  geom_point(data = df.summary, size = 2)

# (2) Bar plots of means + individual jitter points + errors
ggplot(df, aes(dose, len)) +
  geom_col(data = df.summary, fill = NA, color = "black") +
  geom_jitter( position = position_jitter(0.2), color = "black") + 
  geom_errorbar( aes(ymin = len-sd, ymax = len+sd), 
                 data = df.summary, width = 0.2) 

Grouped error bars

Case of one continuous variable (len) and two grouping variables (dose, supp).

• Compute the summary statistics of len grouped by dose and supp:

library(dplyr)
df.summary2 <- df %>%
  group_by(dose, supp) %>%
  summarise(
    sd = sd(len),
    len = mean(len)
  )
df.summary2

## # A tibble: 6 x 4
## # Groups:   dose [?]
##   dose  supp     sd   len
##   <fct> <fct> <dbl> <dbl>
## 1 0.5   OJ     4.46 13.2 
## 2 0.5   VC     2.75  7.98
## 3 1     OJ     3.91 22.7 
## 4 1     VC     2.52 16.8 
## 5 2     OJ     2.66 26.1 
## 6 2     VC     4.80 26.1

• Create error plots for multiple groups:
  1. pointrange colored by groups (supp)
  2. standard error bars + mean points colored by groups (supp)

# (1) Pointrange: Vertical line with point in the middle
ggplot(df.summary2, aes(dose, len)) +
  geom_pointrange(
    aes(ymin = len-sd, ymax = len+sd, color = supp),
    position = position_dodge(0.3)
    )+
  scale_color_manual(values = c("#00AFBB", "#E7B800"))


# (2) Standard error bars
ggplot(df.summary2, aes(dose, len)) +
  geom_errorbar(
    aes(ymin = len-sd, ymax = len+sd, color = supp),
    position = position_dodge(0.3), width = 0.2
    )+
  geom_point(aes(color = supp), position = position_dodge(0.3)) +
  scale_color_manual(values = c("#00AFBB", "#E7B800")) 

• Create simple line/bar plots for multiple groups.
  1. Line plots: change linetype by groups (supp)
  2. Bar plots: change fill color by groups (supp)

# (1) Line plot + error bars
ggplot(df.summary2, aes(dose, len)) +
  geom_line(aes(linetype = supp, group = supp))+
  geom_point()+
  geom_errorbar(
    aes(ymin = len-sd, ymax = len+sd, group = supp),
     width = 0.2
    )

# (2) Bar plots + upper error bars.
ggplot(df.summary2, aes(dose, len)) +
  geom_col(aes(fill = supp), position = position_dodge(0.8), width = 0.7)+
  geom_errorbar(
    aes(ymin = len, ymax = len+sd, group = supp),
    width = 0.2, position = position_dodge(0.8)
    )+
  scale_fill_manual(values = c("grey80", "grey30"))

• Add jitter points:

# Line plots with jittered points
ggplot(df, aes(dose, len, color = supp)) +
  geom_jitter(position = position_jitter(0.2)) + 
  geom_line(aes(group = supp),data = df.summary2) +
  geom_errorbar(aes(ymin = len-sd, ymax = len+sd), data = df.summary2, width = 0.2)+
  scale_color_manual(values = c("#00AFBB", "#E7B800")) +
  theme(legend.position = "top")

# Bar plots + jittered points + error bars
ggplot(df, aes(dose, len, color = supp)) +
  geom_col(data = df.summary2, position = position_dodge(0.8), 
           width = 0.7, fill = "white") +
  geom_jitter(
    position = position_jitterdodge(jitter.width = 0.2, dodge.width = 0.8)
    ) + 
  geom_errorbar(
    aes(ymin = len-sd, ymax = len+sd), data = df.summary2, 
    width = 0.2, position = position_dodge(0.8)
    )+
  scale_color_manual(values = c("#00AFBB", "#E7B800")) +
  theme(legend.position = "top")

Conclusion

This article describes how to add error bars to plots created using the ggplot2 R package.