Articles - R Graphics Essentials

theme_set(
  theme_bw()
)

Data format

• Demo dataset: ToothGrowth
  • Continuous variable: len (tooth length). Used on y-axis
  • Grouping variable: dose (dose levels of vitamin C: 0.5, 1, and 2 mg/day). Used on x-axis.

First, convert the variable dose from a numeric to a discrete factor variable:

data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
head(ToothGrowth)

##    len supp dose
## 1  4.2   VC  0.5
## 2 11.5   VC  0.5
## 3  7.3   VC  0.5
## 4  5.8   VC  0.5
## 5  6.4   VC  0.5
## 6 10.0   VC  0.5

Box plots

• Key function: geom_boxplot()
• Key arguments to customize the plot:
  • width: the width of the box plot
  • notch: logical. If TRUE, creates a notched box plot. The notch displays a confidence interval around the median which is normally based on the median +/- 1.58*IQR/sqrt(n). Notches are used to compare groups; if the notches of two boxes do not overlap, this is a strong evidence that the medians differ.
  • color, size, linetype: Border line color, size and type
  • fill: box plot areas fill color
  • outlier.colour, outlier.shape, outlier.size: The color, the shape and the size for outlying points.

1. Create basic box plots:

• Standard and notched box plots:

# Default plot
e <- ggplot(ToothGrowth, aes(x = dose, y = len))
e + geom_boxplot()
# Notched box plot with mean points
e + geom_boxplot(notch = TRUE, fill = "lightgray")+
  stat_summary(fun.y = mean, geom = "point",
               shape = 18, size = 2.5, color = "#FC4E07")

• Change box plot colors by groups:

# Color by group (dose)
e + geom_boxplot(aes(color = dose))+
  scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))
# Change fill color by group (dose)
e + geom_boxplot(aes(fill = dose)) +
  scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))

Note that, it’s possible to use the function scale_x_discrete() for:

• choosing which items to display: for example c(“0.5”, “2”),
• changing the order of items: for example from c(“0.5”, “1”, “2”) to c(“2”, “0.5”, “1”)

For example, type this:

# Choose which items to display: group "0.5" and "2"
e + geom_boxplot() + 
  scale_x_discrete(limits=c("0.5", "2"))
# Change the default order of items
e + geom_boxplot() +
  scale_x_discrete(limits=c("2", "0.5", "1"))

2. Create a box plot with multiple groups:

Two different grouping variables are used: dose on x-axis and supp as fill color (legend variable).

The space between the grouped box plots is adjusted using the function position_dodge().

e2 <- e + geom_boxplot(
  aes(fill = supp),
  position = position_dodge(0.9) 
  ) +
  scale_fill_manual(values = c("#999999", "#E69F00"))
e2

Split the plot into multiple panel. Use the function facet_wrap():

e2 + facet_wrap(~supp)

Violin plots

Violin plots are similar to box plots, except that they also show the kernel probability density of the data at different values. Typically, violin plots will include a marker for the median of the data and a box indicating the interquartile range, as in standard box plots.

Key function:

• geom_violin(): Creates violin plots. Key arguments:
  • color, size, linetype: Border line color, size and type
  • fill: Areas fill color
  • trim: logical value. If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don’t trim the tails.
• stat_summary(): Adds summary statistics (mean, median, …) on the violin plots.

1. Create basic violin plots with summary statistics:

# Add mean points +/- SD
# Use geom = "pointrange" or geom = "crossbar"
e + geom_violin(trim = FALSE) + 
  stat_summary(
    fun.data = "mean_sdl",  fun.args = list(mult = 1), 
    geom = "pointrange", color = "black"
    )
    
# Combine with box plot to add median and quartiles
# Change color by groups
e + geom_violin(aes(fill = dose), trim = FALSE) + 
  geom_boxplot(width = 0.2)+
  scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))+
  theme(legend.position = "none")

2. Create violin plots with multiple groups:

e + geom_violin(
  aes(color = supp), trim = FALSE,
  position = position_dodge(0.9) 
  ) +
  geom_boxplot(
    aes(color = supp), width = 0.15,
    position = position_dodge(0.9)
    ) +
  scale_color_manual(values = c("#00AFBB", "#E7B800"))

Dot plots

• Key function: geom_dotplot(). Creates stacked dots, with each dot representing one observation.
• Key arguments:
  • stackdir: which direction to stack the dots. “up” (default), “down”, “center”, “centerwhole” (centered, but with dots aligned).
  • stackratio: how close to stack the dots. Default is 1, where dots just just touch. Use smaller values for closer, overlapping dots.
  • color, fill: Dot border color and area fill
  • dotsize: The diameter of the dots relative to binwidth, default 1.

As for violin plots, summary statistics are usually added to dot plots.

1. Create basic dot plots:

# Violin plots with mean points +/- SD
e + geom_dotplot(
  binaxis = "y", stackdir = "center",
  fill = "lightgray"
  ) + 
  stat_summary(
    fun.data = "mean_sdl", fun.args = list(mult=1), 
    geom = "pointrange", color = "red"
    )
# Combine with box plots
e + geom_boxplot(width = 0.5) + 
  geom_dotplot(
    binaxis = "y", stackdir = "center",
    fill = "white"
    ) 
# Dot plot + violin plot + stat summary
e + geom_violin(trim = FALSE) +
  geom_dotplot(
    binaxis='y', stackdir='center',
    color = "black", fill = "#999999"
    ) +
  stat_summary(
    fun.data="mean_sdl",  fun.args = list(mult=1), 
    geom = "pointrange", color = "#FC4E07", size = 0.4
    )

2. Create dot plots with multiple groups:

# Color dots by groups
e + geom_boxplot(width = 0.5, size = 0.4) +
  geom_dotplot(
    aes(fill = supp), trim = FALSE,
    binaxis='y', stackdir='center'
  )+
  scale_fill_manual(values = c("#00AFBB", "#E7B800"))
# Change the position : interval between dot plot of the same group
e + geom_boxplot(
  aes(color = supp), width = 0.5, size = 0.4,
  position = position_dodge(0.8)
  ) +
  geom_dotplot(
    aes(fill = supp, color = supp), trim = FALSE,
    binaxis='y', stackdir='center', dotsize = 0.8,
    position = position_dodge(0.8)
  )+
  scale_fill_manual(values = c("#00AFBB", "#E7B800"))+
  scale_color_manual(values = c("#00AFBB", "#E7B800"))

Stripcharts

Stripcharts are also known as one dimensional scatter plots. These plots are suitable compared to box plots when sample sizes are small.

• Key function: geom_jitter()
• key arguments: color, fill, size, shape. Changes points color, fill, size and shape

1. Create a basic stripchart:

• Change points shape and color by groups
• Adjust the degree of jittering: position_jitter(0.2)
• Add summary statistics:

e + geom_jitter(
  aes(shape = dose, color = dose), 
  position = position_jitter(0.2),
  size = 1.2
  ) +
  stat_summary(
    aes(color = dose),
    fun.data="mean_sdl",  fun.args = list(mult=1), 
    geom = "pointrange",  size = 0.4
    )+
  scale_color_manual(values =  c("#00AFBB", "#E7B800", "#FC4E07"))

2. Create stripcharts for multiple groups. The R code is similar to what we have seen in dot plots section. However, to create dodged jitter points, you should use the function position_jitterdodge() instead of position_dodge().

e + geom_jitter(
  aes(shape = supp, color = supp), 
  position = position_jitterdodge(jitter.width = 0.2, dodge.width = 0.8),
  size = 1.2
  ) +
  stat_summary(
    aes(color = supp),
    fun.data="mean_sdl",  fun.args = list(mult=1), 
    geom = "pointrange",  size = 0.4,
    position = position_dodge(0.8)
    )+
  scale_color_manual(values =  c("#00AFBB", "#E7B800"))

Sinaplot

sinaplot is inspired by the strip chart and the violin plot. By letting the normalized density of points restrict the jitter along the x-axis, the plot displays the same contour as a violin plot, but resemble a simple strip chart for small number of data points (Sidiropoulos et al. 2015).

In this way the plot conveys information of both the number of data points, the density distribution, outliers and spread in a very simple, comprehensible and condensed format.

Key function: geom_sina() [ggforce]:

library(ggforce)
# Create some data
d1 <- data.frame(
  y = c(rnorm(200, 4, 1), rnorm(200, 5, 2), rnorm(400, 6, 1.5)),
  group = rep(c("Grp1", "Grp2", "Grp3"), c(200, 200, 400))
  )
# Sinaplot
ggplot(d1, aes(group, y)) +
  geom_sina(aes(color = group), size = 0.7)+
  scale_color_manual(values =  c("#00AFBB", "#E7B800", "#FC4E07"))

Mean and median plots with error bars

In this section, we’ll show how to plot summary statistics of a continuous variable organized into groups by one or multiple grouping variables.

Note that, an easy way, with less typing, to create mean/median plots, is provided in the ggpubr package. See the associated article at: ggpubr-Plot Means/Medians and Error Bars

Set the default theme to theme_pubr() [in ggpubr]:

theme_set(ggpubr::theme_pubr())

1. Basic mean/median plots. Case of one continuous variable and one grouping variable:

• 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
##     
## 1    0.5  4.50  10.6
## 2      1  4.42  19.7
## 3      2  3.77  26.1

• Create error plots using the summary statistics data. Key functions:
  • 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:

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(aes(color = dose)) +
  geom_errorbarh(aes(color = dose), height=.2)+
  theme_light()

• 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_bar(stat = "identity", 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 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_bar(stat = "identity", 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) 

2. Mean/median plots for multiple groups. 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
##      
## 1    0.5     OJ  4.46 13.23
## 2    0.5     VC  2.75  7.98
## 3      1     OJ  3.91 22.70
## 4      1     VC  2.52 16.77
## 5      2     OJ  2.66 26.06
## 6      2     VC  4.80 26.14

• 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_bar(aes(fill = supp), stat = "identity",
           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"))

• Create easily plots of mean +/- sd for multiple groups. Use the ggpubr package, which will automatically calculate the summary statistics and create the graphs.

library(ggpubr)
# Create line plots of means
ggline(ToothGrowth, x = "dose", y = "len", 
       add = c("mean_sd", "jitter"),
       color = "supp", palette = c("#00AFBB", "#E7B800"))
# Create bar plots of means
ggbarplot(ToothGrowth, x = "dose", y = "len", 
          add = c("mean_se", "jitter"),
          color = "supp", palette = c("#00AFBB", "#E7B800"),
          position = position_dodge(0.8))

• Use the standard ggplot2 verbs, to reproduce the line plots above:

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

Add p-values and significance levels

In this section, we’ll describe how to easily i) compare means of two or multiple groups; ii) and to automatically add p-values and significance levels to a ggplot (such as box plots, dot plots, bar plots and line plots, …).

Key functions:

• compare_means() [ggpubr package]: easy to use solution to performs one and multiple mean comparisons.
• stat_compare_means() [ggpubr package]: easy to use solution to automatically add p-values and significance levels to a ggplot.

The most common methods for comparing means include:

Methods	R function	Description
T-test	t.test()	Compare two groups (parametric)
Wilcoxon test	wilcox.test()	Compare two groups (non-parametric)
ANOVA	aov() or anova()	Compare multiple groups (parametric)
Kruskal-Wallis	kruskal.test()	Compare multiple groups (non-parametric)

1. Compare two independent groups:

• Compute t-test:

library(ggpubr)
compare_means(len ~ supp, data = ToothGrowth,
              method = "t.test")

## # A tibble: 1 x 8
##     .y. group1 group2      p  p.adj p.format p.signif method
##                     
## 1   len     OJ     VC 0.0606 0.0606    0.061       ns T-test

• Create a box plot with p-values. Use the option method = "t.test" or method = "wilcox.test". Default is wilcoxon test.

# Create a simple box plot and add p-values
p <- ggplot(ToothGrowth, aes(supp, len)) +
  geom_boxplot(aes(color = supp)) +
  scale_color_manual(values = c("#00AFBB", "#E7B800"))
p + stat_compare_means(method = "t.test")
# Display the significance level instead of the p-value
# Adjust label position
p + stat_compare_means(
  aes(label = ..p.signif..), label.x = 1.5, label.y = 40
  )

2. Compare two paired samples. Use ggpaired() [ggpubr] to create the paired box plot.

ggpaired(ToothGrowth, x = "supp", y = "len",
         color = "supp", line.color = "gray", line.size = 0.4,
         palette = "jco")+
  stat_compare_means(paired = TRUE)

3. Compare more than two groups. If the grouping variable contains more than two levels, then pairwise tests will be performed automatically. The default method is “wilcox.test”. You can change this to “t.test”.

# Perorm pairwise comparisons
compare_means(len ~ dose,  data = ToothGrowth)

## # A tibble: 3 x 8
##     .y. group1 group2        p    p.adj p.format p.signif   method
##                           
## 1   len    0.5      1 7.02e-06 1.40e-05  7.0e-06     **** Wilcoxon
## 2   len    0.5      2 8.41e-08 2.52e-07  8.4e-08     **** Wilcoxon
## 3   len      1      2 1.77e-04 1.77e-04  0.00018      *** Wilcoxon

# Visualize: Specify the comparisons you want
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len",
          color = "dose", palette = "jco")+ 
  stat_compare_means(comparisons = my_comparisons)+ 
  stat_compare_means(label.y = 50)                   

4. Multiple grouping variables:

• (1/2). Create a multi-panel box plots facetted by group (here, “dose”):

# Use only p.format as label. Remove method name.
ggplot(ToothGrowth, aes(supp, len)) +
  geom_boxplot(aes(color = supp))+
  facet_wrap(~dose) +
  scale_color_manual(values = c("#00AFBB", "#E7B800")) +
  stat_compare_means(label = "p.format")

• (2/2). Create one single panel with all box plots. Plot y = “len” by x = “dose” and color by “supp”. Specify the option group in stat_compare_means():

ggplot(ToothGrowth, aes(dose, len)) +
  geom_boxplot(aes(color = supp))+
  scale_color_manual(values = c("#00AFBB", "#E7B800")) +
  stat_compare_means(aes(group = supp), label = "p.signif")

• Paired comparisons for multiple groups:

# Box plot facetted by "dose"
p <- ggpaired(ToothGrowth, x = "supp", y = "len",
          color = "supp", palette = "jco", 
          line.color = "gray", line.size = 0.4,
          facet.by = "dose", short.panel.labs = FALSE)
# Use only p.format as label. Remove method name.
p + stat_compare_means(label = "p.format", paired = TRUE)

Read more at: Add P-values and Significance Levels to ggplots