How To Annotate Clusters with Circle/Ellipse by a Variable in R ggplot2

In this article, we will discuss how to annotate Clusters with Circle/Ellipse by a categorical variable in the R Programming Language using the ggplot2 package.

To add a circle or ellipse around a cluster of data points, we use the geom_mark_circle() and geom_mark_ellipse() function of the ggforce package. This function automatically computes the circle/ellipse radius to draw around the cluster of points by categorical data.

First, we will plot the data in a scatter plot using the geom_point function of the ggplot2 package. We will use the color parameter of the aes() function to color the plot by a categorical variable group.

Syntax:

ggplot(df, aes( x, y ) ) + geom_point( aes( color ))

Arguments:

• df: determines the data frame to be used.
• x and y: determine the x-axis and y-axis variables respectively.
• color: determines the categorical variable for coloring the data point clusters.

Example:

Here, is a basic scatter plot made using the geom_point() function of the ggplot2 package. We have colored the plot by the categorical variable group.

R

# load library tidyverse
library(tidyverse)

# set theme
theme_set(theme_bw(16))

# create x and y vector
xAxis <- rnorm(1000)
yAxis <- rnorm(1000) + xAxis + 10

# create groups in variable using conditional
# statements
group <- rep(1, 1000)
group[xAxis > -1.5] <- 2
group[xAxis > -0.5] <- 3
group[xAxis > 0.5] <- 4
group[xAxis > 1.5] <- 5

# create sample data frame
sample_data <- data.frame(xAxis, yAxis, group)

# create a scatter plot with points colored by
# group
ggplot(sample_data, aes(x = xAxis,
             y = yAxis))+
  geom_point(aes(color = as.factor(group)))

Output:

Annotate circles around cluster:

To annotate a circle around a cluster of points by the group we use the geom_mark_circle() function of the ggforce package. To use this function we first install & import the ggforce package by using:

install. packages('ggforce')
library(ggforce)

Now, we will annotate the circle around a cluster of data points by using the geom_mark_circle() function.

Syntax:

ggplot(df, aes( x, y ) ) + geom_point( aes( color )) + geom_mark_circle( aes(color) )

Example:

Here, is a basic scatter plot with circles around a cluster of data points colored by a categorical variable group.

R

# load library tidyverse
library(tidyverse)
library(ggforce)

# set theme
theme_set(theme_bw(16))

# create x and y vector
xAxis <- rnorm(500)
yAxis <- rnorm(1000) + xAxis + 10

# create groups in variable using conditional
# statements
group <- rep(1, 500)
group[xAxis > -1.5] <- 2
group[xAxis > -0.5] <- 3
group[xAxis > 0.5] <- 4
group[xAxis > 1.5] <- 5

# create sample data frame
sample_data <- data.frame(xAxis, yAxis, group)

# create a scatter plot with points colored by group
# circles are annotated using geom_mark_circle() function
ggplot(sample_data, aes(x = xAxis,
             y = yAxis))+
  geom_point(aes(color = as.factor(group)))+
  geom_mark_circle(aes(color = as.factor(group)), expand = unit(0.5,"mm"))+
  theme(legend.position = "none")

Output:

Annotate ellipses around cluster:

To annotate an ellipse around a cluster of points by the group we use the geom_mark_ellipse() function of the ggforce package. This function automatically computes the dimensions of the ellipse and overlays it on top of the scatter plot.

Syntax:

ggplot(df, aes( x, y ) ) + geom_point( aes( color )) + geom_mark_ellipse( aes(color) )

Example:

Here, is a basic scatter plot with ellipses around a cluster of data points colored by a categorical variable group.

R

# load library tidyverse
library(tidyverse)
library(ggforce)

# set theme
theme_set(theme_bw(16))

# create x and y vector
xAxis <- rnorm(500)
yAxis <- rnorm(1000) + xAxis + 10

# create groups in variable using conditional
# statements
group <- rep(1, 500)
group[xAxis > -1.5] <- 2
group[xAxis > -0.5] <- 3
group[xAxis > 0.5] <- 4
group[xAxis > 1.5] <- 5

# create sample data frame
sample_data <- data.frame(xAxis, yAxis, group)

# create a scatter plot with points colored by group
# ellipses are annotated using geom_mark_ellipse() function
ggplot(sample_data, aes(x = xAxis,
             y = yAxis))+
  geom_point(aes(color = as.factor(group)))+
  geom_mark_ellipse(aes(color = as.factor(group)), expand = unit(0.5,"mm"))+
  theme(legend.position = "none")

Output:

Customizing the aesthetics

We can customize the aesthetics of the geom_mark_* function by using the color, fill, and alpha property of the aes() function. 

Syntax:

ggplot(df, aes( x, y ) ) + geom_point( aes( color )) + geom_mark_ellipse( aes(color, fill, alpha) )

where,

• color: determines the color of the boundary of the circles or ellipses.
• fill: determines the background color of the circles or ellipses.
• alpha: determines the transparency of the circles or ellipses.

Example:

In this example, we will plot a  scatter plot overlayed by ellipses with a background colored by the group categorical variable.

R

# load library tidyverse
library(tidyverse)
library(ggforce)

# set theme
theme_set(theme_bw(16))

# create x and y vector
xAxis <- rnorm(500)
yAxis <- rnorm(1000) + xAxis + 10

# create groups in variable using conditional
# statements
group <- rep(1, 500)
group[xAxis > -1.5] <- 2
group[xAxis > -0.5] <- 3
group[xAxis > 0.5] <- 4
group[xAxis > 1.5] <- 5

# create sample data frame
sample_data <- data.frame(xAxis, yAxis, group)

# create a scatter plot with points colored by group
# ellipses are annotated using geom_mark_ellipse() function
ggplot(sample_data, aes(x = xAxis,
             y = yAxis))+
  geom_point(aes(color = as.factor(group)))+
  geom_mark_ellipse(aes(fill = as.factor(group)), expand = unit(0.5,"mm"))+
  theme(legend.position = "none")

Output: