A Scatter plot (also known as X-Y plot or Point graph) is used to display the relationship between two continuous variables x and y.
By displaying a variable in each axis, it is possible to determine if an association or a correlation exists between the two variables.
The correlation can be: positive (values increase together), negative (one value decreases as the other increases), null (no correlation), linear, exponential and U-shaped.
This article describes how to create scatter plots in R using the ggplot2 package.
You will learn how to:
- Color points by groups
- Create bubble charts
- Add regression line to a scatter plot
mtcars. The variable
cyl is used as grouping variable.
# Load data data("mtcars") df <- mtcars # Convert cyl as a grouping variable df$cyl <- as.factor(df$cyl) # Inspect the data head(df[, c("wt", "mpg", "cyl", "qsec")], 4)
## wt mpg cyl qsec ## Mazda RX4 2.62 21.0 6 16.5 ## Mazda RX4 Wag 2.88 21.0 6 17.0 ## Datsun 710 2.32 22.8 4 18.6 ## Hornet 4 Drive 3.21 21.4 6 19.4
Loading required R package
Load the ggplot2 package and set the default theme to
theme_bw() with the legend at the top of the plot:
library(ggplot2) theme_set( theme_bw() + theme(legend.position = "top") )
Basic scatter plots
- Key functions:
geom_point()for creating scatter plots.
- Key arguments:
shapeto change point color, size and shape.
# Initiate a ggplot b <- ggplot(df, aes(x = wt, y = mpg)) # Basic scatter plot b + geom_point() # Change color, shape and size b + geom_point(color = "#00AFBB", size = 2, shape = 23)
The different point shapes commonly used in R, include:
Scatter plots with multiple groups
This section describes how to change point colors and shapes by groups. The functions
scale_shape_manual() are used to manually customize the color and the shape of points, respectively.
In the R code below, point shapes and colors are controlled by the levels of the grouping variable cyl :
# Change point shapes by the levels of cyl b + geom_point(aes(shape = cyl)) # Change point shapes and colors by the levels of cyl # Set custom colors b + geom_point(aes(shape = cyl, color = cyl)) + scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))
Add regression lines
- Key R function:
geom_smooth()for adding smoothed conditional means / regression line.
- Key arguments:
linetype: Change the line color, size and type.
fill: Change the fill color of the confidence region.
A simplified format of the function `geom_smooth():
geom_smooth(method="auto", se=TRUE, fullrange=FALSE, level=0.95)
- method : smoothing method to be used. Possible values are lm, glm, gam, loess, rlm.
- method = “loess”: This is the default value for small number of observations. It computes a smooth local regression. You can read more about loess using the R code ?loess.
- method =“lm”: It fits a linear model. Note that, it’s also possible to indicate the formula as formula = y ~ poly(x, 3) to specify a degree 3 polynomial.
- se : logical value. If TRUE, confidence interval is displayed around smooth.
- fullrange : logical value. If TRUE, the fit spans the full range of the plot
- level : level of confidence interval to use. Default value is 0.95
To add a regression line on a scatter plot, the function
geom_smooth() is used in combination with the argument
method = lm.
lm stands for linear model.
# Add regression line b + geom_point() + geom_smooth(method = lm) # Point + regression line # Remove the confidence interval b + geom_point() + geom_smooth(method = lm, se = FALSE) # loess method: local regression fitting b + geom_point() + geom_smooth()
Change point color and shapes by groups:
# Change color and shape by groups (cyl) b + geom_point(aes(color = cyl, shape=cyl)) + geom_smooth(aes(color = cyl, fill = cyl), method = lm) + scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))+ scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07")) # Remove confidence intervals # Extend the regression lines: fullrange b + geom_point(aes(color = cyl, shape = cyl)) + geom_smooth(aes(color = cyl), method = lm, se = FALSE, fullrange = TRUE) + scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))+ scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))
Add marginal rugs to a scatter plot
geom_rug() is used to display display individual cases on the plot.
# Add marginal rugs b + geom_point() + geom_rug() # Change colors by groups b + geom_point(aes(color = cyl)) + geom_rug(aes(color = cyl)) # Add marginal rugs using faithful data data(faithful) ggplot(faithful, aes(x = eruptions, y = waiting)) + geom_point() + geom_rug()
Jitter points to reduce overplotting
mpg data set [in ggplot2] is used in the following examples.
To reduce overplotting, the option
position = position_jitter() with the arguments width and height are used:
- width: degree of jitter in x direction.
- height: degree of jitter in y direction.
# Default plot ggplot(mpg, aes(displ, hwy)) + geom_point() # Use jitter to reduce overplotting ggplot(mpg, aes(displ, hwy)) + geom_point(position = position_jitter(width = 0.5, height = 0.5))
Add point text labels
geom_label(): ggplot2 standard functions to add text to a plot.
geom_label_repel()[in ggrepel package]. Repulsive textual annotations. Avoid text overlapping.
ìnstall.packages("ggrepel")), then type this:
library(ggrepel) # Add text to the plot .labs <- rownames(df) b + geom_point(aes(color = cyl)) + geom_text_repel(aes(label = .labs, color = cyl), size = 3)+ scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))
# Draw a rectangle underneath the text, making it easier to read. b + geom_point(aes(color = cyl)) + geom_label_repel(aes(label = .labs, color = cyl), size = 3)+ scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))
In a bubble chart, points
size is controlled by a continuous variable, here
qsec. In the R code below, the argument alpha is used to control color transparency. alpha should be between 0 and 1.
b + geom_point(aes(color = cyl, size = qsec), alpha = 0.5) + scale_color_manual(values = c("#00AFBB", "#E7B800", "#FC4E07")) + scale_size(range = c(0.5, 12)) # Adjust the range of points size
Color by a continuous variable
- Color points according to the values of the continuous variable: “mpg”.
- Change the default blue gradient color using the function
scale_color_gradientn()[in ggplot2], by specifying two or more colors.
b + geom_point(aes(color = mpg), size = 3) + scale_color_gradientn(colors = c("#00AFBB", "#E7B800", "#FC4E07")) + theme(legend.position = "right")
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