Amazing interactive 3D scatter plots - R software and data visualization


I recently posted an article describing how to make easily a 3D scatter plot in R using the package scatterplot3d.

This R tutorial describes how to perform an interactive 3d graphics using R software and the function scatter3d from the package car.

The function scatter3d() uses the rgl package to draw and animate 3D scatter plots.

3d scatter plot rgl

Install and load required packages

The packages rgl and car are required for this tutorial:

install.packages(c("rgl", "car"))

Note that, on Linux operating system, the rgl package can be installed as follow:

sudo apt-get install r-cran-rgl


Load the packages:

library("car")

Prepare the data

We’ll use the iris data set in the following examples :

data(iris)
head(iris)
  Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1          5.1         3.5          1.4         0.2  setosa
2          4.9         3.0          1.4         0.2  setosa
3          4.7         3.2          1.3         0.2  setosa
4          4.6         3.1          1.5         0.2  setosa
5          5.0         3.6          1.4         0.2  setosa
6          5.4         3.9          1.7         0.4  setosa
sep.l <- iris$Sepal.Length
sep.w <- iris$Sepal.Width
pet.l <- iris$Petal.Length

iris data set gives the measurements of the variables sepal length and width, petal length and width, respectively, for 50 flowers from each of 3 species of iris. The species are Iris setosa, versicolor, and virginica.

The function scatter3d

The simplified formats are:

scatter3d(formula, data)
scatter3d(x, y, z)

  • x, y, z are respectively the coordinates of points to be plotted. The arguments y and z can be optional depending on the structure of x.
  • formula: a model formula of form y ~ x + z. If you want to plot the points by groups, you can use y ~ x + z | g where g is a factor dividing the data into groups
  • data: data frame within which to evaluate the formula


Basic 3D scatter plots

library(car)
# 3D plot with the regression plane
scatter3d(x = sep.l, y = pet.l, z = sep.w)

Scatter3d - R software and data visualization

Note that, the plot can be manually rotated by holding down on the mouse or touchpad. It can be also zoomed using the scroll wheel on a mouse or pressing ctrl + using the touchpad on a PC or two fingers (up or down) on a mac.

Change point colors and remove the regression surface:

scatter3d(x = sep.l, y = pet.l, z = sep.w,
        point.col = "blue", surface=FALSE)

Scatter3d - R software and data visualization

Plot the points by groups

Default plot

scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species)

Scatter3d - R software and data visualization

Remove the surfaces

  • To remove the grids only, the argument grid = FALSE can be used as follow:
scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          grid = FALSE)

Scatter3d - R software and data visualization

Note that, the display of the surface(s) can be changed using the argument fit. Possible values for fit are “linear”, “quadratic”, “smooth” and “additive”

scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          grid = FALSE, fit = "smooth")

Scatter3d - R software and data visualization

  • Remove surfaces. The argument surface = FALSE is used.
scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          grid = FALSE, surface = FALSE)

Scatter3d - R software and data visualization

Add concentration ellipsoids

scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          surface=FALSE, ellipsoid = TRUE)

Scatter3d - R software and data visualization

Remove the grids from the ellipsoids:

scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          surface=FALSE, grid = FALSE, ellipsoid = TRUE)

Scatter3d - R software and data visualization

Change point colors by groups

The argument surface.col is used. surface.col is a vector of colors for the regression planes.

For multi-group plots, the colors are used for the regression surfaces and for the points in the several groups.

scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          surface=FALSE, grid = FALSE, ellipsoid = TRUE,
          surface.col = c("#999999", "#E69F00", "#56B4E9"))

Scatter3d - R software and data visualization

Read more about colors in R: colors in R

It’s also possible to use color palettes from the RColorBrewer package:

library("RColorBrewer")
colors <- brewer.pal(n=3, name="Dark2")
scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          surface=FALSE, grid = FALSE, ellipsoid = TRUE,
          surface.col = colors)

Scatter3d - R software and data visualization

Axes

Change axis labels:

The arguments xlab, ylab and zlab are used:

scatter3d(x = sep.l, y = pet.l, z = sep.w,
        point.col = "blue", surface=FALSE,
        xlab = "Sepal Length (cm)", ylab = "Petal Length (cm)",
        zlab = "Sepal Width (cm)")

Scatter3d - R software and data visualization

Remove axis scales

axis.scales = FALSE

scatter3d(x = sep.l, y = pet.l, z = sep.w,
        point.col = "blue", surface=FALSE, 
        axis.scales = FALSE)

Scatter3d - R software and data visualization

Change axis colors

By default, different colors are used for the 3 axes. The argument axis.col is used to specify colors for the 3 axes:

scatter3d(x = sep.l, y = pet.l, z = sep.w, groups = iris$Species,
          surface=FALSE, grid = FALSE, ellipsoid = TRUE,
          axis.col = c("black", "black", "black"))

Scatter3d - R software and data visualization

Add text labels for the points

The arguments below are used:

  • labels: text labels for the points, one for each point
  • id.n: Number of relatively extreme points to identify automatically
scatter3d(x = sep.l, y = pet.l, z = sep.w, 
          surface=FALSE, labels = rownames(iris), id.n=nrow(iris))

Scatter3d - R software and data visualization

Export images

The plot can be saved as png or pdf.

  • The function rgl.snapshot() is used to save the screenshot as png file:
rgl.snapshot(filename = "plot.png")
  • The function rgl.postscript() is used to saves the screenshot to a file in ps, eps, tex, pdf, svg or pgf format:
rgl.postscript("plot.pdf",fmt="pdf")

See also

The function Identify3d()[ car package] allows to label points interactively with the mouse.

Infos

This analysis has been performed using R software (ver. 3.1.2) and car (ver. 2.0-25)


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