3d scatterplot with R

This post shows how to build a 3d scatterplot with R and the rgl package. It provides the reproducible code and makes it easy to apply it to your own dataset.

3d Section 3d: warning

Building a 3d scatterplot requires a dataset with 3 numeric variables, each being used on an axis. Here, the famous iris dataset is used.

The rgl package comes with the plot3d() function that is pretty close from the base R plot() function. Instead of providing just an x and a y argument, you also have to provide the z coordinate.

Note that the output is interactive by default. If you have X11 or a similar tool installed, you should be able to rotate the chart for a better user experience. A few command line are also provided in case you want to export the chart at .html, .png or .Rmd format.

# library

# This is to output a rgl plot in a rmarkdown document.
# setupKnitr()

# Data: the iris data is provided by R
data <- iris

# Add a new column with color
mycolors <- c('royalblue1', 'darkcyan', 'oldlace')
data$color <- mycolors[ as.numeric(data$Species) ]

# Plot
  x=data$`Sepal.Length`, y=data$`Sepal.Width`, z=data$`Petal.Length`, 
  col = data$color, 
  type = 's', 
  radius = .1,
  xlab="Sepal Length", ylab="Sepal Width", zlab="Petal Length")

# To display in an R Markdown document:
# rglwidget()

# To save to a file:
htmlwidgets::saveWidget(rglwidget(width = 520, height = 520), 
                        file = "HtmlWidget/3dscatter.html",
                        libdir = "libs",
                        selfcontained = FALSE

Related chart types

Data art


This document is a work by Yan Holtz. Any feedback is highly encouraged. You can fill an issue on Github, drop me a message on Twitter, or send an email pasting yan.holtz.data with gmail.com.

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