Understanding rgl-Output in bookdown-html and Its Limitations

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In this article, we will delve into the world of R’s graphics output system, specifically focusing on the rgl package. We’ll explore how to use rgl output within single-file bookdown documents and discuss a common issue with rotating plots.

Introduction to rgl-Output in bookdown-html

Bookdown is an R package that allows us to create HTML documents from R Markdown files. One of the benefits of using Bookdown is its ability to incorporate various graphics output systems, such as rgl, within our documents.

For this article, we will examine how to use rgl output in bookdown-html and discuss a specific issue with rotating plots.

What is rgl?

The rgl package is an R graphics package for 3D visualization. It provides a variety of functions for creating 3D plots, including plot3d, which we’ll be using extensively in this article.

Setting Up the Environment

To get started with rgl output in bookdown-html, we need to ensure that our environment is properly set up. Here’s how you can do it:

# Install required packages
install.packages("bookdown")
install.packages("knitr")
install.packages("rgl")

# Load necessary libraries
library(bookdown)
library(knitr)
library(rgl)

Using rgl-Output in bookdown-html

Let’s create a minimal example of using rgl output within a single-file bookdown document.

---
output: bookdown::html_document2
---

# Introduction to rgl-Output

In this article, we will explore how to use `rgl` output in bookdown-html and discuss a specific issue with rotating plots.

Creating a 3D Plot with rgl

Now that our environment is set up, let’s create a simple 3D plot using the plot3d function from the rgl package.

## Load necessary libraries
library(knitr)
library(rgl)

## Create a 3D plot
with(iris, plot3d(Sepal.Length, Sepal.Width, Petal.Length,
                  type="s", col=as.numeric(Species)))

As you can see, this code creates a simple 3D scatterplot of the Sepal.Length, Sepal.Width, and Petal.Length variables from the built-in iris dataset.

Using rgl-Output in bookdown-html

Now that we’ve created our 3D plot, let’s wrap it within a single-file bookdown document using the bookdown::html_document2 output.

---
output: bookdown::html_document2
---

# Introduction to rgl-Output

In this article, we will explore how to use `rgl` output in bookdown-html and discuss a specific issue with rotating plots.

Rotating 3D Plots with rgl-Output

Now that our environment is set up and we’ve created a simple 3D plot using rgl, let’s examine the rotation functionality.

Rotating the Plot with webgl

By default, Bookdown uses the webgl hook to render 3D plots. However, when using the webgl hook, rotating the plot doesn’t work properly.

## Load necessary libraries
library(knitr)
library(rgl)

# Create a 3D plot that rotates with webgl
with(iris, 
     knit_hooks$set(webgl = hook_webgl))
plot3d(Sepal.Length, Sepal.Width, Petal.Length,
        type="s", col=as.numeric(Species))

In this example, we create a 3D scatterplot using the plot3d function from the rgl package. We then set up the webgl hook to render the plot. However, when we rotate the plot, it doesn’t work properly.

Conclusion

In this article, we explored how to use rgl output in bookdown-html and discussed a specific issue with rotating plots. By understanding how to create 3D plots using rgl, we can leverage its capabilities within our Bookdown documents. However, when using the webgl hook, rotating the plot doesn’t work properly.

Troubleshooting

If you’re experiencing issues with rotating your 3D plot, there are a few things you can try:

• Check that your graphics drivers are up to date and functioning properly.
• Try rendering your 3D plot in a different output format, such as PDF or EPUB.
• Experiment with different webgl hooks, such as the plotly hook, to see if rotating works better.

Further Reading

For more information on using rgl and Bookdown, we recommend checking out the following resources:

• The Bookdown documentation.
• The rgl documentation.

By following these tips and experimenting with different graphics output systems, you can create beautiful and interactive 3D plots within your Bookdown documents.

Last modified on 2023-08-11