rgl Overview

About this document

This document was written in R Markdown, using the knitr package for production. It corresponds to rgl version 1.3.15.

Most of the highlighted function names are HTML links. The internal links should work in any browser; the links to help topics should work if you view the vignette from within the R help system.

The document includes WebGL figures. To view these, you must have Javascript and WebGL enabled in your browser. Some older browsers may not support this – see https://get.webgl.org for tests and links to a discussion.

Primitive shapes

Just as we have points and lines in classic graphics, there are a number of low level functions in rgl to add graphical elements to the currently active plot. The “primitive” shapes are those that are native to OpenGL:

Each of the above functions takes arguments x, y and z, again using xyz.coords for flexibility. They group successive entries as necessary. For example, the triangles3d function takes each successive triple of points as the vertices of a triangle.

You can use these functions to annotate the current graph, or to construct a figure from scratch.

Constructed shapes

rgl also has a number of objects which it constructs from the primitives.

Axes and other “decorations”

The following low-level functions control the look of the graph:

For example, to plot three random triangles, one could use

triangles3d(cbind(x=rnorm(9), y=rnorm(9), z=rnorm(9)), col = "green")
decorate3d()
bg3d("lightgray")

aspect3d(1,1,1)

Besides the *3d functions mentioned above, there are deprecated functions rgl.abclines, rgl.bbox, rgl.bg, rgl.clipplanes, rgl.lines, rgl.linestrips, rgl.planes, rgl.points, rgl.primitive, rgl.quads, rgl.setAxisCallback, rgl.spheres, rgl.sprites, rgl.surface, rgl.texts, rgl.triangles. You should avoid using all of these functions, which do not work properly with the *3d functions and will soon be removed from rgl. See the ?r3d help topic for details.

The function rgl.getAxisCallback provides low-level support for setAxisCallbacks.

Camera angle

By default when you open a new plot with open3d:

• The x axis goes from left to right.
• The y axis goes from near the camera to far away.
• The z axis goes from down to up.

You can change the camera angle simply by dragging the picture with the mouse.

To set the camera angle programmatically, use view3d. This uses polar coordinates:

• theta sets the rotation around the vertical axis, in degrees.
• phi sets the “vertical” rotation around the horizontal axis, from -90 to 90 degrees.

The default angle is roughly theta = 0, phi = -70. Starting from this position:

• As you increase theta, the graph will spin anticlockwise from your point of view.
• As you increase phi to 0, you start to look down at the scene from the top. If you increase phi above 0, you continue over and start to see the graph from the “back” (and upside down).

You can also use observer3d to change the camera location using x,y,z coordinates. In particular, increasing the z coordinate lets you zoom out, and decreasing it zooms you in.

One useful approach is to use the mouse to find a nice viewing angle. You can then save it using par3d("userMatrix") and restore the same view later:

myview <- par3d("userMatrix")
# ... later ...
par3d(userMatrix = myview)

Lighting

In most scenes, objects are “lit”, meaning that their appearance depends on their position and orientation relative to lights in the scene. The lights themselves don’t normally show up, but their effect on the objects does.

Use the light3d function to specify the position and characteristics of a light. Lights may be infinitely distant, or may be embedded within the scene. Their characteristics include ambient, diffuse, and specular components, all defaulting to white. The ambient component appears the same from any direction. The diffuse component depends on the angle between the surface and the light, while the specular component also takes the viewer’s position into account.

The deprecated rgl.light function should no longer be used; use light3d instead.

Materials

The mental model used in rgl is that the objects being shown in scenes are physical objects in space, with material properties that affect how light reflects from them (or is emitted by them). These are mainly controlled by the material3d function, or by arguments to other functions that are passed to it.

The material properties that are recognized in calls to material3d are described in detail in the ?material3d help page, and listed in the rgl.material.names variable. All of them can be set except the ones in rgl.material.readonly. Here we give an overview.

Other properties include “texmipmap”, “texmagfilter”, “texminfilter”, “texenvmap”, “fog”, “point_antialias”, “line_antialias”, “depth_mask”, “depth_test”, “polygon_offset”, “margin”, “floating”, “tag” and “blend”; see the help page for details.

There is also a deprecated rgl.material function that works at a lower level; users should avoid it.

Textures

As described in the previous section, one of the material properties is texture, the name of a bitmap file (in .png format) containing an image to be displayed on the surface. This section gives more details about textures.

In OpenGL, each vertex in a polygon may be associated with a particular location in the bitmap. The interior of the polygon interpolates within the bitmap. There are two conventions in rgl functions for specifying these coordinates.

Functions which specify primitives (triangles3d, etc.) accept an optional matrix argument texcoords which gives s (horizontal) and t (vertical) locations within the bitmap in columns with one row per vertex. The coordinates are (0,0) for the lower left, and (1,1) for the upper right. If values outside this range are given, the image repeats, i.e. (1.1, 1.2) would specify the same point in the image as (0.1, 0.2).

Other functions such as surface3d that take matrices for each vertex coordinate accept texture coordinates as matrices as well, in arguments texture_s and texture_t.

For example, the following code displays four copies of a 2D plot on a quad, because the texture coordinates run from 0 to 2 in both s and t:

filename <- tempfile(fileext = ".png")
png(filename = filename)
plot(rnorm(1000), rnorm(1000))
safe.dev.off()

## png 
##   2

open3d()

## null 
##   59

xyz <- cbind(c(0,1,1,0), 0, c(0,0,1,1))
quads3d(xyz, texture = filename, texcoords = xyz[,c(1, 3)]*2, 
        col = "white", specular = "black")

Some other notes:

• The color in quads3d() above was specified to be white. By default, the colors in the bitmap will modify the color of the surface. If col is black (a common default), you won’t see anything, so a warning may be issued.
  
• You usually don’t want specular reflections (which show up as glare). Setting specular to black prevents those.
• The material property "texmode" allows texture colors to be used differently. The default is "modulate", where the texture values combine multiplicatively with the underlying values.
• Another aspect of how the bitmap is handled is controlled by the material property "textype". The default is "rgb", which takes the red-green-blue colors from the bitmap and uses them to modify the corresponding colors in the polygon.
  
• Other possibilities for "textype" and "texmode" are described in the material3d help page.
• The other "tex*" material properties control how the interpolation within the image is done.
• Modern OpenGL supports 1- and 3-dimensional textures; these are not currently supported in rgl.

Fonts

rgl uses the same ideas as base graphics for drawing text: there are font families named "sans", "serif", and "mono" for drawing text of those types. In rgl, the "symbol" family is not supported.

New font families can be defined using the low-level function rglFonts, or more simply using the higher level function rglExtrafonts. The latter function requires the extrafont package to be installed.

par3d: Miscellaneous graphical parameters

The par3d function, modelled after the classic graphics par function, sets or reads a variety of different rgl internal parameters, listed in the rgl.par3d.names variable. All of them can be set except the ones in rgl.par3d.readonly. Some parameters are completely read-only; others are fixed at the time the window is opened, and others may be changed at any time.

The deprecated rgl.viewpoint function should not be used.

Default settings

The r3dDefaults list and the getr3dDefaults function control defaults in new windows opened by open3d.
The function looks for the variable in the user’s global environment, and if not found there, finds the one in the rgl namespace. This allows the user to override the default settings for new windows.

Once found, the r3dDefaults list provides initial values for par3d parameters, as well as defaults for material3d and bg3d in components "material" and "bg" respectively.

Specific solids

These functions generate specific shapes. Optional arguments allow attributes such as color or transformations to be specified.

cols <- rainbow(7)
layout3d(matrix(1:16, 4,4), heights=c(1,3,1,3))
text3d(0,0,0,"tetrahedron3d"); next3d()
shade3d(tetrahedron3d(col=cols[1])); next3d()
text3d(0,0,0,"cube3d"); next3d()
shade3d(cube3d(col=cols[2])); next3d()
text3d(0,0,0,"octahedron3d"); next3d()
shade3d(octahedron3d(col=cols[3])); next3d()
text3d(0,0,0,"dodecahedron3d"); next3d()
shade3d(dodecahedron3d(col=cols[4])); next3d()
text3d(0,0,0,"icosahedron3d"); next3d()
shade3d(icosahedron3d(col=cols[5])); next3d()
text3d(0,0,0,"cuboctahedron3d"); next3d()
shade3d(cuboctahedron3d(col=cols[6])); next3d()
text3d(0,0,0,"oh3d"); next3d()
shade3d(oh3d(col=cols[7]))

A very large collection of polyhedra is contained in the Rpolyhedra package.

Generating new shapes

These functions generate new shapes:

A related function is triangulate, which takes a two dimensional polygon and divides it up into triangles using the “ear-clipping” algorithm.

The generic function as.mesh3d is provided to allow data structures produced by other code to be converted to mesh structures. Currently the following classes are supported:

The checkDeldir function checks that a compatible version of the deldir package is installed.

The default as.mesh3d.default method is a simple way to construct a mesh from a matrix of vertices; it can use mergeVertices (which can also be used on its own) to merge repeated vertices within the matrix, allowing addNormals to be used to give a smooth appearance.

The as.tmesh3d generic is a variation that guarantees the resulting object will have no quad entries.

Functions tmesh3d, qmesh3d are now obsolete; use mesh3d instead.

The underlying class structure for shapes

"shape3d" is the basic abstract type. Objects of this class can be displayed by shade3d (which shades faces), wire3d (which draws edges), or dot3d (which draws points at each vertex.)

"mesh3d" is a descendant type. Objects of this type contain the following fields:

Contouring and clipping shapes

These functions compute and plot contours of functions on surfaces, or clip objects along a contour of a function.

Manipulating shapes

These functions manipulate and modify mesh objects:

The individual steps in subdivision3d are also available: deform.mesh3d, divide.mesh3d, normalize.mesh3d. These are mainly intended for internal use.

The recommended method

Currently the best way to embed an rgl scene in a document is to produce the document in HTML using R Markdown. Early in the document, you should have code like this in one of the setup code chunks:

```{r echo=FALSE, include=FALSE}
library(rgl)
setupKnitr(autoprint = TRUE)
```

The call to setupKnitr() will install a number of hooks and set options in knitr so that rgl code is handled properly. The autoprint = TRUE argument makes rgl act in the document almost the same way it would act in the console, or the way base graphics are handled by knitr: If you print the value of high level rgl functions, a plot will be inserted into the output, but maybe only after low level modifications to it are complete. For example, this code block prints both triangles and spheres in a single plot at the end:

xyz <- matrix(rnorm(27), ncol = 3)
triangles3d(xyz, col = rainbow(9))
spheres3d(xyz, col = rainbow(9), radius = 0.1)

There are a few differences if you have a complicated situation:

• The mechanism depends on the result of the rgl function calls being automatically printed. If the calls are in a loop or other code block where automatic printing doesn’t happen, you’ll need some trickery to get things to print. For example, this will print three plots:

plots <- NULL
for (i in 1:3) {
  plot3d(rnorm(10), rnorm(10), rnorm(10))
  plots <- htmltools::tagList(plots, rglwidget())
  close3d()
}
plots

• It also depends on the fact that rgl functions return results using lowlevel() or highlevel() to mark which kind of plot they are. If you are using a function from another package to produce the plot, you may need to insert an explicit call to one of those to get it to print. Use lowlevel() if the function just modifies an existing plot, highlevel() if it starts a new one. For example,

foreignHigh()   # Produces a high level plot, but doesn't return
                # an appropriate value
highlevel()
foreignLow()    # Modifies the previous plot
lowlevel()

This should display the output at the end of the code chunk, when modifications are assumed complete.

Producing PDF output

While some PDF previewers support interactive 3D graphics, most don’t. To produce a screenshot of an rgl scene in an R Markdown document with PDF output, simply follow the directions given above. The auto-printing will detect PDF output and use snapshot3d to produce a PNG file to insert. (See below if you want to insert a different format of graphic.)

If you really need interactive output, see the writeASY function.

Manual insertion of plots

You may not want to use the setupKnitr(autoprint = TRUE) method described above. It is very new, and may still have bugs; you may have an older document and not want to edit it to work that way.

In this case, you can insert plots manually. Use setup code

```{r echo=FALSE, include=FALSE}
library(rgl)
setupKnitr()
```

and call rglwidget() at top level whenever you want to insert a plot.

There are a couple of other differences in default behaviour if you are not using autoprint:

• By default, each code chunk continues the rgl scene from earlier chunks. You’ll need an explicit open3d call to get a clean window.

• Also by default, the rgl window is not closed at the end of the chunk. This probably doesn’t matter, but you may find you run out of memory if your scenes are really big.

Older methods

The original way to insert an rgl scene in a document was to use the deprecated writeWebGL function to write HTML code to insert in a document. Later, Sweave and knitr hooks were added. These are no longer supported, and you should update old documents to use the newer methods. If you are reading documents that suggest using those methods, let the author know they need updating!

User interaction

By default, rgl detects and handles mouse clicks within your scene, and uses these to control its appearance. You can find out the current handlers using the following code:

par3d("mouseMode")

##        none        left       right      middle       wheel 
##      "none" "trackball"      "zoom"       "fov"      "pull"

The labels c("left", "right", "middle") refer to the buttons on a three button mouse, or simulations of them on other mice. "wheel" refers to the mouse wheel, and "none" refers to actions that take place when the mouse is moved without pressing any button.

The button actions generally correspond to click and drag operations. Possible values for “mouseMode” for the mouse pointer or wheel are as follows:

The following functions make use of the mouse for selection within a scene.

selectionFunction3d produces the selection function from information about the projection and mouse selection region; it is used internally in the functions above.

The deprecated rgl.select3d function is an obsolete version of select3d, and rgl.select is a low-level support function.

Animations

rgl has several functions that can be used to construct animations. These are based on functions that update the scene according to the current real-world time, and repeated calls to those. The functions are:

See the movie3d function for a way to output an animation to a file on disk.
Animations are not currently supported in the HTML written by rglwidget, though the playwidget function provides equivalent functionality.

Integration with TCL/TK

There are three functions in rgl that support control of an rgl scene using the TCL/TK framework.

These functions were formerly contained (without the tk prefixes on their names) in the tkrgl package. That package is now deprecated.

Exporting and importing scenes

rgl contains several functions to write scenes to disk for use by other software, or to read them in.

In order from highest fidelity to lowest, the functions are:

The rgl2gltf package can read or write GLTF and GLB files. It includes an as.rglscene method to convert GLTF objects to rgl scenes. The code in rgl’s Buffer R6 class is based on the GLTF format. It is used by rglwidget to make output webpages somewhat smaller than they were previously.

There are also functions to save snapshots or other recordings of a scene, without any 3D information being saved:

The rgl.snapshot function is a low level version of snapshot3d(); it requires that the rgl display be onscreen and copies from there. snapshot3d() tries to use the webshot2 package so it will work even with no display. The functions rgl.Sweave.off, Sweave.snapshot are involved in Sweave processing and not normally called by users.

Default display

There are two ways in which rgl scenes are normally displayed within R. The older one is in a dedicated window. In Unix-alikes this is an X11 window; it is a native window in Microsoft Windows. On macOS, the XQuartz system (see https://www.xquartz.org) needs to be installed to support this.

To suppress this display, set options(rgl.useNULL = TRUE) before opening a new rgl window. See the help page for the rgl.useNULL function for how to set this before starting R.

The newer way to display a scene is by using WebGL in a browser window or in the Viewer pane in RStudio. To select this, set options(rgl.printRglwidget = TRUE). Each operation that would change the scene will return a value which triggers a new WebGL display when printed.

Working with WebGL scenes

You should use the following scheme for exporting a scene to a web page. There’s also an older scheme, which is no longer supported.

The recommended approach works with the htmlwidgets framework (see http://www.htmlwidgets.org/). In an R Markdown document in knitr, use the rglwidget function. (You can also use chunk option webgl=TRUE; we recommend the explicit use of rglwidget.) This approach also allows display of rgl scenes in RStudio. Besides rgl scenes, various controls for them can be displayed, and there are a few utility functions that can be useful:

These functions work with the above scheme in Shiny apps:

The selectionFunction3d function is also likely to be involved in mouse interactions when using Shiny.

Some functions are mainly for internal use: elementId2Prefix, playwidgetOutput, renderPlaywidget, rglwidgetOutput, renderRglwidget, registerSceneChange. More details are given in the vignette User Interaction in WebGL. The functions lowlevel, highlevel, rglId are also for internal use, marking function results for automatic printing. Finally, the function setUserShaders allows you to use hand-written shaders in WebGL, and getShaders allows you to see what shader would be used.

Working with the scene

rgl maintains internal structures for all the scenes it displays. The following functions allow users to find information about them and manipulate them. In cases where there are both *3d and rgl.* versions of functions, most users should use the *3d version: the rgl.* functions are more primitive and are mainly intended for internal use.

Some of these functions have alternate names for back compatibility:
rgl.cur, rgl.ids, rgl.pop. Either name will work, but the *3d version is recommended for new code. Some have deprecated versions: rgl.clear, rgl.set. Those should not be called.

These functions are mainly intended for programming, and have no corresponding *3d counterparts:

The as.triangles3d generic function is intended to extract coordinates in a form suitable for passing to triangles3d. Currently a method is provided for rglId objects.

In addition to these, there are some deprecated functions which should not be called: rgl.init, rgl.open, rgl.close, rgl.quit.

Working with 3-D vectors

Most rgl functions work internally with “homogeneous” coordinates. In this system, 3-D points are represented with 4 coordinates, generally called (x, y, z, w). The corresponding Euclidean point is (x/w, y/w, z/w), if w is nonzero; zero values of w correspond to “points at infinity”. The advantage of this system is that affine transformations including translations and perspective shifts become linear transformations, with multiplication by a 4 by 4 matrix.

rgl has the following functions to work with homogeneous coordinates:

There is also a function GramSchmidt, mainly for internal use: it does a Gram-Schmidt orthogonalization of a 3x3 matrix, with some specializations for its use in cylinder3d.

Working with other packages

Sometimes it may be convenient to interactively rotate a scene to a particular view, then display it in lattice or base graphics. The rglToLattice and rglToBase functions support this.

For example, we first display the volcano data in rgl:

persp3d(volcano, col = "green")

This display is interactive, but we can reproduce the initial view using the lattice wireframe or base graphics persp functions:

# Only evaluated if the lattice & orientlib packages are installed
lattice::wireframe(volcano, col = "green", 
           screen = rglToLattice())

angles <- rglToBase()
persp(volcano, col = "green", shade = TRUE,
      theta = angles$theta, phi = angles$phi)

Note that the orientlib package must be available for these functions to work.

Creating pkgdown websites

The “Using RGL in pkgdown web sites” vignette describes how to use rgl in a pkgdown web site. The utility function in_pkgdown_example can be used to detect that pkgdown is being used.

Working with testthat

The testthat package is widely used for unit tests in packages. Such tests are hard to write with rgl, because the output is visual and interactive rather than a simple value. The expect_known_scene, compare_proxy.mesh3d and all.equal.mesh3d functions help with this by removing system-dependent features of rgl output.

Working with Javascript

The WebGL displays created using rglwidget rely on a large body of Javascript code included in this package. To help in development of this code, the makeDependency function was written. It may be useful in other packages that include Javascript.

Other functions and objects

This section is for miscellaneous functions and objects that don’t fall in any of the other categories in this document.

The setGraphicsDelay function is designed to work around what appears to be a bug on macOS: if a standard plot window is opened too quickly after an rgl window, R can crash. This function inserts a one second delay when it appears to be needed.

The gltfTypes vector contains constants used in OpenGL and glTF.