## Warning in rgl.init(initValue, onlyNULL): RGL: unable to open X11 display## Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.Introduction
The rgl package is used to produce interactive 3-D plots. It contains high-level graphics commands modelled loosely after classic R graphics, but working in three dimensions. It also contains low level structure inspired by (but incompatible with) the grid package.
This document gives an overview. See the help pages for details.
For installation instructions, see the README file in the top level directory of the source tarball rgl_1.3.10.tar.gz (or a later version).
About this document
This document was written in R Markdown, using the knitr package for production. It corresponds to rgl version 1.3.10.
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.
Basics and High Level Functions
The plot3d function plots points within an RGL window. It is similar to the classic plot function, but works in 3 dimensions.
For example
with(iris, plot3d(Sepal.Length, Sepal.Width, Petal.Length,
type="s", col=as.numeric(Species)))plot3d() example.
can be used to plot three columns of the iris data. Allowed plot types include "p", "l", "h", "s", meaning points, lines, segments from z=0, and spheres. There’s a lot of flexibility in specifying the coordinates; the xyz.coords function from the grDevices package is used for this.
You can use your mouse to manipulate the plot. The default is that if you click and hold with the left mouse button, you can rotate the plot by dragging it. The right mouse button is used to resize it, and the middle button changes the perspective in the point of view.
If you call plot3d again, it will overwrite the current plot. To open a new graphics window, use open3d.
The other high level function is persp3d to draw surfaces. It is similar to the classic persp function, but with greater flexibility. First, any of x, y or z can be specified using matrices, not just z. This allows parametric surfaces to be plotted. An even simpler specification is possible: x may be a function, in which case persp3d will work out the grid itself. See ?persp3d.function for details. For example, the MASS package estimates Gamma parameters using maximum likelihood in a ?MASS::fitdistr example. Here we show the log likelihood surface.
# This example requires the MASS package
library(MASS)
# from the fitdistr example
set.seed(123)
x <- rgamma(100, shape = 5, rate = 0.1)
fit <- fitdistr(x, dgamma, list(shape = 1, rate = 0.1), lower = 0.001)
loglik <- function(shape, rate) sum(dgamma(x, shape=shape, rate=rate,
log=TRUE))
loglik <- Vectorize(loglik)
xlim <- fit$estimate[1]+4*fit$sd[1]*c(-1,1)
ylim <- fit$estimate[2]+4*fit$sd[2]*c(-1,1)
mfrow3d(1, 2, sharedMouse = TRUE)
persp3d(loglik,
xlim = xlim, ylim = ylim,
n = 30)
zlim <- fit$loglik + c(-qchisq(0.99, 2)/2, 0)
next3d()
persp3d(loglik,
xlim = xlim, ylim = ylim, zlim = zlim,
n = 30)persp3d() example.
On the left, the whole surface over a range of the parameters; on the right, only the parts of the surface with log likelihood values near the maximum.
Note: this example used the knitr hook functions (see setupKnitr) to insert the scene into this vignette; the previous example used the rglwidget function. We generally recommend the newer rglwidget approach.
Note that both plot3d and persp3d are generic functions, with the following methods defined:
methods(plot3d)## [1] plot3d.ashape3d* plot3d.default* plot3d.deldir*
## [4] plot3d.formula* plot3d.function* plot3d.lm*
## [7] plot3d.mesh3d* plot3d.rglbackground* plot3d.rglbboxdeco*
## [10] plot3d.rglobject* plot3d.rglscene* plot3d.rglsubscene*
## [13] plot3d.rglWebGL* plot3d.tri* plot3d.triSht*
## see '?methods' for accessing help and source code
methods(persp3d)## [1] persp3d.ashape3d* persp3d.default* persp3d.deldir* persp3d.formula*
## [5] persp3d.function* persp3d.tri* persp3d.triSht*
## see '?methods' for accessing help and source codeAdding Graphical Elements
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:
| Function | Description |
|---|---|
points3d: |
adds points |
lines3d: |
adds lines |
segments3d: |
adds line segments |
triangles3d: |
adds triangles |
quads3d: |
adds quadrilaterals |
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.
| Function | Description |
|---|---|
text3d, texts3d: |
adds text |
abclines3d: |
adds straight lines to plot (like abline) |
arc3d: |
adds spherical arcs or spirals to plot |
planes3d: |
adds planes to plot |
clipplanes3d: |
add clipping planes to plot |
sprites3d, particles3d: |
add sprites (fixed shapes or images) to plot |
spheres3d: |
adds spheres |
surface3d, terrain3d: |
a surface (as used in persp3d) |
drape3d: |
drapes lines on a surface or object(s) |
shadow3d: |
projects mesh onto a surface |
arrow3d: |
add an arrow to a scene |
pch3d: |
draw base-style plotting symbols |
plotmath3d: |
used by text3d for math text |
Axes and other “decorations”
The following low-level functions control the look of the graph:
| Function | Description |
|---|---|
axes3d, axis3d: |
add axes to plot |
box3d, bbox3d: |
add box around plot |
title3d: |
add title to plot |
mtext3d: |
add marginal text to plot |
decorate3d: |
add multiple “decorations” (scales, etc.) to plot |
aspect3d: |
set the aspect ratios for the plot |
bg3d, bgplot3d: |
set the background of the scene |
show2d: |
show a 2D plot or image in a 3D scene |
legend3d: |
set a legend for the scene |
grid3d: |
add a reference grid to a graph |
thigmophobe3d: |
choose label positions to avoid overlap |
setAxisCallbacks: |
set user-defined axis annotations |
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")triangles3d() example.
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.
Controlling the Look of the Scene
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:
-
thetasets the rotation around the vertical axis, in degrees. -
phisets 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
phito 0, you start to look down at the scene from the top. If you increasephiabove 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:
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.
| Property | Default | Meaning |
|---|---|---|
| color | white | vector of surface colors to apply to successive vertices for diffuse light |
| alpha | 1 | transparency: 0 is invisible, 1 is opaque |
| lit | TRUE | whether lighting calculations should be done |
| ambient | black | color in ambient light |
| specular | white | color in specular light |
| emission | black | color emitted by the surface |
| shininess | 50 | controls the specular lighting: high values look shiny |
| smooth | TRUE | whether shading should be interpolated between vertices |
| texture | NULL | optional path to a “texture” bitmap to be displayed on the surface |
| front, back | fill | should polygons be filled, or outlined? |
| size | 3 | size of points in pixels |
| lwd | 1 | width of lines in pixels |
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()## agg_png
## 2
open3d()## null
## 11
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")Texture example.
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. Ifcolis 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
specularto 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
OpenGLsupports 1- and 3-dimensional textures; these are not currently supported inrgl.
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.
| Name | Changeable? | Description |
|---|---|---|
| antialias | fixed | Amount of hardware antialiasing |
| cex | Default size for text | |
| family | Device-independent font family name; see ?text3d | |
| font | Integer font number | |
| useFreeType | Should FreeType fonts be used if available? | |
| fontname | read-only | System-dependent font name set by rglFonts
|
| FOV | Field of view, in degrees. Zero means isometric perspective | |
| ignoreExtent | Should rgl ignore the size of new objects when computing the bounding box? |
|
| skipRedraw | Should rgl suppress updates to the display? |
|
| maxClipPlanes | read-only | How many clip planes can be defined? |
| modelMatrix | read-only | The OpenGL ModelView matrix; partly set by view3d
|
| projMatrix | read-only | The OpenGL Projection matrix |
| bbox | read-only | Current bounding-box of the scene |
| viewport | Dimensions in pixels of the scene within the window | |
| windowRect | Dimensions in pixels of the window on the whole screen | |
| listeners | Which subscenes respond to mouse actions in the current one | |
| mouseMode | What the mouse buttons do. See “mouseMode”
|
|
| observer | read-only | The position of the observer; set by observer3d
|
| scale | Rescaling for each coordinate; see aspect3d
|
|
| zoom | Magnification of the scene |
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.
Meshes: Constructing Shapes
rgl includes a number of functions to construct and display various solid shapes. These generate objects of class "shape3d", "mesh3d" or "shapelist3d". The details of the classes are described below. We start with functions to generate them.
Specific solids
These functions generate specific shapes. Optional arguments allow attributes such as color or transformations to be specified.
| Function | Description |
|---|---|
tetrahedron3d, cube3d, octahedron3d, dodecahedron3d, icosahedron3d: |
Platonic solids |
cuboctahedron3d, oh3d: |
other solids |
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]))Solids example.
A very large collection of polyhedra is contained in the Rpolyhedra package.
Generating new shapes
These functions generate new shapes:
| Function | Description |
|---|---|
cylinder3d: |
generate a tube or cylinder |
polygon3d: |
generate a flat polygon by triangulation |
extrude3d: |
generate an “extrusion” of a polygon |
turn3d: |
generate a solid of rotation |
ellipse3d: |
generate an ellipsoid in various ways |
mesh3d: |
generate a shape from indexed vertices |
shapelist3d: |
generate a shape by combining other shapes |
as.mesh3d: |
a generic function; see below |
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:
| Class | Package | Description |
|---|---|---|
deldir
|
deldir |
Delaunay triangulations of irregular point clouds |
triSht
|
interp |
Also Delaunay triangulations |
tri
|
tripack |
Generalized Delaunay triangulations |
ashape3d
|
alphashape3d |
Alpha-shapes |
rglId |
rgl |
rgl object identifiers |
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:
| Field | Meaning |
|---|---|
| vb | A 4 by n matrix of vertices in homogeneous coordinates. Each column is a point. |
| ip | (optional) A vector of vertex indices for points. |
| is | (optional) A 2 by s matrix of vertex indices. Each column is a line segment. |
| it | (optional) A 3 by t matrix of vertex indices. Each column is a triangle. |
| ib | (optional) A 4 by q matrix of vertex indices. Each column is a quadrilateral. |
| material | (optional) A list of material properties. |
| normals | (optional) A matrix of the same shape as vb, containing normal vectors at each vertex. |
| texcoords | (optional) A 2 by n matrix of texture coordinates corresponding to each vertex. |
| values | (optional) A vector of length n holding values at each vertex |
| meshColor | (optional) A text value indicating how colors and texture coordinates should be interpreted. |
| tags | (optional) A vector added by some functions (e.g. clipMesh3d) to relate output parts to input parts. |
Contouring and clipping shapes
These functions compute and plot contours of functions on surfaces, or clip objects along a contour of a function.
| Function | Description |
|---|---|
contourLines3d: |
draw contour lines on surface |
filledContour3d: |
fill between contours on surface |
clipMesh3d: |
clip mesh object using curved boundary |
clipObj3d: |
clip general object using curved boundary |
Manipulating shapes
These functions manipulate and modify mesh objects:
| Function | Description |
|---|---|
addNormals: |
add normal vectors to make a shape look smooth |
subdivision3d: |
add extra vertices to make it look even smoother |
merge: |
merge mesh objects |
facing3d: |
subset of mesh facing “up” |
getBoundary3d: |
get the boundary of a mesh object |
The individual steps in subdivision3d are also available: deform.mesh3d, divide.mesh3d, normalize.mesh3d. These are mainly intended for internal use.
Multi-figure Layouts
rgl has several functions to support displaying multiple different “subscenes” in the same window. The high level functions are
| Function | Description |
|---|---|
mfrow3d: |
Multiple figures (like par(“mfrow”) |
layout3d: |
Multiple figures (like layout) |
next3d: |
Move to the next figure (like plot.new or frame) |
subsceneList: |
List all the subscenes in the current layout |
clearSubsceneList: |
Clear the current list and revert to the previous one |
There are also lower level functions.
| Function | Description |
|---|---|
newSubscene3d: |
Create a new subscene, with fine control over what is inherited from the parent |
currentSubscene3d: |
Report on the active subscene |
subsceneInfo: |
Get information on current subscene |
useSubscene3d: |
Make a different subscene active |
addToSubscene3d, delFromSubscene3d: |
Add objects to a subscene, or delete them |
gc3d: |
Do “garbage collection”: delete objects that are not displayed in any subscene |
Documents with rgl Scenes
The rgl package can produce output that can be embedded in other documents. The recommended way to do this has changed several times over the years. We will start with the current recommendation, then list older methods.
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)Autoprint example.
There are a few differences if you have a complicated situation:
- The mechanism depends on the result of the
rglfunction 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
rglfunctions return results usinglowlevel()orhighlevel()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. Uselowlevel()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
rglscene from earlier chunks. You’ll need an explicitopen3dcall to get a clean window.Also by default, the
rglwindow 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!
Utility Functions
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:
| Mode | Description |
|---|---|
"none" |
No action |
"trackball" |
The mouse acts as a virtual trackball. Clicking and dragging rotates the scene |
"xAxis", "yAxis", "zAxis"
|
Like "trackball", but restricted to rotation about one axis |
"polar" |
The mouse affects rotations by controlling polar coordinates directly |
"selecting" |
The mouse is being used by the select3d function |
"zoom" |
The mouse zooms the display |
"fov" |
The mouse affects perspective by changing the field of view |
"pull" |
Rotating the mouse wheel towards the user “pulls the scene closer” |
"push" |
The same rotation “pushes the scene away” |
"user" |
A user action set by setUserCallbacks, rgl.setMouseCallbacks, rgl.setWheelCallback. Use rgl.getMouseCallbacks and rgl.getWheelCallback to retrieve. |
The following functions make use of the mouse for selection within a scene.
| Function | Description |
|---|---|
identify3d: |
like the classic graphics identify function |
select3d: |
returns a function that tests whether a coordinate was selected |
selectpoints3d: |
selects from specific objects |
hover3d: |
displays “hover” info about points |
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:
| Function | Description |
|---|---|
play3d: |
Repeatedly call the update function |
spin3d: |
Update the display by rotating at a constant rate |
par3dinterp: |
Compute new values of some par3d parameters by interpolation over time |
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.
| Function | Description |
|---|---|
tkspin3d: |
Set up buttons in a window to control a scene |
tkspinControl: |
Embed the control buttons in a separate TCL/TK frame |
tkpar3dsave: |
Create a dialog to interactively save mouse actions |
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:
| Function | Description |
|---|---|
scene3d: |
Save a scene to an R variable, which can be saved and reloaded |
rglwidget: |
Prints as HTML and Javascript to display a scene in a web browser. (See also User Interaction in WebGL.) |
writeASY: |
Write files for Asymptote |
writePLY: |
Write PLY files (commonly used in 3D printing) |
readOBJ, writeOBJ: |
Read or write OBJ files (commonly used in 3D graphics) |
readSTL, writeSTL: |
Read or write STL files (also common in 3D printing) |
as.rglscene: |
Generic function, no methods in rgl
|
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:
| Function | Description |
|---|---|
snapshot3d: |
Save a PNG file bitmap of the scene |
rgl.postscript: |
Save a Postscript, LaTeX, PDF, SVG or PGF vector rendering of the scene |
movie3d: |
Save a series of bitmaps to be assembled into a movie |
rgl.pixels: |
Obtain pixel-level information about the scene in an R variable |
rgl.Sweave: |
Driver function for inserting a snapshot into a Sweave document. |
hook_rgl, hook_webgl: |
knitr hook functions for inserting images into a document. |
setupKnitr: |
Function to set up knitr hooks |
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:
| Function | Description |
|---|---|
propertyControl: |
set individual properties |
clipplaneControl: |
control a clipping plane |
subsetControl: |
control which objects are displayed |
ageControl: |
“age” vertices of an object |
vertexControl: |
control properties of vertices |
par3dinterpControl: |
WebGL control like par3dinterp
|
playwidget: |
display and automate controls |
toggleWidget: |
display a button to toggle some items |
| %>%: |
magrittr pipe |
figHeight, figWidth: |
Dimensions of figures in R Markdown document |
rglShared: |
share data using crosstalk package |
rglMouse: |
change mouse mode in RGL scene |
asRow: |
arrange multiple objects in an HTML display |
getWidgetId: |
get the elementId from a widget |
These functions work with the above scheme in Shiny apps:
| Function | Description |
|---|---|
sceneChange: |
used in Shiny for large scene changes |
shinyGetPar3d, shinySetPar3d: |
get or set par3d values from Shiny |
shinyResetBrush: |
reset the mouse brush in Shiny |
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.
| Function | Description |
|---|---|
open3d: |
open a new window |
close3d: |
close the current window |
cur3d: |
id of the active device |
set3d: |
set a particular device to be active |
pop3d: |
delete objects from the scene |
clear3d: |
delete all objects of certain classes |
ids3d: |
ids, types and tags of current objects |
tagged3d: |
find tags or objects with tags |
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:
| Function | Description |
|---|---|
rgl.bringtotop: |
bring the current window to the top |
rgl.dev.list: |
ids of all active devices |
rgl.attrib, rgl.attrib.info, rgl.attrib.count: |
attributes of objects in the scene |
rgl.projection: |
return information about the current projection |
rgl.user2window, rgl.window2user: |
convert between coordinates in the current projection |
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:
| Function | Description |
|---|---|
asEuclidean, asHomogeneous: |
convert between homogeneous and Euclidean coordinates when x, y and z are columns |
asEuclidean2, asHomogeneous2: |
convert when x, y and z are rows |
rotate3d, scale3d, translate3d: |
apply a transformation |
transform3d: |
apply a general transformation |
rotationMatrix, scaleMatrix, translationMatrix: |
compute the transformation matrix |
identityMatrix: |
return a 4 x 4 identity matrix |
projectDown: |
a 3D to 2D projection down a vector |
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")Volcano in rgl
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.
Warning: Work in Progress!
This vignette is always a work in progress. Some aspects of the rgl package are not described, or do not have examples. There may even be functions that are missed completely, if the following list is not empty:
## [1] "safe.dev.off" "textureSource"Index of Functions
The following functions and constants are described in this document: