vrmlgen (version 1.4.9)

cloud3d: Draw a 3D scatter plot

Description

cloud3d creates dynamic 3D scatter plot visualizations in the VRML- or Livegraphics3D-format.

Usage

cloud3d(x, y = NULL, z = NULL, labels = rownames(data), filename = "out.wrl", type = "vrml", pointstyle = c("s", "b", "c"), metalabels = NULL, hyperlinks = NULL, cols = rainbow(length(unique(labels))), scalefac = 4, autoscale = "independent", lab.axis = c("X-axis", "Y-axis", "Z-axis"), col.axis = "black", showaxis = TRUE, col.lab = "black", col.bg = "white", cex.lab = 1, htmlout = NULL, hwidth = 1200, hheight = 800, showlegend = TRUE, vrml_navigation = "EXAMINE", vrml_showdensity = FALSE,  vrml_fov = 0.785, vrml_pos = rep(scalefac + 4, 3), vrml_dir = c(0.19, 0.45, 0.87, 2.45), vrml_transparency = 0, lg3d_ambientlight = 0.5)

Arguments

x

a 3-column numeric matrix of coordinates or a numeric vector of x-coordinates (not used if parameter obj\_infile or xfun is specified)

y

a numeric vector of y-coordinates (only needed if x is a vector)

z

a numeric vector of z-coordinates (only needed if x is a vector)

labels

a vector of size n containing optional class labels (strings or numbers) for the data points

filename

filename of the generated output file

type

the output type ("vrml" or "lg3d"), this will be set automatically if mesh3d is called after vrml.open() or lg3d.open()

pointstyle

a vector of point style types. Possible types are "s" for spheres, "b" for boxes and "c" for cone. To draw all points in the same style, use a vector of size 1, otherwise the number of used point styles must be greater or equal to the number of different labels (i.e. length(pointstyles) >= length(unique(labels)))

metalabels

a vector of strings or numbers containing optional metalabels for the rows which can be accessed by hovering the mouse over a data point in the plot (in VRML)

hyperlinks

a vector of strings specifying hyperlinks that will be triggered, when the user clicks on the corresponding datapoint

cols

a vector of colors to visualize different classes among the data points. The number of colors should either be one or at least as large as the number of different labels (i.e. length(col) >= length(unique(labels))

scalefac

a numerical scaling factor to increase/decrease the size of the plotted 3D objects

autoscale

the scaling type. "independent" means all axes are auto-scaled independently. "equidist" means all axes are scaled by the same factor and "equicenter" additionally positions the drawn object in the center. "none" means no scaling is applied

lab.axis

a vector of size 3 containing the axis labels

col.axis

color of the axis

showaxis

if FALSE, the coordinate axes are hidden in the output

col.lab

a vector of colors specifying the axis labels

col.bg

background color

cex.lab

scaling factor for axis label font size

htmlout

a filename for generating an HTML-file to embed the VRML-output

hwidth

width of the embedded visualization in the HTML-output

hheight

height of the embedded visualization in the HTML-output

showlegend

if TRUE, a data legend will be drawn based on the group labels

vrml_navigation

type of mouse navigation in the VRML file, can be "EXAMINE", "WALK", "SLIDE", "FLY" or "PAN" (VRML only)

vrml_showdensity

if TRUE, semi-transparent density estimation contour surfaces will be drawn to identify regions of high data density (requires misc3d-package)

vrml_transparency

a number between 0 and 1 specifying the transparency level of plotted objects (VRML only)

vrml_fov

a scalar defining the field of view angle in the VRML file in radians (VRML only)

vrml_pos

a vector of size 3 corresponding to the position of the viewpoint (VRML only)

vrml_dir

a vector of size 4 specifying the viewing direction (first 3 components) and the rotation of the camera around the direction vector (last component in radians, VRML only)

lg3d_ambientlight

ambient light gray level (value between 0 and 1, LG3D only)

Value

The function is used for its side-effect (creating a VRML- or Livegraphics3D-file) and has no return value.

Details

cloud3d creates dynamic 3D-scatterplots with optional features like density estimation contour surfaces and hyperlinks for each datapoint in the VRML- or Livegraphics3D-format. The plots can automatically be embedded in a HTML-file to allow users to inspect the data interactively and from different 3D-perspectives and scalings on a webpage. To add additional shapes and objects to the final 3D scene, this plotting function can also be called within a VRML- or Livegraphics3D-environment created by calling the vrml.open() or lg3d.open() function. In this case, cloud3d will inherit all global parameters set in the vrml.open- or lg3d.open- function (e.g. filename, type, htmlout, etc.) and the user does not need to specify these options anymore.

References

Bowman, A. W. and Azzalini, A. (2007). R package 'sm': Nonparametric smoothing methods (version 2.2) URL: http://www.stats.gla.ac.uk/~adrian/sm, http://azzalini.stat.unipd.it/Book_sm

Feng, D. and Tierney, L. (2009). R package 'misc3d": Miscellaneous 3D plots (version 0.6-1) URL: http://cran.r-project.org/web/packages/misc3d/index.htm Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor (2010). vrmlgen: An R Package for 3D Data Visualization on the Web. Journal of Statistical Software, 36(8), p. 1-18. URL: http://www.jstatsoft.org/v36/i08/

See Also

mesh3d, bar3d

Examples

curdir <- getwd()
outdir <- tempdir()
setwd(outdir)


# example 1: visualize random 3D input data
mat <- matrix(runif(99, 0, 3), ncol = 3)

# create random class assignment vector with three classes
y <- round(runif(33, 0, 2))
y <- ifelse(y == 0, "class 1", ifelse(y == 1, "class 2", "class 3"))

# create ouput using numbers from 1 to length(y) as metalabels
cloud3d(mat, labels = y, metalabels = 1:length(y), col.axis = "black",
        col.lab = "blue", col.bg = "white", type = "vrml",
        filename = "result.wrl", htmlout = "result.html")

# show the output in a web-browser 
# (VRML-plugin must be installed!)
if(file.exists(paste("file://",file.path(outdir,
                "result.html"), sep = "")))
{
  browseURL(paste("file://",file.path(outdir,
                  "result.html"), sep = ""))
}


# example 2: visualization of Edgar Anderson's Iris data
# using density estimation contour surfaces (requires misc3-package!)
irismat <- iris[,1:3]
cloud3d(irismat, labels = iris[,5], vrml_showdensity = TRUE,
        col.axis = "blue", col.lab = "black", lab.axis = colnames(irismat),
        type = "vrml", filename = "result2.wrl", htmlout = "iris.html")

# show the output in a web-browser 
# (VRML-plugin must be installed!)
if(file.exists(paste("file://",file.path(outdir,
                "iris.html"), sep = "")))
{
  browseURL(paste("file://",file.path(outdir,
                  "iris.html"), sep = ""))
}
 
setwd(curdir)