bar3d: Draw a 3D bar chart

Description

bar3d creates 3D barplots and height map visualizationsin the VRML- or Livegraphics3D-format.

Usage

bar3d(data, row.labels = rownames(data), col.labels = colnames(data), metalabels = NULL, filename = "out.wrl", type = "vrml", space = 0.5, cols = rainbow(length(as.matrix(data))), rcols = NULL, ccols = NULL, origin = c(0, 0, 0), scalefac = 4, lab.axis = c("X-axis", "Y-axis", "Z-axis"), lab.vertical = FALSE, col.axis = "black", showaxis = TRUE, autoscale = TRUE,  ignore_zeros = TRUE, col.lab = "black", col.bg = "white", cex.lab = 1, cex.rowlab = 1, cex.collab = 1, htmlout = NULL, hwidth = 1200, hheight = 800, showlegend = TRUE, vrml_navigation = "EXAMINE", vrml_transparency = 0, vrml_fov = 0.785, vrml_pos = rep(scalefac + 4, 3), vrml_dir = c(0.19, 0.45, 0.87, 2.45), lg3d_ambientlight = 0.5)

Arguments

data

a numerical matrix with 3 columns and n rows

row.labels

a vector containing the row labels (strings or numbers)

col.labels

a vector containing the column labels (strings or numbers)

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)

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()

space

space between single bars in a bar plot (as a fraction of the average bar width)

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))

rcols

specifies the bar colors per row of the input matrix (the cols- and ccols paramter can remain undefined). The number of colors must correspond to the numbers of rows of the data matrix.

ccols

specifies the bar colors per column of the input matrix (the cols- and rcols-parameter can remain undefined). The number of colors must correspond to the numbers of columns of the data matrix.

origin

a vector of length 3 specifying the coordinates of the plot origin (can be used to translate the plot)

scalefac

a scaling factor for the size of the entire plot

lab.axis

a vector of size 3 containing the axis labels

col.axis

color of the axis

lab.vertical

if TRUE, the data labels will be plotted in vertical instead of horizontal orientation

showaxis

if FALSE, the coordinate axes are hidden in the output

autoscale

if TRUE, the data is automatically scaled to fill the volume between the axes

ignore_zeros

if TRUE, for height values equal to zero no bar will be plotted

col.lab

a vector of colors for the axis labels

col.bg

background color

cex.lab

scaling factor for axis label font size

cex.rowlab

scaling factor for matrix row labels font size

cex.collab

scaling factor for matrix column labels font size

htmlout

a filename for generating an HTML-file to embed the 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 added to the 3D plot

vrml_navigation

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

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

bar3d generates 3D barplots and height map visualizationsin 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

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/

Examples

Run this code


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

# Height map visualization of geographical data
# with colors corresponding to different height levels
colpalette <- terrain.colors(max(volcano)-min(volcano)+1)
cols <- colpalette[as.vector(t(volcano))-min(volcano)+1]
bar3d(volcano, col.bg = "white", cols = cols,
      type = "vrml", space = 0, showaxis = FALSE,
      filename = "volcano.wrl", htmlout = "volcano.html")

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

# bar plot for a data matrix with numerical metalabels
mat <- matrix(9:1, nrow = 3)
rownames(mat) <- paste('row',1:3)
colnames(mat) <- paste('col',1:3)
bar3d(mat, space = 1, metalabels = 1:9, col.bg = "white",
      col.axis = "blue", col.lab = "black", type = "vrml",
      filename = "barplot.wrl", htmlout = "barplot.html")
      
# show the output in a web-browser 
# (VRML-plugin must be installed!)
if(file.exists(paste("file://",file.path(outdir,
                "barplot.html"), sep = "")))
{
  browseURL(paste("file://",file.path(outdir,
                  "barplot.html"), sep = ""))
}

# Height map visualization of very rough and highly
# simplified topographic data for the United Kingdom

data(uk_topo)

bar3d(uk_topo, autoscale = FALSE, cols = "blue",
     space = 0, showaxis = FALSE, filename = "uk_topo.wrl",
     htmlout = "uk_topo.html")

setwd(curdir)

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