do3d: Generate 3D graph(s) using scatterplot3d

In made4: Multivariate analysis of microarray data using ADE4

Description

do3d is a wrapper for scatterplot3d. do3d will draw a single 3D xyz plot and will plot each group of points in a different colour, given a factor.

rotate3d calls do3d to draw multiple 3D plots in which each plot is marginally rotated on the x-y axis.

Usage

do3d(dataset, x = 1, y = 2, z = 3, angle = 40, classvec = NULL, classcol
= NULL, col = NULL, cex.lab=0.3, pch=19, cex.symbols=1, ...)
rotate3d(dataset, x = 1, y = 2, z = 3, beg = 180, end = 360, step = 12, 
savefiles = FALSE, classvec = NULL, classcol = NULL, col = NULL, ...)

Arguments

dataset	XYZ coordinates to be plotted. A matrix or data.frame with 3 or more columns. Usually results from multivariate analysis, such as the \$co or \$li coordinates from a PCA dudi.pca, or COA dudi.coa or the \$ls, \$co coordinates from bga.
x	Numeric, the column number for the x-axis, the default is 1 (that is dataset[,1])
y	Numeric, the column number for the y-axis, the default is 2 (that is dataset[,2])
z	Numeric, the column number for the z-axis, the default is 3 (that is dataset[,3])
angle	Numeric, the angle between x and y axis. Note the result depends on scaling. See scatterplot3d
classvec	A factor or vector which describes the classes in dataset
classcol	A factor or vector which list the colours for each of the classes in the dataset. By default NULL. When NULL, getcol is used to obtain an optimum set of colours of the classes in classvec.
cex.lab	Numeric. The magnification to be used for the axis annotation relative to the current default text and symbol size. Default is 0.3
pch	Integer specifying a symbol or single character to be used when plotting points. The default is pch= 19
cex.symbols	Numeric. The magnification to be used for the symbols relative to the current default text size. Default is 1
col	A character indicating a colour. To be used if all points are to be one colour. If classvec, classcol and col are all NULL. all points will be drawn in red by default.
beg	Numeric. The starting angle between the x and y axis for rotate3d. Rotate3d will draw plots in which they are rotated from angle beg to angle end
end	Numeric. The final angle between the x and y axis for rotate3d. Rotate3d will draw plots in which they are rotated from angle beg to angle end
step	Numeric. Increment of the sequence between the starting angle beg and the final angle end.
savefiles	Logical, indicating whether the plot should be saved as a pdf file. The default is FALSE
...	further arguments passed to or from other methods

Details

This calls scatterplot3d to plot a 3d representation of results.

It is also worth exploring the package rgl which enables dynamic 3d plot (that can be rotated)

library(rgl) plot3d(khan.coa$co[,1], khan.coa$co[,2],khan.coa$co[,3], size=4, col=khan$train.classes) rgl.snapshot(file="test.png", top=TRUE) rgl.close()

Value

Produces plots of the xyz coordinates.

Author(s)

Aedin Culhane

See Also

See Also scatterplot3d

Examples

data(khan)
if (require(ade4, quiet = TRUE)) {
khan.coa<-dudi.coa(khan$train, scannf=FALSE, nf=5)
}
par(mfrow=c(2,1))
do3d(khan.coa$co, classvec=khan$train.classes)
do3d(khan.coa$co, col="blue")
rotate3d(khan.coa$co,classvec=khan$train.classes)
khan.bga<-bga(khan$train, khan$train.classes)
plot.new()
par(bg="black")
do3d(khan.bga$bet$ls, classvec=khan$train.classes)

Example output

Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: scatterplot3d

made4 documentation built on Nov. 8, 2020, 6:49 p.m.