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Last data update: 2014.03.03

R: Generate 3D graph(s) using scatterplot3d

do3d	R Documentation

Generate 3D graph(s) using scatterplot3d

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(made4)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/made4/do3d.Rd_%03d_medium.png", width=480, height=480)
> ### Name: do3d
> ### Title: Generate 3D graph(s) using scatterplot3d
> ### Aliases: do3d rotate3d
> ### Keywords: hplot
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>