R and 3D plots

The R Project for Statistical Computing is a convenient tool for plotting experimental data. If you are using Debian, you can find the R core .deb package, otherwise you can download the R source code and compile it yourself.

Basics

Starting R: Once R is installed you start it by typing R. This will give you an R prompt.

Quitting R: q()

HTML help: help.start()

Searching online help: help.search("what you don't know")

Assignment: variable <- value, eg. x <- 42

Show content of a variable: variable, eg. x

Loading data from a file: read.table("filename") (assuming that your data file contains data only, where each line describes one point in a multi-dimensional space).

Loading data from a file into a variable: xyz <- read.table("filename") (you knew that!)

3D Plots

In order to plot in 3D you need to add a package called scatterplot3d to R. You should download scatterplot3d package from one of the CRAN mirrors and leave it as a .tar.gz file. Then as root type the following from command-line:

# R CMD INSTALL scatterplot3D_version.tar.gz

Now, to use the package you start R and type:

> library(scatterplot3d)

In order to load the package. Hereafter, you can use the function scatterplot3d(). Assume that you have a file in the following format:

# an example file for 3D plots with R and scatterplot3d
x1 y1 z1
x2 y2 z2
x3 y3 z3
..
..

To do the plot the following sequence of commands will do the trick:

# R
> library(scatterplot3d)
> xyz <- read.table("examplefile.data")
> scatterplot3d(xyz)
> xyz
x1 y1 z1
x2 y2 z2
x3 y3 z3

Assuming everything looks good and you want to save the plot:

> postscript("greatlookinggraph.eps")
> scatterplot3d(xyz)
> dev.off()
> q()

The command dev.off() turns off the postscript device and flushes unwritten data. There are multiple devices, the default on UNIX is the x11 device, which produces nice windows. A device is started and set to the default graphical output device by simply typing the name of the device followed by brackets. Remember to issue a dev.off() when you are done with a device. A list of available devices is shown if you type help(Devices) -- lookout by the way R is case-sensitive hence, help(devices) will leave you with nothing but an error message.

Use help(scatterplot3d) to get the full list of parameters and options for the function.