View source for R and 3D plots

[http://www.r-project.org 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 [http://cran.r-project.org/mirrors.html 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 [http://mirrors.sunsite.dk/cran/src/contrib/Descriptions/scatterplot3d.html download scatterplot3d package] from one of the [http://cran.r-project.org/mirrors.html CRAN mirrors] and leave it as a .tar.gz file. Then as root type the following from command-line:
<pre>
# R CMD INSTALL scatterplot3D_version.tar.gz
</pre>

Now, to use the package you start R and type:
<pre>
> library(scatterplot3d)
</pre>
In order to load the package. Hereafter, you can use the function scatterplot3d(). Assume that you have a file in the following format:
<pre>
# an example file for 3D plots with R and scatterplot3d
x1 y1 z1
x2 y2 z2
x3 y3 z3
..
..

</pre>

To do the plot the following sequence of commands will do the trick:
<pre>
# R
> library(scatterplot3d)
> xyz <- read.table("examplefile.data")
> scatterplot3d(xyz)
> xyz
x1 y1 z1
x2 y2 z2
x3 y3 z3
</pre>


Assuming everything looks good and you want to save the plot:
<pre>
> postscript("greatlookinggraph.eps")
> scatterplot3d(xyz)
> dev.off()
> q()
</pre>

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.


=== 3D and colors ===
Replace the '''scatterplot3d''' parameters with the following in order to get (nicer) colorful 3D plots:
<pre>
scatterplot3d(xyz, highlight.3d=TRUE, col.axis="blue", col.grid="lightblue", main="scatterplot3d", pch=20)
</pre>