GnuPlot

[http://www.gnuplot.info/]

GnuPlot is the best plotting program I've seen so far. It is easy to use and very powerful.

The easiest way to install it on a Mac is to use the Fink package installer (here).

Demo: plotting data from the file

set terminal postscript landscape color 20;
set out "myplot.ps";
#set multiplot;# allows multiple plots on the same page
#set nokey;#omits the legend in the right hand corner
set ylabel 'excess';
set xlabel 'position';
set title 'Frankia cumulative nucleotide skews';

# set xr [0:1766];
# set yr [0:1];

plot "my_table" using 1:2 title "1vs2" with lines, \
"my_table" using 1:3 title "1vs3" with lines, \
"my_table" using 1:4 title "1vs4" with lines ;

#set nomultiplot;

Save all these commands into a file, e.g. "plot.p". Now at the command prompt execute "gnuplot plot.p". File "myplot.ps" will contain your plot in PostScript format.

To illustrate the power and beauty of gnuplot try the following on a system where gnuplot works interactively. I used gnuplot4.0 under MacOSX 10.4, but there is no reason this shouldnot work on other systems.

Start gnuplot (open terminal, type gnuplot)

Then excute the following:

• set isosample 50
• set samples 1000
• splot ((sin (sqrt(x**2 + y**2))))/sqrt((x**2+y**2))
• set yrange [-20:20]
• set xrange [-20:20]
• replot
• set hidden3d
• replot
• set contour
• show view
• set view 65,30
• replot

You could also execute load "test.p" from within gnuplot, after you copied test.p into the working directory.

Links:

A good article from IBM introducing gnuplot (to plot data, draw functions with examples, change terminals)
The Best Tutorial on GnuPlot (excellent, learning by doing, see for example here)
Official GnuPlot Manual (too complicated)

For those on PCs:
GhostView - free PostScript viewer for PCs (you also can use Adobe PDF writer)