I use gnuplot and Stata to generate a heatmap representation of a square matrix containing a measure of closeness between 26 departments in a university. gnuplot is a general-purpose plotting program, and can be wheedled into doing a lot of things, but Stata’s graphics routines are also very general. Given data in i, j, n format (in blocks, that is with a blank line inserted before every change of value of i), gnuplot can generate a heatmap with code like the following: