2D density plot using gnuplot of x y z data

 set hidden3d
 set dgrid3d 50,50 qnorm 2
 set view map
 splot 'data_file' u 1:2:3 palette



courtesy: http://superuser.com/questions/716014/create-a-smooth-surface-using-x-y-z-data-gnuplot
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make both point size and point color a function of a variable

This can be useful in plotting the wavefunctions on a bunch of sites. For example say the 1 and 2 column has the x and y coordinates of the sites. The 3 rd column contains the wavefunction amplitude.

pl ‘./fort.80’ u 1:2:($3)*10:3 w p pt 7 ps variable palette

The above command will make both the size of the point and the color bar a function of the wavefunction amplitude.