Gnuplot can make great scattered plots, including the use of circles instead of just dots. The circles are typically filled, with their radious depending on a numerical value on the data being plotted. In addition, it is also possible to draw a border in the circle using different colors. Here is an example using characters from Grey’s Anatomy TV show.

These are the gnuplot commands to create the scattered plot:

set term jpeg size 700,800
set output 'plot_scattered.jpeg'
set xtics rotate ( "Meredith" 1, "Avery" 2, "Teddy" 3, "Karev" 4, "Bailey" 5, "Burke" 6, "Lexie" 7, "Owen" 8, "Addison" 9, "O'Malley" 10, "Arizona" 11, "Derek" 12, "April" 13, "Sloan" 14, "Izzie" 15, "Webber" 16, "Christina" 17, "Callie" 18 ) scale 0
set ytics ( "Meredith" 1, "Avery" 2, "Teddy" 3, "Karev" 4, "Bailey" 5, "Burke" 6, "Lexie" 7, "Owen" 8, "Addison" 9, "O'Malley" 10, "Arizona" 11, "Derek" 12, "April" 13, "Sloan" 14, "Izzie" 15, "Webber" 16, "Christina" 17, "Callie" 18 ) scale 0
plot [0:19][0:23] "homerun.txt" using 3:5:1 title 'homerun' with circles linecolor rgb "#9ACD32" fill solid noborder \
, "gender.txt" using 3:5:1 title 'homerun same gender' with circles linecolor rgb "#9400D3" lw 3 fill solid border lt 3 \
, "firstbase.txt" using 3:5:1 title 'first-base' with circles linecolor rgb "#A9A9A9" lw 3

These are the text files with the data being plotted: homerun, gender, firstbase.

One great thing about Gnuplot is that it can create SVG files, this is the SVG file of the same plot: svg_file (rename it to .svg instead of .txt so that a web browser can open it).