In gnuplot i can draw a rectangle via
set object rect from x0,y0 to x1,y1
How to read the coordinates x0,x1,y0,y1 from a file?
One way would be to put the line of code that sets the rectangle into a separate file and call that file from within the gnuplot script. So you have a file called "coord.txt" that contains the one line
set object rect from 2,2 to 4,40
and you have a gnuplot script called "rect.gp" that says
set title "call rectangle coordinates"
load "coord.txt"
plot x**2
If you now from within gnuplot type load "rect.gp" you get your graph with the rectangle.
That may not be exactly what you are looking for but maybe a first step.