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When mousing is active, clicking in the active window will set several user variables that can be accessed from the gnuplot command line. The coordinates of the mouse at the time of the click are stored in MOUSE_X MOUSE_Y MOUSE_X2 and MOUSE_Y2. The mouse button clicked, and any meta-keys active at that time, are stored in MOUSE_BUTTON MOUSE_SHIFT MOUSE_ALT and MOUSE_CTRL. These variables are set to undefined at the start of every plot, and only become defined in the event of a mouse click in the active plot window. To determine from a script if the mouse has been clicked in the active plot window, it is sufficient to test for any one of these variables being defined.
plot 'something' set pause mouse if (defined(MOUSE_BUTTON)) call 'something_else'; \ else print "No mouse click."