Every graph window is set to display graphs for a particular sub-portfolio. This sub-portfolio is referred to as the "active portfolio" for that graph window. Graph windows are independent, so each graph window can have a different active portfolio. The active portfolio is the one that will be graphed for portfolio based graph types. For investment based graph types the investments in the active portfolio will be graphed.
From within a graph window you can view/select the active portfolio from the top level Portfolio menu command.