Seems like Plotly doesn't support chart selection the way I would like to, and I have to use HTML Canvas, but that's not really a problem. I just grouped the charts together with Plotly's subplots and created a Canvas above the whole chart. Since I know where the user clicks and where the diagrams are, it's not too hard to calculate the maths needed and draw the rectangles on the Canvas accordingly. May have performance issues with a larger data set and multiple subplots, but that needs further investigation. The idea is basically this and the question is solved.