Create a click through window for Linux

Question

I want to make a click through window. A window which I click but the click pass to the window below it.

I've found this two solutions for windows:

How to make click-through windows PyQt
I have a form that can "click through", i.e. direct clicks to the window below. How can I undo my changes after the event?

But I want it to work in linux. I study the xlib mechanisms but cannot understand how the window stack works. Actually I can get all the windows with XQueryTree() and found the ones under my window. But I don't know witch one are above.