How do I intercept rqt plugin mouse events?

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Yes there is a standard way.

Taking rqt python plugin tutorial as an example, you can replace QWidget with your main python modoule, give it to qt_gui.PluginContext.add_widget method.

A little more about concept, rqt framework provides:

1. An "interface" between your own python components and rqt itself.

2. Standard procedures for GUI (shutdown etc.)

3. Nice features for GUI design (ex. loadUi that enables to use UI definition in xml (.ui file)

This means you can easily utilize your own stuff without even modifying. You just add a class that extends qt_gui.plugin.Plugin where you define #1 & #2 above. Currently detailed API document doesn't exist but API Review might give you more insight.