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There is a way to get subplots working - not a very convenient one though. @dirk-thomas 's comment in this thread points in the right direction: https://github.com/ros-visualization/rqt_common_plugins/issues/86#issuecomment-21653925

You can load multiple plugins/instances of a plugin into the same rqt window. The command provided in the comment didn't work for me, but you can do it manually.

Start rqt

$ rqt

Then on the top left select Plugins -> Visualization -> Plot to add a rqt_plot. Repeat this to add more plots.

Note that every plot is independent. For example, if you pause one, the other continues to run.

This does the trick for me. Hope it helps you, too!