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With rqt_plot you need specify what data (message attribute) you're trying to plot, as messages can be composed of many other messages (which the Navdata message is). If it were to just plot an entire message you could end up with a big mess of plot lines crossing over each other. Besides, some data are strings and arrays. How do you plot a string or an array?

rostopic will happily print whatever message it receives because it's not plotting the data, just printing out what it receives.

So, to plot the information that you want (altitude for instance) you can use

rosrun rqt_plot rqt_plot /ardrone/navdata/altd

and then rqt_plot will plot the time vs. altitude for you. You can follow the same pattern at the top of rqt_plot by entering the topic then specifying the message attribute you want to plot.