Consider these examples:
cows eat grass
This example is a clause, because it contains the subject "cows" and the predicate "eat grass."
cows eating grass
What about "cows eating grass"? This noun phrase could be a subject, but it has no predicate attached to it: the adjective phrase "eating grass" show which cows the writer is referring to, but there is nothing here to show why the writer is mentioning cows in the first place.
cows eating grass are visible from the highway
This is a complete clause again. The subject "cows eating grass" and the predicate "are visible from the highway" make up a complete thought.
This single-word command is also a clause, even though it does seem to have a subject. With a direct command, it is not necessary to include the subject, since it is obviously the person or people you are talking to: in other words, the clause really reads "[You] run!". You should not usually use direct commands in your essays, except in quotations.