I think PEP20: The zen of Python is relevant here:

"In the face of ambiguity, refuse the temptation to guess."

So instead of guessing whether we are dealing with multichannel data or not, I think a good option is to raise an exception, forcing the user to be explicit about hers or his intentions. With a well written warning message, most users will be able to deal with such an exception without even looking up the function in the documentation.