"This morning" is in the past
Your suggestion is completely correct if "this morning" is in the past:
- She didn't look very happy this morning
- She wasn't! Someone had phoned while she was sleeping.
The phone call was completed before the looking-unhappy, hence past perfect can be used. It was during a continuous past duration of sleeping.
You don't have to specify that the phone call was before the appearance, as they were around the same time or if it's immaterial: so you can also use simple past here, which would be a more common way to put it:
- She wasn't! Someone phoned while she was sleeping.
"This morning" is the present
If "this morning" is the present:
- She doesn't look very happy this morning
- She isn't! Someone phoned while she was sleeping.
The phone call was completed in the past, but not before any other event in the past. The sleeping is still a duration, in the past.
Following are from EF:
past continuous: to describe an unfinished action that was interrupted by another event or action, e.g. "I was having a beautiful dream when the alarm clock rang."
past perfect: The past perfect refers to a time earlier than before now. It is used to make it clear that one event happened before another in the past. It does not matter which event is mentioned first - the tense makes it clear which one happened first.
simple past: The simple past tense, sometimes called the preterite, is used to talk about a completed action in a time before now. The simple past is the basic form of past tense in English. The time of the action can be in the recent past or the distant past and action duration is not important.