My wife has cancer I file separately her income bracket goes low enough to qualify for special treatment. will this show her as low income without looking at my income?

You will need to ask the organization that offers that "special treatment" for low income people.

However, MOST organizations will still look at your combined Household income if you are married and live together.  But again, you need to ask the organization that is offering the special treatment how they determine eligibility for that "special treatment".