If part of the wisdom tooth has appeared through the gum and part of it is still covered, the gum may become sore and perhaps swollen. Food particles and bacteria can collect under the gum edge, and it will be difficult to clean the area effectively.
Your dentist will tell you whether this is a temporary problem that can be dealt with by using mouthwashes and special cleaning methods (and possibly antibiotics), or whether it is better to have the tooth removed.