Can the company keep the passport with visa for 2...

We would like to inform you that if you are an expat in UAE and the employer took your passport, then the employer doesn't have the right to take it. So you can claim for it, and if they refuse then you can file a complaint with the police and provide a copy of that complaint to the Ministry of Labor to prove the violation.
Note that the law allows the governmental departments that belong to the Ministry of Interior to take the passport, otherwise it is legal violation such as the private sector.