You can add atan2 as a custom function in the Function|Custom functions/constants dialog:
atan2(y,x) = if(x>0, atan(y/x), y>0, pi/2 - atan(x/y), y<0, -pi/2 - atan(x/y), x<0, atan(y/x) + pi)

Alternatively if you don't want to add it every time you need it, you can create it in a plugin. I have attached a pugin that defines the atan2 function. You can install it with the Plugin Manager in the beta version of Graph 4.5.

It is an incredibly useful software. 

I have one major request that would substantially widen its usefulness for me :

Please implement the atan2(y,x) function.

Using atan(y/x) is NOT a work-around for this, because of domain issues.

Thank you !!