How do I add a flowclust 2d gate to an existing gatingset? I am able to do this successfully for rectangle gates using add(gs,myrectgate,...) but I can't figure out how to do a similar thing with a flowclust gate. 

If you are using the function 'gate_flowClust_2d' from openCyto package, it returns a polygonGate, which can be added as it is to `GatingSet` by `add` method. If you were talking about using `flowClust` package directly (e.g. through 'flowClust` function), you need to convert the tmixFilter result to `ellipseGate`. It can be done through the convenient internal wrapper  'openCyto:::.getEllipseGate`. Alternatively, you can use another helper function ('cytoUtils::tmix2DGate') to invoke the `flowClust` and get the multiple (depends on your input of 'K') polygonGates .