How can I close the two windows that the following MATLAB SOM example creates, from the command line?
>> x = simplecluster_dataset;
>> net = selforgmap([8 8]);
>> net = train(net,x);
>> view(net)
>> y = net(x);
>> classes = vec2ind(y);
Your code opens two windows which are: Neural Network Training Window and Self-Organizing Map.
As mentioned in the documentation, nntraintool close is for closing Neural Network Training Window and as answered here, nnet.guis.closeAllViews() is for closing all diagrams of the Neural Networks.
If you are using multiple nnet guis views and want to close only a specific view, assign a handle to that particular view and then use close to close it. i.e. replace view(net) with h = view(net), now when you use, close(h), it'll close that particular nnet gui view.