I don’t have your code, but if you want a plot in a new figure window, precede the plot call with a figure call:
figure(1)
subplot(2,1,1)
plot( ...)
subplot(2,1,2)
plot
The numbers in the figure call are not absolutely necessary, but since MATLAB will put all subsequent plots in the existing figure window if you do not create a new figure window each time, it helps to keep track of them.
