You might be interested to have different plots in seperate figures in your code. when you create a figure make sure you assign it to a handle:
fig1=figure(1)
fig2=figure(2)
Then later in your code when you want to plot that particular figure. first make that figure your current figure:
figure(fig1)
subplot(2,1,1)
then continue with your code and and for the other figure again change to that figure:
figure(fig2)
plot(x)
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