The NaN values themselves will not plot. This may produce breaks in the plotted line, so if you don’t want the breaks, your only option is to interpolate.
The easiest way to interpolate is to keep your original independent variable to be your interpolating variable, the eliminate all the NaN values from your dependent variable and the corresponding values of you independent variable, then use interp1.
Example:
x = 1:10;
y = [2 4 2 9 NaN 3 1 NaN 6 10];
xs = x(~isnan(y));
ys = y(~isnan(y));
yi = interp1(xs, ys, x, 'Linear');
figure(1)
subplot(2,1,1)
plot(x, y)
grid
subplot(2,1,2)
plot(x, yi)
grid
