It is safer and in my opinion easier to specify the parents explicitly:
Fig1 = figure;
Axes1_1 = subplot(1,2,1, 'Parent', Fig1, 'NextPlot', 'add'); % Equivalent to: hold on
Axes1_2 = subplot(1,2,2, 'Parent', Fig1, 'NextPlot', 'add');
Fig2 = figure(2);
Axes2_1 = subplot(1,2,1, 'Parent', Fig2, 'NextPlot', 'add');
Axes2_2 = subplot(1,2,2, 'Parent', Fig2, 'NextPlot', 'add');
j=0;
while j<=Niter % A FOR loop might be nicer
(...)
plot(tspan,H_v_c, 'Parent', Axes1_1);
stem(j,J_new, 'Parent', Axes1_2);
plot(tspan, xout(:,1)+xout(:,2), 'r', 'Parent', Axes2_1);
plot(tspan, xout(:,3), 'g', 'Parent', Axes2_1);
plot(tspan, xout(:,4), 'b', 'Parent', Axes2_1);
plot(tspan, xout(:,5), 'c', 'Parent', Axes2_1);
plot(tspan, v_chemo, 'Parent', Axes2_2);
j=j+1;
end
Note that in modern Matlab versions (HG2, 2014b) this is safe also to define the parent:
plot(Axes2_2, ...)
This should be faster also, because it avoids the switching of the active figures and axes.
