Here's a trick for doing precisely what you are looking for, run the example:
data1 = randi([0,100],100,1);
data2 = randi([0,10],100,1);
plot(1:100, data1,'-r*')
hold on
data2_complement = 100 - data2;
data2 = [data2_complement data2];
b = bar(data2,'stacked');
b(1).FaceAlpha = 0;
b(1).EdgeAlpha = 0;
In words - what happens here is the following: 1. You plot the data set you want on the top, as a stacked bar, ranging the entire span of the yaxis limits. Do so by adding to your real vector a complementary vector that holds up space (in my example this was data2_complement). 2. Now all you need to do is set the Alpha (transparency) to zero so you won't actually see this complementary vector
Hope this helps
p.s. if you post your real data, I can try adjusting this example to fit with your real task
