From what I understand, you are trying to plot the curve (x1, y1) along with the deviations of the curve (x2, y2) from (x1, y1).
This could be done with the "errorbar(x,y,neg,pos)" function which draws a vertical error bar at each data point, where 'neg' determines the length below the data point and 'pos' determines the length above the data point, respectively.
The following code snippet demonstrates the use of this function, to plot sin(x) against x along with the deviation of cos(x) from sin(x).
x = linspace(-2*pi, 2*pi, 100);
f1_x = sin(x);
f2_x = cos(x);
err = f2_x - f1_x;
pos = zeros(1, length(x));
neg = zeros(1, length(x));
pos(f2_x < f1_x) = err(f2_x < f1_x);
neg(f2_x > f1_x) = err(f2_x > f1_x);
errorbar(x, f1_x, pos, neg);
For further reference, consider going through the following document:
