Here is one way to create such a plot. Assume you have the point matrix created by the PDE Toolbox mesher, p, and a solution vector, u. The function below will create a plot of that solution along a line defined by the x and y locations of the two end points. My example is for a solution on a unit square and I want a plot along the line (0,.5) to (1,.5). I want to include 25 points in the plot. As you can see, the real work is being done by the TriScatteredInterp function from core MATLAB.
plotAlongLine(p, u, [0,.5], [1,.5], 25);
function plotAlongLine(p, u, xy1, xy2, numpts)
x = linspace(xy1(1),xy2(1),numpts);
y = linspace(xy1(2),xy2(2),numpts);
F = TriScatteredInterp(p(1,:)', p(2,:)', u);
uxy = F(x,y);
figure; plot(x, uxy);