So you want to just call:
plot(x, y)
then change the plotted line to have a different line style or color? Call plot with an output, so you have a handle to the line, then change its properties.
x = 0:0.1:2*pi;
y = sin(x);
h = plot(x, y);
pause % So you can see how the plot looks before its properties change
h.Color = 'r';
