Plot function doesn't have support to tune transparency. You can use scatter to do that
scat = scatter(x,y,'MarkerFaceColor','b','MarkerEdgeColor','r');
scat.MarkerFaceAlpha = .5;
scat.MarkerEdgeAlpha = .5;
You can manipulate the color values, if you wish to use plot function.
hand = plot(X,Y,'r');
hand.LineWidth = 2;
hand.Color(4)=0.2; % this would act as your alpha value or transparency factor.
