It's not the wrong function, but applying it very inefficiently. Each call to plot() produces another line object so you're creating a zillion of 'em.
Rearrange the code with logical addressing to plot all of one linestyle in one call using hold on after first to add to the same axis.
Something more like
) A filled 'o' if the entry is 1
2) An empty(very lightly shaded) 'o' if the entry is 0
3) A 'x' if the entry is 2
for i=1:numberLines
is1=(H{i}==1); % logical for case 1
is0=(H{i}==0); % logical for case 2
is2=(H{i}==2); % logical for case 3
plot(time_EWS{i}(is1),H{i}(is1),'o','MarkerSize',5,'MarkerFaceColor', PS.Grey4, 'MarkerEdgeColor', PS.Grey5);
hold on
plot(time_EWS{i}(is0),H{i}(is0),'x','MarkerSize',5,'MarkerFaceColor', PS.Red1, 'MarkerEdgeColor', PS.Red2);
plot(time_EWS{i}(is2),H{i}(is2),'o','MarkerSize',5,'MarkerFaceColor', PS.Grey1,'MarkerEdgeColor', PS.Grey2);
end
is the crux of what need to do instead.
The above can be streamlined significantly more by use of arrays to hold the various pieces such as the colors and markers and logical vectors to use a loop for the plot() call instead of multiple individual calls.
It would also be best practice to save the line handles into an array of handles to be able to use for legends or other manipulations after the initial plotting is done.
The above would plot the actual values; your code would plot a straight line -- if that is really what was wanted, then create the Y vector as Y=[N:-1:1] and use it instead with the logical indexing arrays.
