If the lines you want in the legend are the first things you plot (i.e., you plot all of them before you add the extra lines and annotations), you can call legend after everything is plotted with only the legend entries you want to be shown. Example below:
% Sample data to plot
x = 0:10;
y1 = x.^2;
y2 = x.^3;
% Plot data
plot(x,y1);
hold on;
plot(x,y2);
% Add other lines and annotations
line(xlim, [10 10]);
% Create legend for y1 and y2
% Since there are only two entries, nothing is shown in the legend for the reference line
legend('y1', 'y2');
If you're plotting additional annotations between lines of plotting data, you should save plots to variables, as below:
% Plot line 1
h1 = plot(x,y1);
hold on;
% Other lines and annotations
line(xlim, [10 10]);
% Plot line 2
h2 = plot(x,y2);
% Create legend
legend([h1 h2], 'y1', 'y2');
Hope this helps!
