You can specify a vector of plot handles to use in the legend. For example:
h1 = plot(rand(1,10)); % Blue line
hold on;
h2 = plot(rand(1,10),'r'); % Red line
h3 = plot(rand(1,10),'g'); % Green line
legend([h1 h3],{'hello','world'}); % Only the blue and green lines appear
% in the legend
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