Multiple colors: set color order define in the beginning the color-order for all plots set(0,'DefaultAxesColorOrder',[1 0 0;0 1 0;0 0 1]) or, for an individual plot h = plot(...) set(h,'DefaultAxesColorOrder',[1 0 0;0 1 0;0 0 1]) plot selected samples in different color X = randn(2,100); % data set Xidx = 1:10; % select first 10 samples to highlight in redh1 = plot(X(1,:),X(2,:),'.','Color',[0.7,0.7,0.7]); hold on % plot all samples in greyh2 = plot(X(1,idx),X(2,idx),'.','Color','red'); hold off % plot selected samples (idx) in red |