Try something like this —
x = 1:10;
y = rand(size(x));
figure
stem(x, y)
hold on
stem(x([1 3 5]),y([1 3 5]),'g', 'MarkerEdgeColor','b')
hold off
grid
It changes the stem colour to green, and keeps the marker colour blue.
It is also possible to change the other properties of the chosen (and other) stems and markers.
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