Another option is to set the color after plotting via the cell array set syntax:
c = [...
1 0 0
0 1 0
0 0 1];
h = plot(rand(100,3));
set(h, {'color'}, num2cell(c,2));
It requires an extra line of code, but I've always found this much easier than messing with default color order, hold settings, etc.
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