Complete examples always help ince we have no way of knowing what the
points data structures look like, but I'll hazard a gues.  The x and y
arguments to "plot" need to be sequences.  Ie, something like

  plot([0.5], [0.5], 'ro')

It can be inefficient to plot many separate points this way -- if you
have a lot of points, use a
matplotlib.collections.RegularPolyCollection or scatter.

Thank you for your answer :)

OK, I'll try to wrap them :|. The best solution would indeed be to paint them all at once, but I didn't manage to do that, even when I looked in the scatter_demo2 example :(
What I have is a set of points in a numpy.array - for instance size (2000, 2) -. What I have as well is a nump.array of size (2000, 3). How can I make plot understand that each line of the set points must be painted with the corresponding line in the colour array ?