I think I found a bug in how scatter() handles the alpha transparency of the plotted points. If the color array passed in is composed of integers, then the alpha is applied to the points like it should. But if the color array is floats, then the alpha parameter is ignored. Here is some sample code to demonstrate. I tested with the latest svn code.
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
ax.scatter([1,2,3,4], [1,2,3,4])
#alpha ignored
ax.scatter([1,2], [1,2],
s = 120,
c = [(1.0, 0.0, 0.0, 1.0), (0.0, 1.0, 0.0, 1.0)],
edgecolor = 'none',
alpha = 0.4)
#alpha used
ax.scatter([3,4], [3,4],
s = 120,
c = [(1, 0, 0, 1), (0, 1, 0, 1)],
edgecolor = 'none',
alpha = 0.4)
plt.show()
Thanks,
-Ben