In R, you can set the alpha channel by
rgb(r=.1,g=.5,b=.5,alpha=.5,max=1)
for any object that takes a color argument. patch objects in pyplot have a set_alpha method, but can this be done for lines on a plot, for instance? like pyplot.plot(x,y,color=???) or h = pyplot.plot(x,y) and do something with h.