Use the matplotlib savefig function with the keyword argument transparent=True to save the image as a png file.
In [30]: x = np.linspace(0,6,31)
In [31]: y = np.exp(-0.5*x) * np.sin(x)
In [32]: plot(x, y, 'bo-')
Out[32]: [<matplotlib.lines.Line2D at 0x3f29750>]
In [33]: savefig('demo.png', transparent=True)
Result:
Of course, that plot doesn't demonstrate the transparency. Here's a screenshot of the PNG file displayed using the ImageMagick display command. The checkerboard pattern is the background that is visible through the transparent parts of the PNG file.
