Png files can handle transparency.
So you could use this question Save plot to image file instead of displaying it using Matplotlib so as to save you graph as a png file.
And if you want to turn all white pixel transparent, there's this other question : Using PIL to make all white pixels transparent?
If you want to turn an entire area to transparent, then there's this question: And then use the PIL library like in this question Python PIL: how to make area transparent in PNG? so as to make your graph transparent.