Programmatically save plots

[mofojed]

For data analysis code, need to be able to programmatically save plots (eg. plot.save("file.png") should write out a file).

[mofojed]

This may be related to #8 and #287 , in that we need to have a clear instructions for the user to mount a directory for usage (or some way of getting their files in and out of the Docker container).

[mofojed]

I think this will work once plotting works. Right now getting an error when trying to create a plot, with missing classes.