Add analysis module

[roshankern]

@gwaybio This is ready for review!

[roshankern]

Just realized it might be useful to show well or plate for UMAP colors, which could indicate/disprove any plate/image effects on features. I will implement this and let you know when done.

[gwaybio]

LGTM! A couple general comments:

1. I like that you saved the UMAP coordinates, will you use these to generate publication-ready figures later? (I noticed that you didn't save the actual UMAP images)
2. Does format_training_data.ipynb need a number prefix? (i.e. does it need to be executed in a specific order?)

[roshankern]

1. I was just being thorough saving the UMAP coordinates (in case we wanted to analyze/visualize these differently). The publication-ready figures are accessible through the executed jupyter notebook html file. Should I also save the images in results/?
2. format_training_data.ipynb does not need to be executed in a specific order so I will remove the number prefix.

[gwaybio]

Should I also save the images in results/?

Probably. It wouldn't hurt.