Initial visualization notebooks for sourmash outputs

Sourmash is a tool for rapidly comparing sequencing data. We've used sourmash in this repository to analyze and compare the content of cheese metagenomes. However the purpose of this repo is to create a generalized pipeline and set of visualizations that could work to look at any new metagenome sequencing data -- regardless of metadata associated with those new samples, complexity of the underlying community, or the number of samples.

It's difficult to generate a generalized set of visualizations that show something interesting and are interprettable, but I've taken a stab at it here.

What I'm looking for at this point is feedback on the visualizations that exist and help identifying anything that is obviously missing or that would be super helpful.

A general point to keep in mind is that I think sourmash fits very early on in the get to know you phase of data analysis. The hope is that these visualizations help you identify interesting patterns that you would want to dig into more with more in depth tools. If these visualizations spark a lot of interesting biological questions for you that you can't wait to learn more about, they've done their job. If the visualizations just make you confused and you have no idea what's going on, then I failed :)

@borgesadair1, I know you're most interested in viruses. I've held off on adding the virus viz to this PR because I want to make sure we're getting quality results from sourmash first. That being said, I think some of the visualizations in other notebooks could be applied to viruses, so I would love your opinions on what would be best to dev there.

@ecpierce, I know you're most interested in fungi. I started a fungi notebook but it's currently very sparse. It would be helpful if you could see what other visualization I have implemented that you would like to see specifically for fungi, or to hear what you think is just missing from this space at all.

@JAArc, @Manon-Morin welcome to GitHub! I haven't shown you how to go over a pull request yet. The easiest way to view the content in the PR is to either use the NB review button below, or to navigate back to the home page of this repository, click on the branch drop down mean (by default it will say main), and select init_viz. Then navigate to the notebooks folder and scroll through all of the the ipynb notebooks. These are files that have code, text, and figures all combined together. I would love any comments you have. You can use the comment feature on the PR to add your thoughts if you don't want to use the full review feature, or we can set up a time to go over how to use those features.

Arcadia-Science / 2022-prjna853785-sourmash

Initial visualization notebooks for sourmash outputs #8