Extract PC matrix within clustering function (2/2)

[sjspielman]

Closes #754

This PR does the second half of #754 and allows calculate_clusters() to take a single-cell object instead of only a matrix.
I'm opening this as a draft because I couldn't pick between two ways of doing this..so I implemented them both. Which general approach should we go with (noting it might be a little bit "why not both"!)?

• First, in 01d538a, I primarily updated the calculate_clusters() function and left the extract pc function alone. While writing docs for it though, it felt odd strange to describe the default pc_name argument behavior in the clustering function when the extract function was actually defining those defaults. I then wondered if too much was getting duplicated, so I then...
• Implemented the most recent commit shown in the PR, where I moved a decent amount of the behavior out of the extract function and into the clustering function. Here, the extract function requires all arguments.

[jashapiro]

I think you may have overcomplicated things! The extract function you had already did all the conversions and checks, so let it handle that. I made a suggestion that I feel like ought to work with pretty minimal code changes, if you revert the extract function to its previous form.

[sjspielman]

I think you may have overcomplicated things!

Me?!

But in all seriousness, yes. What you have suggested is more or less my first commit, so I'll just revert and get back on track there!

[jashapiro]

• While writing docs for it though, it felt odd strange to describe the default pc_name argument behavior in the clustering function when the extract function was actually defining those defaults.

Just write something like "optional pc_name argument passed to extract_pc_matrix"

[sjspielman]

Should be ready for a real look now. Note that I ended up exporting extract_pc_matrix (so I also wrote some quick examples) since we refer to it in the calculate_cluster docs now.

[jashapiro]

LGTM, with one little comment about column name checks.