Add -r flag to specify Leiden clustering resolution parameter.

[gjbaker]

No description provided.

[jmuhlich]

@gjbaker I had not actually read through Edward's actual code changes before proposing you submit this as a PR here. It looks like he changed quite a lot of the code, rather than just adding the -r feature and fixing the sc.pp.neighbors call. Let's go over this in detail this week to see if there's a less invasive subset of changes we can integrate.