Add first basic scrublet integration

pinin4fjords commented 3 years ago

First-level Scrublet integration. This should handle all arguments and produce the object output and call the main scrublet() function.

To do:

[x] allow filtering of object based on doublet status
[x] add some optional non-object outputs (e.g. tabular)
[x] Add CLI for functions other than main scrublet() (plot, simulate etc) to allow intelligent operation

1/7/2021: Now complete following release of Scanpy 1.8 with a change I was waiting on. To summarise, changes in this PR:

write_cluster() renamed to write_obs(). I needed to export the doublet obs data and the existing function works, but needed a rename to reflect wider utility.
Commands added to run overall scrublet function, and associated functions for plotting, simulating doublets independently etc.
Factored out existing neighbour metric argument so it can be used for scrublet without duplicating it.

pinin4fjords commented 3 years ago

Proposed https://github.com/theislab/scanpy/pull/1741 to plotting function in Scanpy to allow better integration with established plotting patterns in this package.

pinin4fjords commented 3 years ago

Thanks for the review @pcm32

ebi-gene-expression-group / scanpy-scripts