extensions to support supervised project

[SabrinaRichter]

PR Checklist

• This comment contains a description of changes (with reason)
• Referenced issue is linked
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

Description of changes

• added functionality for self-supervision models to the GraphTools class, should not affect the remaining project

Technical details

Additional context

[github-actions]

Hi @SabrinaRichter,

It looks like this pull-request is has been made against the theislab/ncem master or main branch.
The master/main branch should always contain code from the latest release.
Because of this, PRs to master/main are only allowed if they come from any theislab/ncem release or patch branch.

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Thanks again for your contribution!

[SabrinaRichter]

@AnnaChristina the supervised manuscript works on binary cell types for schuerch (https://github.com/theislab/tissue/blob/b53bcd6bbeefb10f2930fc5c55e51d6d4cfefa4c/tissue/data.py#L1641)
any idea how you want different coarseness levels being handled? multiple cluster_col_xxx columns and then optionally selecting another cluster_col for node_type one-hot encoding set to 'cluster_col_preprocessed' by default?

[AnnaChristina]

I would define this as an additional column in obs of celldata, and I'll check how we ensure this is then subsequently used.

Yes would also go for the set default als many plotting function in ncem require the preprocessed cell names

[SabrinaRichter]

see my edit above?

[AnnaChristina]

Yes also just edited!

[SabrinaRichter]

Can you check out the latest commit? should not have any effect on your code. currently only one level is saved in obs, but one can select which one in the init method

[AnnaChristina]

Looks good to me.