search

saeyslab / napari-sparrow

Other
18 stars 0 forks source link

Analyze multirun results #61

Closed berombau closed 2 years ago

berombau commented 2 years ago

A cleaned-up version of https://github.com/saeyslab/napari-spongepy/blob/Lotte/experiments/join_to_adata.ipynb should serve as an example of how to analyze the result folder of a multirun.

The .adata's should be concatenated and the metadata of the dataset should be added in .obs.

berombau commented 2 years ago

We can use the experimental AnnCollection API https://anndata.readthedocs.io/en/latest/generated/anndata.experimental.AnnCollection.html. The lazy loading would be nice and it also supports .to_adata() to gain the same concatenated output.

KoenDesplenter commented 2 years ago

I made a cleaned-up version of the notebook named analysis.ipynb in the branch analyse. The notebooks is able to perform the whole analysis by just adjusting the path of the multirun folder. I will look into the Anncollection API.

berombau commented 2 years ago

We'll come back to the AnnCollection API later, when it's less experimental