Keep unstructured annotation for manually defining a root_key

[maximilian-heeg]

Hi,

thanks for that wonderful package. I have encountered a issue with one dataset where I wanted to manually define the starting cell of the latent time.

The python package allows to specify a root_key and end_key for the calculation of the pseudotime and latent time.
https://scvelo.readthedocs.io/scvelo.tl.latent_time.html#scvelo.tl.latent_time

The root_key is stored in the unstructured annotation of the adata object. See also here: https://github.com/theislab/scvelo/blob/master/scvelo/tools/dynamical_model.py#L758-L766

Currently, the adata object in this package is created from scratch.
adata <- and$AnnData(X, layers=list(spliced=spliced, unspliced=unspliced))
https://github.com/kevinrue/velociraptor/blob/master/R/scvelo.R#L191

Therefore it is currently not possible to store any information in the unstructured annotation. Could the metadata of a sce object be potentially converted to the unstructured annotation?

Thanks you very much for your help!
Max

[kevinrue]

Hi Max

Thank you for the kind words.

Indeed that sounds entirely feasible, simply an overlook at this stage.

We'll look into it for the next version shortly and get back to you.

Thank you for the feedback!
Kevin

[LTLA]

Sounds like we should be using zellkonverter's conversion utilities to handle the AnnData construction for us.