User provided latent space

[UCDNJJ]

Enable the user to provide a latent representation within anndata.obsm for clustering. If latent rep. is provided also ignore PCA computation steps in onestep_clust.

Code updates can be found at: https://github.com/UCDNJJ/tc_latent.

TODO:

• Update onestep_clust to handle new user input specifying latent space (projection) and extracting from anndata obsm.
• New tests for use-case
• Ensure all prior tests pass

Validation:

• Pull request with code coverage, passing all tests.

[UCDNJJ]

@MatthewAitken I'm having trouble passing a test in the test_merging.py due to issues with reading tasic_normed_select.h5ad. Is it possible this file is corrupted on the main branch?

[MatthewAitken]

@MatthewAitken I'm having trouble passing a test in the test_merging.py due to issues with reading tasic_normed_select.h5ad. Is it possible this file is corrupted on the main branch?

The large test files are stored as git lfs objects, do you have git lfs installed? Check the file itself - if it's just a string of characters, it needs to be pulled from git lfs. See here for installation and usage instructions https://git-lfs.com/

[UCDNJJ]

Ah, I haven't used git-lfs before. Just installed git-lfs and re-cloned this repo. Working as expected now, thanks!