User provided latent space

AllenInstitute / transcriptomic_clustering

improved clustering pipeline for transcriptomic data

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User provided latent space #127

Open UCDNJJ opened 1 year ago

UCDNJJ commented 1 year ago

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:

[x] 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 commented 1 year ago

@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?

example

MatthewAitken commented 1 year ago

@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 commented 1 year ago

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