scanpy icon indicating copy to clipboard operation
scanpy copied to clipboard

Add layer support to sc.tl.score_genes

Open gokceneraslan opened this issue 5 years ago • 3 comments

... so that we can do crazy things like scoring velocities or scoring "unspliced expression".

gokceneraslan avatar Dec 25 '19 05:12 gokceneraslan

@gokceneraslan I've been thinking we should have options like layer and obsm in many more places. I've started trying to implement this in a systemic way with an internal API and some test helpers in: #1173.

What would you think of using that here?

ivirshup avatar Apr 21 '20 07:04 ivirshup

@ivirshup is there an elegant way to get subset of genes with _get_obs_rep? because in the current code there are things like:

    _adata = adata.raw if use_raw else adata
    _adata_subset = _adata[:, gene_pool]

gokceneraslan avatar Nov 06 '20 22:11 gokceneraslan

Not much beyond _get_obs_rep(adata[:, genes], ...) or something like _get_obs_rep(adata.raw.to_adata()[:, genes], ...).

ivirshup avatar Dec 13 '20 06:12 ivirshup