Error in inline usage

[jenzopr]

Hi!

I'm trying to use Solo inline on an Anndata object with 4 hashtag features. My code looks roughly like this:

# Load adata, filter cells and genes on min_counts = 1
...

# Subset on hashtag features
hdata = adata[:, hashtag_features].copy()

from solo import hashsolo

hashsolo.hashsolo(hdata)

Initially, the error from solo was NotImplementedError: adding a nonzero scalar to a sparse matrix is not supported - I assume because hdata.X is a sparse matrix. Then I tried to do

hdata.X = hdata.X.todense()

prior to the hashsolo call, but now I'm getting a IndexError: boolean index did not match indexed array along dimension 1; dimension is 4 but corresponding boolean dimension is 1. Any ideas how to proceed?

Thanks,
Jens

[jenzopr]

Funnily, saving the hdata object with force_dense = True (as_dense = True in scanpy >=1.5.1) and reloading the object seems to do the trick.

Nevertheless, can hashsolo be easily written to take sparse matrices as well?

[njbernstein]

Hi Jens,

Let me take a look. It will probably just convert the sparse matrix under the hood into a dense matrix because I don't think cell hashing matrices should cause memory issues. Its interesting the

hdata.X = hdata.X.todense()

didnt work.

[jenzopr]

Any update? Maybe a workaround? :-)

[njbernstein]

@jenzopr I merged a fix just now let me know if it works.

Some of the indexing I do in hashsolo doesn't work with a dense matrix so the code needs to be:

if issparse(cell_hashing_adata.X):
    cell_hashing_adata.X = np.array(cell_hashing_adata.X.todense())

[njbernstein]

If you need this fix released to pypi let me know otherwise you can install the fix from cloning the master branch and pip installing from there

[jenzopr]

Thats great! Thanks a lot for your support 🎉

[apredeus]

Same error still appears to happen in the newest version. Saving the .h5ad file using as_dense='X' option, followed by reading it back in again seems to solve the issue, while

adata.X = adata.X.todense()

does not work.