TypeError: np.matrix is not supported.

[andrewdchen]

Hello!
Running into the following error while running scanorama through scanpy's sc.pp.scanorama_integrate. Couldn't find any related issues/discussions so wondering if anyone had some pointers?

Thanks!

Traceback (most recent call last):
  File "/restricted/projectnb/brcameta/brca_atlas/scripts/05_scvi_scanvi_integration.py", line 92, in <module>
    sce.pp.scanorama_integrate(adata_new, 'batch')
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scanpy/external/pp/_scanorama_integrate.py", line 121, in scanorama_integrate
    integrated = scanorama.assemble(
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scanorama/scanorama.py", line 933, in assemble
    bias = transform(curr_ds, curr_ref, ds_ind, ref_ind, sigma=sigma,
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scanorama/scanorama.py", line 762, in transform
    avg_bias = batch_bias(curr_ds, match_ds, bias, sigma=sigma,
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scanorama/scanorama.py", line 723, in batch_bias
    weights = rbf_kernel(curr_ds, match_ds, gamma=0.5*sigma)
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/sklearn/utils/_param_validation.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/sklearn/metrics/pairwise.py", line 1474, in rbf_kernel
    X, Y = check_pairwise_arrays(X, Y)
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/sklearn/metrics/pairwise.py", line 165, in check_pairwise_arrays
    X = check_array(
  File "/rprojectnb2/montilab-p/personal/andrewdr/mambaforge/envs/scvi-env/lib/python3.9/site-packages/sklearn/utils/validation.py", line 753, in check_array
    raise TypeError(
TypeError: np.matrix is not supported. Please convert to a numpy array with np.asarray. For more information see: https://numpy.org/doc/stable/reference/generated/numpy.matrix.html

[Shashankti]

Hey Andrew, did you figure out the reason behind this error. I am currently facing the same issue and cant figure out whats going wrong