fixed neighbors key bug

[jjia1]

Pull request type

Please check the type of change your PR introduces:

• Bugfix
• Feature
• Code style update (formatting, renaming)
• Refactoring (no functional changes, no api changes)
• Build related changes
• Documentation content changes
• Other (please describe):

What is the current behavior?

Issue Number: welch-lab#6

Current error status

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[46], line 4
      2 keys = ['fullvb']
      3 grid_size = (1,2)
----> 4 res, res_type = vv.post_analysis(adata,
      5                                  'continuous',
      6                                  methods,
      7                                  keys,
      8                                  compute_metrics=True,
      9                                  raw_count=False,
     10                                  #genes=gene_plot,
     11                                  grid_size=(1,2),
     12                                  #figure_path=figure_path,
     13                                  cluster_key='celltype')

File ~/miniconda3/envs/velovae/lib/python3.10/site-packages/velovae/analysis/evaluation.py:455, in post_analysis(adata, test_id, methods, keys, gene_key, compute_metrics, raw_count, genes, plot_type, cluster_key, cluster_edges, nplot, frac, embed, grid_size, sparsity_correction, figure_path, save, **kwargs)
    453 for i, method in enumerate(methods):
    454     if compute_metrics:
--> 455         stats_i, stats_type_i = get_metric(adata,
    456                                            method,
    457                                            keys[i],
    458                                            vkeys[i],
    459                                            cluster_key,
    460                                            gene_key,
    461                                            cluster_edges,
    462                                            embed,
    463                                            n_jobs=(kwargs['n_jobs']
    464                                                    if 'n_jobs' in kwargs
    465                                                    else None))
    466         stats_type_list.append(stats_type_i)
    467         # avoid duplicate methods with different keys

File ~/miniconda3/envs/velovae/lib/python3.10/site-packages/velovae/analysis/evaluation.py:273, in get_metric(adata, method, key, vkey, cluster_key, gene_key, cluster_edges, embed, n_jobs)
    266 stats['Vel Consistency (Velocity Genes)'] = mean_vel_consistency_sub
    268 # Compute velocity metrics on all genes
    269 (iccoh, mean_iccoh,
    270  cbdir_embed, mean_cbdir_embed,
    271  cbdir, mean_cbdir,
    272  tscore, mean_tscore,
--> 273  mean_vel_consistency) = get_velocity_metric(adata,
    274                                              key,
    275                                              vkey,
    276                                              cluster_key,
    277                                              cluster_edges,
    278                                              None,
    279                                              embed,
    280                                              n_jobs)
    281 stats['CBDir (Embed)'] = mean_cbdir_embed
    282 stats['CBDir'] = mean_cbdir

File ~/miniconda3/envs/velovae/lib/python3.10/site-packages/velovae/analysis/evaluation.py:80, in get_velocity_metric(adata, key, vkey, cluster_key, cluster_edges, gene_mask, embed, n_jobs)
     35 def get_velocity_metric(adata,
     36                         key,
     37                         vkey,
   (...)
     41                         embed='umap',
     42                         n_jobs=None):
     43     """
     44     Computes Cross-Boundary Direction Correctness and In-Cluster Coherence.
     45     The function calls scvelo.tl.velocity_graph.
   (...)
     78             - float: Velocity Consistency
     79     """
---> 80     mean_constcy_score = velocity_consistency(adata, vkey, gene_mask)
     81     if cluster_edges is not None:
     82         try:

File ~/miniconda3/envs/velovae/lib/python3.10/site-packages/velovae/analysis/evaluation_util.py:1621, in velocity_consistency(adata, vkey, gene_mask)
   1607 def velocity_consistency(adata, vkey, gene_mask=None):
   1608     """Velocity Consistency as reported in scVelo paper
   1609 
   1610     Args:
   (...)
   1619         float: Average score over all cells.
   1620     """
-> 1621     nbs = adata.uns['neighbors']['indices']
   1623     velocities = adata.layers[vkey]
   1624     nan_mask = ~np.isnan(velocities[0]) if gene_mask is None else gene_mask

KeyError: 'indices'

What is the new behavior?

Current version evaluation_utils.py calls the neighbor indices as adata.uns['neighbors']['indices'].
This doesn't work with newer versions of anndata and/or Scanpy where adata.uns['neighbors'].keys()
will print out:

dict_keys(['connectivities_key', 'distances_key', 'params'])

where the indices are inside of the connectivities_key. I found the offending behavior in the following functions:

1. velocity_consistency
2. inner_cluster_coh
3. cross_boundary_correctness
4. gen_cross_boundary_correctness
5. gen_cross_boundary_correctness_test
6. calibrated_cross_boundary_correctness
7. also added import to include csr_matrix from scipy.sparse

Other information

Output from

# Get all module names in the current namespace
module_names = set(sys.modules) & set(globals())

# Print the name and version of each module
for name in module_names:
    module = sys.modules[name]
    if hasattr(module, '__version__'):
        print(f"{name}=={module.__version__}")
    elif hasattr(module, 'VERSION'):
        print(f"{name}=={module.VERSION}")
    else:
        print(f"{name}")

logging==0.5.1.2
torch==2.3.1
math
random
warnings
textwrap
sys
anndata==0.10.7
os
cellrank==2.0.4
gc

Other package dependencies are available upon request.