TypeError (unsupported operand type(s) for +:) issue with 'Calculating TF-eGRNs AUC correlation'

[SidG13]

Describe the bug
Hi, I'm copying this issue to discussion since I believe it may be more appropriate here. First off, I'm pretty sure this is a similar issue as mentioned in #112 . My understanding is that there is a minor problem in a line concerning using the '+' operation on a string and int but I'm not entirely sure.

I actually changed the code locally so that cistromes.py:214

cell_names.append(category + '_' + str(x))

becomes

cell_names.append(str(category) + '_' + str(x))

However, this now produces no markers for my clusters, presumably because each cell cluster/type is now treated as a string (my cell clusters are called '0-7', a holdover from Seurat's annotation)?

I'm able to run the function fully (no obvious errors) by using:

scplus_obj.metadata_cell['GEX_cell_cluster'] = scplus_obj.metadata_cell['GEX_cell_cluster'].astype(str)

But my cluster names are now "0.0, 1.0, 2.0" etc. Since this didn't fix the underlying issue I believe, I reverted my change.

To Reproduce
I was running the following command, the scenicplus wrapper:

from scenicplus.wrappers.run_scenicplus import run_scenicplus
try:
    run_scenicplus(
        scplus_obj = scplus_obj,
        variable = ['GEX_cell_cluster'],
        species = None,
        assembly = None,
        tf_file = '/home/administrator/Desktop/ExtraDrive1/Sid/sc_multiome/SCENICplus_multiome/data_manipulation/utoronto_human_tfs_v_1.01.txt',
        save_path = os.path.join(work_dir, 'scenicplus'),
        upstream = [1000, 150000],
        downstream = [1000, 150000],
        calculate_TF_eGRN_correlation = True,
        calculate_DEGs_DARs = True,
        export_to_loom_file = True,
        export_to_UCSC_file = True,
        path_bedToBigBed = '/home/administrator/Desktop/ExtraDrive1/Sid/sc_multiome/SCENICplus_multiome/data_manipulation',
        n_cpu = 12,
        _temp_dir = os.path.join(tmp_dir, 'ray_spill'))
except Exception as e:
    #in case of failure, still save the object
    dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=4) # change dill protocol to 4
    raise(e)

Error output
Much of the wrapper worked correctly, it breaks at "Calculating TF-eGRNs AUC correlation". I've put the error message from only this section below.

2023-02-20 12:22:25,821 SCENIC+_wrapper INFO     Calculating TF-eGRNs AUC correlation
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In [18], line 22
     19 except Exception as e:
     20     #in case of failure, still save the object
     21     dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=4)
---> 22     raise(e)

Cell In [18], line 3
      1 from scenicplus.wrappers.run_scenicplus import run_scenicplus
      2 try:
----> 3     run_scenicplus(
      4         scplus_obj = scplus_obj,
      5         variable = ['GEX_cell_cluster'],
      6         species = None,
      7         assembly = None,
      8         tf_file = '/home/administrator/Desktop/ExtraDrive1/Sid/sc_multiome/SCENICplus_multiome/data_manipulation/utoronto_human_tfs_v_1.01.txt',
      9         save_path = os.path.join(work_dir, 'scenicplus'),
     10         upstream = [1000, 150000],
     11         downstream = [1000, 150000],
     12         calculate_TF_eGRN_correlation = True,
     13         calculate_DEGs_DARs = True,
     14         export_to_loom_file = True,
     15         export_to_UCSC_file = True,
     16         path_bedToBigBed = '/home/administrator/Desktop/ExtraDrive1/Sid/sc_multiome/SCENICplus_multiome/data_manipulation',
     17         n_cpu = 12,
     18         _temp_dir = os.path.join(tmp_dir, 'ray_spill'))
     19 except Exception as e:
     20     #in case of failure, still save the object
     21     dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=4)

File ~/Desktop/ExtraDrive1/Sid/sc_multiome/SCENICplus_multiome/scenicplus/src/scenicplus/wrappers/run_scenicplus.py:240, in run_scenicplus(scplus_obj, variable, species, assembly, tf_file, save_path, biomart_host, upstream, downstream, region_ranking, gene_ranking, simplified_eGRN, calculate_TF_eGRN_correlation, calculate_DEGs_DARs, export_to_loom_file, export_to_UCSC_file, tree_structure, path_bedToBigBed, n_cpu, _temp_dir)
    238 log.info('Calculating TF-eGRNs AUC correlation')
    239 for var in variable:
--> 240     generate_pseudobulks(scplus_obj, 
    241                      variable = var,
    242                      auc_key = 'eRegulon_AUC',
    243                      signature_key = 'Gene_based',
    244                      nr_cells = 5,
    245                      nr_pseudobulks = 100,
    246                      seed=555)
    247     generate_pseudobulks(scplus_obj, 
    248                              variable = var,
    249                              auc_key = 'eRegulon_AUC',
   (...)
    252                              nr_pseudobulks = 100,
    253                              seed=555)
    254     TF_cistrome_correlation(scplus_obj,
    255                     variable = var, 
    256                     auc_key = 'eRegulon_AUC',
    257                     signature_key = 'Gene_based',
    258                     out_key = var+'_eGRN_gene_based')

File ~/Desktop/ExtraDrive1/Sid/sc_multiome/SCENICplus_multiome/scenicplus/src/scenicplus/cistromes.py:214, in generate_pseudobulks(scplus_obj, variable, normalize_expression, auc_key, signature_key, nr_cells, nr_pseudobulks, seed)
    212         cistrome_auc_agg_list.append(sub_auc)
    213         dgem_agg_list.append(sub_dgem)
--> 214         cell_names.append(category + '_' + str(x))
    215 cistrome_auc_agg = pd.concat(cistrome_auc_agg_list, axis=1)
    216 cistrome_auc_agg.columns = cell_names

TypeError: unsupported operand type(s) for +: 'int' and 'str'

Expected behavior
I'm not too sure what category is at line 214, but this is where it is adding an integer and a string. My variable 'GEX_cell_cluster' is an integer, does this cause an issue? If so, is there an easy way to fix this at this stage?

Version (please complete the following information):

• Python: 3.8.13
• SCENIC+: 0.1.dev453+gf322c5b

Additional context
Thank you!

[SeppeDeWinter]

Hi @SidG13

Sorry I missed this question.

Can you try converting 'GEX_cell_cluster' in your metadata_cell to strings (e.g. 'cluster_1', 'cluster_3', ... etc.).

Best,

Seppe

[SidG13]

No problem! I'm really not too familiar with anndata, so here's how I went about it (I don't know how to append a string to a slot like you said), just converting directly to a string.

scplus_obj.metadata_cell['GEX_cell_cluster']=scplus_obj.metadata_cell['GEX_cell_cluster'].astype(str)

I still get the output:

where my clusters are called "0.0, 1.0, 2.0" etc. and there are no markers for them. But notice that scenicplus does work properly, which is good, I'm just not sure if this is hinting at an underlying problem.

[SidG13]

I was able to do it in the end, adding the cluster_ as a string did help! Thanks!