Issue with loom file export function

[SteveTur]

Hi, I run the following function on my date:

from scenicplus.loom import * export_to_loom(scplus_obj, signature_key = 'Gene_based', tree_structure = ('Patient 1', 'SCENIC+'), title = 'Gene based eGRN', nomenclature = "hg38", out_fname='/Users/stur/Paper_Results/SCIENCE/Loom_Files.loom')

However i got the following error:

---

Exception Traceback (most recent call last) Cell In[54], line 2 1 from scenicplus.loom import * ----> 2 export_to_loom(scplus_obj, 3 signature_key = 'Gene_based', 4 tree_structure = ('Patient 1', 'SCENIC+'), 5 title = 'Gene based eGRN', 6 nomenclature = "hg38", 7 out_fname='/Users/stur/Paper_Results/SCIENCE/Loom_Files.loom')

File ~/scenicplus/scenicplus/src/scenicplus/loom.py:214, in export_to_loom(scplus_obj, signature_key, out_fname, eRegulon_metadata_key, auc_key, auc_thr_key, keep_direct_and_extended_if_not_direct, selected_features, selected_cells, cluster_annotation, tree_structure, title, nomenclature) 212 # Create minimal loom 213 log.info('Creating minimal loom') --> 214 _export_minimal_loom(ex_mtx=ex_mtx, 215 cell_names=cell_names, 216 feature_names=feature_names, 217 out_fname=out_fname, 218 regulons=regulon_mat, 219 cell_annotations=None, 220 tree_structure=tree_structure, 221 title=title, 222 nomenclature=nomenclature, 223 embeddings=embeddings, 224 auc_mtx=auc_mtx, ... --> 307 raise Exception('The embedding should have two columns.') 309 # Default embedding must have id == -1 for SCope. 310 embedding_id = idx - 1

Exception: The embedding should have two columns.

I would like to use my own representation which is store here:

dr_cell:'GEX_X_draw_graph_fa'

Is it possible? Where does the error came from exactly ?

Thank you for your help.

Best,

Steven

[SteveTur]

It appears that deleting all other dr_cell files worked, and I was able to retrieve the loom files. However, when I attempted to load them onto the scope, nothing happened.

[SeppeDeWinter]

Hi @SteveTur

What do you mean with nothing happened? Did the files upload? Sometimes you need to click on another embedding (or reload the page) in order that the file properly displays.

All the best,

Seppe

[SteveTur]

Hello Seppe,

Thank you for your response. I followed your suggestion and loaded the loomfile, but there was still no output. I'm wondering whether the issue could be related to the object generation process. By no output, I mean that I managed to load the object correctly; however, the webpage has no options available, like the object is not loaded properly.

Also, I have an unrelated question. Can I manually add another gene to the TF database from Toronto TF database? If I do, will the analysis still work for this particular gene?

Best,

Steven

[SeppeDeWinter]

Hi @SteveTur

Also, I have an unrelated question. Can I manually add another gene to the TF database from Toronto TF database? If I do, will the analysis still work for this particular gene?

Yes, you can do that. As long as there is a motif annotated to that gene in the database it will be included in the analysis.

[SeppeDeWinter]

Regarding this question:

Thank you for your response. I followed your suggestion and loaded the loomfile, but there was still no output. I'm wondering whether the issue could be related to the object generation process. By no output, I mean that I managed to load the object correctly; however, the webpage has no options available, like the object is not loaded properly.

Could you share your Scope session ID, you can find it in the url of your uploaded loom file (if you are unsure, just send the whole link).

Best,

Seppe