Starlitnightly/omicverse

TypeError: enrichr() got an unexpected keyword argument 'description'

Closed this issue · 2 comments

When i run the code:
deg_genes=dds.result.loc[dds.result['sig']!='normal'].index.tolist()
enr=ov.bulk.geneset_enrichment(gene_list=deg_genes,
pathways_dict=pathway_dict,
pvalue_type='auto',
organism='mouse')

The error:

TypeError Traceback (most recent call last)
/home/linux/data/python_code/omic_analysis/omic_learn_bulk_different_expression.ipynb Cell 16 line 2
1 deg_genes=dds.result.loc[dds.result['sig']!='normal'].index.tolist()
----> 2 enr=ov.bulk.geneset_enrichment(gene_list=deg_genes,
3 pathways_dict=pathway_dict,
4 pvalue_type='auto',
5 organism='mouse')

File ~/data/miniconda3/envs/pyomic/lib/python3.8/site-packages/omicverse/bulk/_Enrichment.py:211, in geneset_enrichment(gene_list, pathways_dict, pvalue_threshold, pvalue_type, organism, description, background, outdir, cutoff)
208 elif (organism == 'Human') or (organism == 'human') or (organism == 'hs'):
209 background='hsapiens_gene_ensembl'
--> 211 enr = gp.enrichr(gene_list=gene_list,
212 gene_sets=pathways_dict,
213 organism=organism, # don't forget to set organism to the one you desired! e.g. Yeast
214 description=description,
215 background=background,
216 outdir=outdir,
217 cutoff=cutoff # test dataset, use lower value from range(0,1)
218 )
219 if pvalue_type=='auto':
220 if enr.res2d.shape[0]>100:

TypeError: enrichr() got an unexpected keyword argument 'description'

Maybe you need to downgrade pyGSEA, refer to the following code

pip install gseapy==0.10.8

Maybe you need to downgrade pyGSEA, refer to the following code

pip install gseapy==0.10.8

Thanks for your reply!

It's solved the problem.

My sincere thanks again!

With best wishes.