Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Sfaira field names in _convert_and_set_var_names #32

Closed
le-ander opened this issue Dec 10, 2020 · 2 comments
Closed

Sfaira field names in _convert_and_set_var_names #32

le-ander opened this issue Dec 10, 2020 · 2 comments
Assignees
@davidsebfischer

Comments

@le-ander
Copy link
Member

I'm a bit unsure why we would use attributes of ADATA_IDS_SFAIRA to define symbol_col= and ensembl_col= in _convert_and_set_var_names() these should always be independent, no?

sfaira/sfaira/data/human/kidney/human_kidney_2020_10x_liao_001.py

Line 116 in 273d7b6

self._convert_and_set_var_names(symbol_col=ADATA_IDS_SFAIRA.gene_id_names, ensembl_col=ADATA_IDS_SFAIRA.gene_id_ensembl, new_index=ADATA_IDS_SFAIRA.gene_id_ensembl)

@davidsebfischer
Copy link
Contributor

Yes true, these we could keep as strings there!

@le-ander
Copy link
Member Author

I guess the only instance where we could have ADATA_IDS_SFAIRA fields in _convert_and_set_var_names() would be when we have just created a new var column of the name ADATA_IDS_SFAIRA.... in the dataloader above

This was referenced Dec 10, 2020
Closed
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@davidsebfischer davidsebfischer

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

_convert_and_set_var_names only receives strings explicitly set in data loader theislab/sfaira
2 participants
@davidsebfischer @le-ander