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Exporting raw data in CSV

See original GitHub issue

Hi Guys,

this it perhaps rather a question than issue, Is there a way to export raw data in csv format? If I do this adata.write_csvs("filename", skip_data=False)

it works perfectly fine

but with adata.raw.write_csvs("filename", skip_data=False)

I get this error AttributeError: 'Raw' object has no attribute 'write_csvs'

Thanks,

Issue Analytics

State:
Created 5 years ago
Reactions:1
Comments:12 (7 by maintainers)

Top GitHub Comments

12reactions

tsotnechcommented, Mar 1, 2019

@LuckyMD @maximilianh Thanks guys for your help and sorry for misunderstanding I think I wasn’t explaining correctly my issue.

So at the end this worked perfectly well to export raw data matrix

t=adata.raw.X.toarray()
pd.DataFrame(data=t, index=adata.obs_names, columns=adata.raw.var_names).to_csv('adata_raw_x.csv')

1reaction

LuckyMDcommented, Mar 1, 2019

I think I understand what you mean. The “coordinate” representation you are referring to is a sparse matrix format. If you don’t want that representation, you can densify your data using the function: adata.X.toarray(). I think you should be able to do the same with adata.X.raw as well.

Scaling removes the sparse matrix formatting, as the matrix is no longer sparse after scaling. In other words, scaling replaces (nearly) all of the 0s, so you get a dense format.

I hope that is what you’re looking for.