`scgen.batch_removal` doesn't save `adata.raw` about scgen HOT 3 CLOSED

Like Carlos mentioned, he was trying to add a .raw attribute to the resulting object, and the expression plots did not have the genes show up where he was expecting them to. Looking at batch_removal(), I understand why. You subset and concatenate the object, reshuffling the order of the cells within it, and then at the end you paste the original .obs_names over the current ordering, essentially scrambling the index.

This can be amended quite easily - just add index_unique=None to each of your .concat() calls. At the end, you can re-sort the final corrected object to match the original's cell ordering rather than overwrite the .obs_names, and if you do that you can just copy the .raw over if you feel like it.

from scgen.

Like Carlos mentioned, he was trying to add a .raw attribute to the resulting object, and the expression plots did not have the genes show up where he was expecting them to. Looking at batch_removal(), I understand why. You subset and concatenate the object, reshuffling the order of the cells within it, and then at the end you paste the original .obs_names over the current ordering, essentially scrambling the index.

This can be amended quite easily - just add index_unique=None to each of your .concat() calls. At the end, you can re-sort the final corrected object to match the original's cell ordering rather than overwrite the .obs_names, and if you do that you can just copy the .raw over if you feel like it.

Hi @ktpolanski ,

Yes, this can be easily added, At the moment I am busy with something else, I would be happy if you guys would be interested to fix it and I will happily merge your pull requests.

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Thanks to @ktpolanski now correc_data also has .raw file of the original adata. @cartal I also updated the example [here(https://nbviewer.jupyter.org/github/M0hammadL/scGen_notebooks/blob/master/notebooks/scgen_batch_removal.ipynb) to show that you can use .raw file after correction.

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