mousepixels
Fix: Integration step's labeling of samples
Why:
In the integration section, we looped through all of the csv files and saved the sample names in adata.obs['Sample']. However, the sample name was being stored as 'raw' for every sample, due to an error in where the delimiter was.
Example filename: 'raw_counts/GSM5226574_C51ctr_raw_counts.csv'
How:
Changed csv_path.split('_')[1] to split after the first _, which would return C51ctr. Previously, it would return raw.
Note: the git diff is picking up changes to the figures, which are not related to this PR. I believe this is a git artifact of jupyter notebooks which may have detected a permission change after cloning. The only line which was changed by me was line 17 of the cell currently labeled as In [89]
Tags:
scanpy, scvi
