Fix: Integration step's labeling of samples #16
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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
Tags: scanpy, scvi
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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 diffis 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 asIn [89]Tags:
scanpy, scvi