Closed liboxun closed 4 years ago
Thanks for reporting this issue!
You're running harmonypy version 0.0.3, but that version does not support multiple covariates.
Here's the code from version 0.0.3:
The new code should support multiple covariates. I just pushed version 0.0.4 to pypi right now.
I started tracking changes in CHANGELOG.md, so I hope that helps to see what has changed between versions.
Right now, you should be able to upgrade to 0.0.4 with:
pip install harmonypy
If you want to try the latest code available on GitHub, try:
pip install git+https://github.com/slowkow/harmonypy
Please let me know if you run into any other issues!
Appreciate the quick response the update! I'll post new results when I have them.
This update (0.0.4) fixed it! Thanks!
From reading the documentation at https://github.com/immunogenomics/harmony, it seems that feeding a list of multiple covariates to the argument
vars_use
would harmonize the data over these covariates. However when I tried to do this using:where
adata
is my dataset in AnnData format, I got this error:Was there something I overlooked? Please advise. Thanks!