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calico / scnym

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
https://scnym.research.calicolabs.com
Apache License 2.0
74 stars 11 forks source link

domain_groupby argument missing #12

Closed MariekeL closed 3 years ago

MariekeL commented 3 years ago

Thank you for developing scNym. I've been using it to infer cell populations between datasets. However, after going over your guidelines on how to use scNym I noticed that the argument domain_groupby seems to be missing from the scnym_api function. As such, I'm wondering which steps I need to take in order to be able to run scNym using multiple domains. I've been using the scNym version 0.3.0 in python 3.8.5.

jacobkimmel commented 3 years ago

Hi @MariekeL, thanks for your interest! This looks like a bad PR on my end. It will be fixed by EOD and I'll tag you. Thanks for the heads up!

jacobkimmel commented 3 years ago

@MariekeL : For now, you can use multidomain training with the following edit to the model config file.

config_name = "no_new_identity" # or other valid config
config = scnym.api.CONFIGS[config_name]
config["domain_groupby"] = "your_domain_column"

scnym.api.scnym_api(
  adata=adata, groupby=groupby, out_path=out_path, config=config,
)
jacobkimmel commented 3 years ago

@MariekeL Apologies for the trouble. This should be fixed now if you update your Github checkout to master or pip install --upgrade scnym. Double check that your final installed version now reads 0.3.1.