Predict cell states using Astir. This package requires the python library `astir` and `reticulate` to work. The function returns a `condor` object with automatically annotated cell states and QC of the annotation, the results are also saved in a folder specified by the user.
Usage
runAstir_cellstates(
fcd,
data_slot,
analysis_path,
manifest_name,
max_epochs,
learning_rate,
initial_epochs
)Arguments
- fcd
Flow cytometry dataset.
- data_slot
Data slot to use for the analysis (e.g. "orig" or "norm").
- analysis_path
Full path to the output folder of astir analysis.
- manifest_name
Filename of the manifest file, this file must be located in the `analysis_path` folder.
- max_epochs
Maximum number of epochs.
- learning_rate
Learning Rate.
- initial_epochs
Initial Epochs.