Predict cell types using 'Astir'. This package requires the python library `astir` and `reticulate` to work. The function returns a `condor` object with automatically annotated cell types and QC of the annotation, the results are also saved in a folder specified by the user.
Usage
runAstir_celltype(
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, for details see `Astir` documentation.
- learning_rate
Learning Rate.
- initial_epochs
initial epochs, for details see `Astir` documentation.
Details
Run Astir cell type prediction
Predict cell types using 'Astir'. This package requires the python library `astir` and `reticulate`. This function is still experimental and was not extensively tested in cyCONDOR. In one of the next release we will document it's usage in more details on a dedicated vignette. For the moment if you want to know more feel free to reach out on our `Slack` channel. For more details on the different parameters refer to `Astir` documentation.