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# Run Astir cell type prediction

Source: `R/astir.R`
`runAstir_celltype.Rd`

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,
      prefix = NULL
    )

## 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.

prefix

  Optional prefix for the slot name of the output.

## Value

runAstir_celltype

## 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.