scripts.apply_umap#

Functions#

process_file(file, species_name, n_events, stain_1, ...)

Processes import .fcs files by first gating (if asked) and then sampling their entries

process_files([TrainPanel])

Main function for UMAP application.

Module Contents#

scripts.apply_umap.process_file(file, species_name, n_events, stain_1, stain_2, model_dir)#

Processes import .fcs files by first gating (if asked) and then sampling their entries to only keep a subset of them for the training step.

Parameters:

  • (str) (model_dir) – Path to the .fcs file

  • (str) – Name of the species corresponding to the .fcs file

  • (int) (n_events) – Number of entries of the .fcs file to keep for model training

  • (Strain) (stain_1) – User parameters for the (live/dead) staining

  • (Stain) (stain_2) – User parammeters for the (cells/debris) staining

  • (str) – Path for model-related output files to be saved

Return sampled_df:

The gated (if asked) and sampled entris of the .fcs file to be used for the model training

scripts.apply_umap.process_files(TrainPanel=None, **kwargs)#

Main function for UMAP application.