API

Import the patpy package:

import patpy

• Preprocessing: pp
  • patpy.pp.prepare_data_for_phemd
  • patpy.pp.convert_cell_types_to_phemd_format
  • patpy.pp.calculate_compositional_metrics
  • patpy.pp.calculate_cell_qc_metrics
  • patpy.pp.calculate_n_cells_per_sample
  • patpy.pp.filter_small_samples
  • patpy.pp.filter_small_cell_groups
  • patpy.pp.subsample
  • patpy.pp.is_count_data
  • patpy.pp.fill_nan_distances
• Tools: tl
  • patpy.tl.PILOT
  • patpy.tl.GroupedPseudobulk
  • patpy.tl.CellGroupComposition
  • patpy.tl.MrVI
  • patpy.tl.RandomVector
  • patpy.tl.SCPoli
  • patpy.tl.Pseudobulk
  • patpy.tl.WassersteinTSNE
  • patpy.tl.SampleRepresentationMethod
  • patpy.tl.describe_metadata
  • patpy.tl.test_distances_significance
  • patpy.tl.predict_knn
  • patpy.tl.evaluate_prediction
  • patpy.tl.test_proportions
  • patpy.tl.evaluate_representation
• Plotting: pl