Index

A

activation_frequencies() (flagx.gating.SOMClassifier method) align_channel_names() (flagx.io.FlowDataManager method)

anndata_list_ (flagx.io.FlowDataManager attribute) annotate_som() (flagx.gating.SOMClassifier method)

B

binary_classes_ (flagx.pipeline.GatingPipeline attribute)

C

channel_names_alignment_kwargs (flagx.pipeline.GatingPipeline attribute) channels (flagx.pipeline.GatingPipeline attribute) check_class_balance() (flagx.io.FlowDataManager method) check_og_channel_names_df() (flagx.io.FlowDataManager method) check_sample_sizes() (flagx.io.FlowDataManager method) class_counts_ (flagx.gating.MLPClassifier attribute) (flagx.gating.SOMClassifier attribute)

class_counts_per_unit_ (flagx.gating.SOMClassifier attribute) class_priors_ (flagx.gating.MLPClassifier attribute) (flagx.gating.SOMClassifier attribute) classes_ (flagx.gating.MLPClassifier attribute) (flagx.gating.SOMClassifier attribute) compensate (flagx.pipeline.GatingPipeline attribute) compensation_log_ (flagx.io.FlowDataManager attribute) criterion_ (flagx.gating.MLPClassifier attribute)

D

data (flagx.io.FlowDataset attribute) data_loader_ (flagx.gating.MLPClassifier attribute)

data_set_ (flagx.gating.MLPClassifier attribute) dataset (flagx.io.FlowDataLoaders attribute) downsampling_kwargs (flagx.pipeline.GatingPipeline attribute)

E

export_to_fcs() (in module flagx.io)

F

FCNNModel (class in flagx.gating) file_path (flagx.io.FlowDataset attribute) fit() (flagx.gating.MLPClassifier method) (flagx.gating.SOMClassifier method) flagx.gating module

flagx.io module FlowDataLoaders (class in flagx.io) FlowDataManager (class in flagx.io) FlowDataset (class in flagx.io) forward() (flagx.gating.FCNNModel method)

G

gating_method (flagx.pipeline.GatingPipeline attribute) gating_method_kwargs (flagx.pipeline.GatingPipeline attribute) gating_module_ (flagx.pipeline.GatingPipeline attribute)

GatingPipeline (class in flagx.pipeline) get_data_loader() (flagx.io.FlowDataManager method) grid_search_ (flagx.gating.SOMClassifier attribute)

H

hyperparameter_tuning() (flagx.gating.SOMClassifier method)

I

includes_labels (flagx.io.FlowDataset attribute) inference() (flagx.pipeline.GatingPipeline method) invalid_files_ (flagx.io.FlowDataManager attribute)

is_fitted_ (flagx.gating.MLPClassifier attribute) (flagx.gating.SOMClassifier attribute) is_trained_ (flagx.pipeline.GatingPipeline attribute)

L

label_idx (flagx.io.FlowDataset attribute) label_key (flagx.pipeline.GatingPipeline attribute) layers (flagx.gating.FCNNModel attribute)

load() (flagx.gating.MLPClassifier class method) (flagx.gating.SOMClassifier class method) (flagx.pipeline.GatingPipeline class method) load_data_files_to_anndata() (flagx.io.FlowDataManager method)

M

mean_impurity() (flagx.gating.SOMClassifier method) MLPClassifier (class in flagx.gating) model_ (flagx.gating.MLPClassifier attribute)

module flagx.gating flagx.io

N

new_to_og_classes_dict_ (flagx.gating.MLPClassifier attribute)

O

og_channel_names_ (flagx.io.FlowDataManager attribute) og_classes_ (flagx.gating.MLPClassifier attribute) (flagx.gating.SOMClassifier attribute)

on_disk (flagx.io.FlowDataset attribute) optimizer_ (flagx.gating.MLPClassifier attribute)

P

perform_data_split() (flagx.io.FlowDataManager method) plot_class_balance_df() (flagx.io.FlowDataManager static method) plot_sample_size_df() (flagx.io.FlowDataManager static method) predict() (flagx.gating.MLPClassifier method) (flagx.gating.SOMClassifier method)

predict_proba() (flagx.gating.MLPClassifier method) (flagx.gating.SOMClassifier method) prediction_threshold (flagx.pipeline.GatingPipeline attribute) preprocessing_kwargs (flagx.pipeline.GatingPipeline attribute) pytorch_dataloader (flagx.io.FlowDataLoaders attribute) pytorch_np_dataloader (flagx.io.FlowDataLoaders attribute)

Q

quantization_error() (flagx.gating.SOMClassifier method)

R

relabel_data() (flagx.io.FlowDataManager method)

relabel_data_kwargs (flagx.pipeline.GatingPipeline attribute) reset() (flagx.gating.SOMClassifier method)

S

sample_sizes_ (flagx.io.FlowDataManager attribute) sample_wise_compensation() (flagx.io.FlowDataManager method) sample_wise_downsampling() (flagx.io.FlowDataManager method) sample_wise_preprocessing() (flagx.io.FlowDataManager method) save() (flagx.gating.MLPClassifier method) (flagx.gating.SOMClassifier method) (flagx.pipeline.GatingPipeline method)

save_path (flagx.pipeline.GatingPipeline attribute) save_to_numpy_files() (flagx.io.FlowDataManager method) score() (flagx.gating.MLPClassifier method) (flagx.gating.SOMClassifier method) som_ (flagx.gating.SOMClassifier attribute) som_unit_labels_ (flagx.gating.SOMClassifier attribute) SOMClassifier (class in flagx.gating)

T

test_data_ (flagx.io.FlowDataManager attribute) topographic_error() (flagx.gating.SOMClassifier method) train() (flagx.pipeline.GatingPipeline method) train_data_ (flagx.io.FlowDataManager attribute)

train_data_file_names (flagx.pipeline.GatingPipeline attribute) train_data_file_path (flagx.pipeline.GatingPipeline attribute) train_data_file_type (flagx.pipeline.GatingPipeline attribute) training_log_ (flagx.gating.MLPClassifier attribute) transform() (flagx.gating.SOMClassifier method)

U

unit_impurity() (flagx.gating.SOMClassifier method)

unpredictable_classes() (flagx.gating.SOMClassifier method)

V

val_data_ (flagx.io.FlowDataManager attribute)

verbosity (flagx.pipeline.GatingPipeline attribute)