Index

A

add_handle() (pyInfinityFlow.InfinityFlow_Utilities.InfinityFlowFileHandler method) anndata_to_df() (in module pyInfinityFlow.InfinityFlow_Utilities) apply_inverse_logicle() (in module pyInfinityFlow.Transformations)

apply_inverse_logicle_to_anndata() (in module pyInfinityFlow.InfinityFlow_Utilities) apply_logicle() (in module pyInfinityFlow.Transformations) apply_logicle_to_anndata() (in module pyInfinityFlow.InfinityFlow_Utilities) assign_rainbow_colors_to_groups() (in module pyInfinityFlow.Plotting_Utilities)

B

byte_locations (pyInfinityFlow.fcs_io.FCSFileObject attribute)

byteord_format (pyInfinityFlow.fcs_io.FCSFileObject attribute)

C

check_infinity_flow_annotation_dataframes() (in module pyInfinityFlow.InfinityFlow_Utilities)

CombinedRegressionModels (class in pyInfinityFlow.InfinityFlow_Utilities)

D

data (pyInfinityFlow.fcs_io.FCSFileObject attribute)

delimiter (pyInfinityFlow.fcs_io.FCSFileObject attribute)

F

FCSFileObject (class in pyInfinityFlow.fcs_io)

file_path (pyInfinityFlow.fcs_io.FCSFileObject attribute) find_markers_from_anndata() (in module pyInfinityFlow.InfinityFlow_Utilities)

H

handles (pyInfinityFlow.InfinityFlow_Utilities.InfinityFlowFileHandler attribute)

I

infinity_channels (pyInfinityFlow.InfinityFlow_Utilities.CombinedRegressionModels attribute) infinity_markers (pyInfinityFlow.InfinityFlow_Utilities.CombinedRegressionModels attribute)

InfinityFlowFileHandler (class in pyInfinityFlow.InfinityFlow_Utilities) isotype_control_names (pyInfinityFlow.InfinityFlow_Utilities.InfinityFlowFileHandler attribute)

L

list_fcs_channels() (in module pyInfinityFlow.fcs_io) list_infinity_markers (pyInfinityFlow.InfinityFlow_Utilities.InfinityFlowFileHandler attribute)

list_par_n (pyInfinityFlow.fcs_io.FCSFileObject attribute) load_data_from_pd_df() (pyInfinityFlow.fcs_io.FCSFileObject method)

M

make_flow_regression_predictions() (in module pyInfinityFlow.InfinityFlow_Utilities) make_pca_elbo_plot() (in module pyInfinityFlow.InfinityFlow_Utilities)

marker_finder() (in module pyInfinityFlow.InfinityFlow_Utilities) move_features_out_of_silent() (in module pyInfinityFlow.InfinityFlow_Utilities) move_features_to_silent() (in module pyInfinityFlow.InfinityFlow_Utilities)

N

named_par (pyInfinityFlow.fcs_io.FCSFileObject attribute)

named_par_channel (pyInfinityFlow.fcs_io.FCSFileObject attribute)

O

ordered_reference_backbone (pyInfinityFlow.InfinityFlow_Utilities.InfinityFlowFileHandler attribute)

ordered_training_channels (pyInfinityFlow.InfinityFlow_Utilities.CombinedRegressionModels attribute)

P

par_count (pyInfinityFlow.fcs_io.FCSFileObject attribute) parameter_annotations (pyInfinityFlow.InfinityFlow_Utilities.CombinedRegressionModels attribute) perform_background_correction() (in module pyInfinityFlow.InfinityFlow_Utilities)

plot_feature_over_x_y_coordinates_and_save_fig() (in module pyInfinityFlow.Plotting_Utilities) plot_leiden_clusters_over_umap() (in module pyInfinityFlow.Plotting_Utilities) plot_markers_df() (in module pyInfinityFlow.Plotting_Utilities)

R

read_annotation_table() (in module pyInfinityFlow.InfinityFlow_Utilities) read_fcs() (pyInfinityFlow.fcs_io.FCSFileObject method)

read_fcs_into_anndata() (in module pyInfinityFlow.InfinityFlow_Utilities) regression_models (pyInfinityFlow.InfinityFlow_Utilities.CombinedRegressionModels attribute)

S

save_fcs_flow_anndata() (in module pyInfinityFlow.InfinityFlow_Utilities) save_umap_figures_all_features() (in module pyInfinityFlow.InfinityFlow_Utilities) scale_feature() (in module pyInfinityFlow.Transformations) setup_output_directories() (in module pyInfinityFlow.InfinityFlow_Utilities)

single_chunk_testing() (in module pyInfinityFlow.InfinityFlow_Utilities) single_chunk_training() (in module pyInfinityFlow.InfinityFlow_Utilities) spillover (pyInfinityFlow.fcs_io.FCSFileObject attribute) struct_format_string (pyInfinityFlow.fcs_io.FCSFileObject attribute)

T

text_segment (pyInfinityFlow.fcs_io.FCSFileObject attribute)

text_segment_values (pyInfinityFlow.fcs_io.FCSFileObject attribute) to_fcs() (pyInfinityFlow.fcs_io.FCSFileObject method)

U

use_isotype_controls (pyInfinityFlow.InfinityFlow_Utilities.InfinityFlowFileHandler attribute)

V

validation_metrics (pyInfinityFlow.InfinityFlow_Utilities.CombinedRegressionModels attribute)

var_annotations (pyInfinityFlow.InfinityFlow_Utilities.CombinedRegressionModels attribute) version (pyInfinityFlow.fcs_io.FCSFileObject attribute)

W

write_anndata_to_fcs() (in module pyInfinityFlow.InfinityFlow_Utilities)