Index

A

add_ctrl_file() (cytopy.data.fcs.FileGroup method) add_experiment() (cytopy.data.project.Project method) add_population() (cytopy.data.fcs.FileGroup method) add_subject() (cytopy.data.project.Project method) adjusted_functions (cytopy.flow.fda_norm.LandmarkReg attribute)

apply_transform() (in module cytopy.flow.transform) apply_transform_map() (in module cytopy.flow.transform) AsinhTransformer (class in cytopy.flow.transform) assert_population_labels() (in module cytopy.flow.cell_classifier.utils) auto_weights() (in module cytopy.flow.cell_classifier.utils)

B

build_keras_model() (in module cytopy.flow.build_models)

build_model() (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier method) build_sklearn_model() (in module cytopy.flow.build_models)

C

calc_metrics() (in module cytopy.flow.cell_classifier.utils) calculate_optimal_neighbours() (in module cytopy.flow.neighbours) case_sensitive (cytopy.data.experiment.NormalisedName attribute) CellClassifier (class in cytopy.flow.cell_classifier.cell_classifier) channel (cytopy.data.mapping.ChannelMap attribute) ChannelMap (class in cytopy.data.mapping) channels (cytopy.data.experiment.Panel attribute) check_downstream_populations() (in module cytopy.flow.cell_classifier.utils) check_duplication() (in module cytopy.data.experiment) check_excel_template() (in module cytopy.data.experiment) check_matched_pair() (cytopy.data.mapping.ChannelMap method) check_pairing() (in module cytopy.data.experiment) chunks() (in module cytopy.data.read_write) class_weights (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute) cluster_landmarks() (in module cytopy.flow.fda_norm) collection_datetime (cytopy.data.fcs.FileGroup attribute) comp_matrix (cytopy.data.read_write.FCSFile attribute) compensate() (cytopy.data.read_write.FCSFile method) compenstate() (in module cytopy.data.experiment) confusion_matrix_plots() (in module cytopy.flow.cell_classifier.utils) construct_tree() (in module cytopy.flow.tree) control_counts() (cytopy.data.experiment.Experiment method) create_convex_hull() (in module cytopy.data.geometry) create_from_dict() (cytopy.data.experiment.Panel method) create_from_excel() (cytopy.data.experiment.Panel method) create_polygon() (in module cytopy.data.geometry) cytopy.data.errors module cytopy.data.experiment module cytopy.data.fcs module cytopy.data.geometry module

cytopy.data.mapping module cytopy.data.population module cytopy.data.project module cytopy.data.read_write module cytopy.data.setup module cytopy.data.subject module cytopy.flow.build_models module cytopy.flow.cell_classifier.cell_classifier module cytopy.flow.cell_classifier.keras_classifier module cytopy.flow.cell_classifier.sklearn_classifier module cytopy.flow.cell_classifier.utils module cytopy.flow.clustering.flowsom module cytopy.flow.fda_norm module cytopy.flow.neighbours module cytopy.flow.sampling module cytopy.flow.transform module cytopy.flow.tree module

D

data_directory (cytopy.data.project.Project attribute) data_loaded() (in module cytopy.data.fcs) definition (cytopy.data.population.Population attribute) delete() (cytopy.data.experiment.Experiment method) (cytopy.data.fcs.FileGroup method) (cytopy.data.project.Project method) delete_all_populations() (cytopy.data.experiment.Experiment method) delete_experiment() (cytopy.data.project.Project method)

delete_populations() (cytopy.data.fcs.FileGroup method) density_dependent_downsampling() (in module cytopy.flow.sampling) density_probability_assignment() (in module cytopy.flow.sampling) duplicate_mappings() (in module cytopy.data.experiment) DuplicateExperimentError DuplicateGateError DuplicatePopulationError DuplicateSampleError DuplicateSubjectError

E

ellipse_to_polygon() (in module cytopy.data.geometry) estimate_pdfs() (in module cytopy.flow.fda_norm) Experiment (class in cytopy.data.experiment) Experiment.DoesNotExist

Experiment.MultipleObjectsReturned experiment_id (cytopy.data.experiment.Experiment attribute) experiments (cytopy.data.project.Project attribute) explore_channel_mappings() (in module cytopy.data.read_write)

F

faithful_downsampling() (in module cytopy.flow.sampling) fcs_files (cytopy.data.experiment.Experiment attribute) fcs_mappings() (in module cytopy.data.read_write) FCSFile (class in cytopy.data.read_write) features (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute) FileGroup (class in cytopy.data.fcs) FileGroup.DoesNotExist

FileGroup.MultipleObjectsReturned filepath (cytopy.data.read_write.FCSFile attribute) files (cytopy.data.fcs.FileGroup attribute) filter_by_closest_centroid() (in module cytopy.flow.fda_norm) filter_fcs_files() (in module cytopy.data.read_write) filter_samples_by_subject() (cytopy.data.experiment.Experiment method) flags (cytopy.data.experiment.Experiment attribute) (cytopy.data.fcs.FileGroup attribute) FlowSOM (class in cytopy.flow.clustering.flowsom)

G

gates (cytopy.data.fcs.FileGroup attribute) generate_panel() (cytopy.data.experiment.Experiment method) geom (cytopy.data.population.Population attribute) get_experiment() (cytopy.data.project.Project method) get_fcs_file_paths() (in module cytopy.data.read_write)

get_population() (cytopy.data.fcs.FileGroup method) get_population_by_parent() (cytopy.data.fcs.FileGroup method) get_sample() (cytopy.data.experiment.Experiment method) get_subject() (cytopy.data.project.Project method) global_init() (in module cytopy.data.setup)

H

HyperlogTransformer (class in cytopy.flow.transform)

I

index (cytopy.data.population.Population attribute) init_new_file() (cytopy.data.fcs.FileGroup method) initiation_date (cytopy.data.experiment.Panel attribute) inside_ellipse() (in module cytopy.data.geometry) inside_polygon() (in module cytopy.data.geometry) InsufficientEventsError

InvalidDataDirectory inverse (cytopy.flow.transform.Transformer attribute) inverse() (cytopy.flow.transform.Normalise method) (cytopy.flow.transform.Scaler method) inverse_scale() (cytopy.flow.transform.LogTransformer method) (cytopy.flow.transform.Transformer method)

K

KerasCellClassifier (class in cytopy.flow.cell_classifier.keras_classifier)

knn() (in module cytopy.flow.neighbours) kwargs (cytopy.flow.transform.Transformer attribute)

L

landmark_shift_deltas (cytopy.flow.fda_norm.LandmarkReg attribute) LandmarkReg (class in cytopy.flow.fda_norm) landmarks (cytopy.flow.fda_norm.LandmarkReg attribute) list_channels() (cytopy.data.experiment.Panel method) list_downstream_populations() (cytopy.data.fcs.FileGroup method) list_experiments() (cytopy.data.project.Project method) list_markers() (cytopy.data.experiment.Panel method) list_populations() (cytopy.data.fcs.FileGroup method) list_samples() (cytopy.data.experiment.Experiment method) list_subjects() (cytopy.data.project.Project method) load_control_population_from_experiment() (in module cytopy.data.experiment)

load_ctrl_population_df() (cytopy.data.fcs.FileGroup method) load_model() (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier method) load_population_data_from_experiment() (in module cytopy.data.experiment) load_population_df() (cytopy.data.fcs.FileGroup method) load_training_data() (cytopy.flow.cell_classifier.cell_classifier.CellClassifier method) load_validation() (cytopy.flow.cell_classifier.cell_classifier.CellClassifier method) logger (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute) LogicleTransformer (class in cytopy.flow.transform) LogTransformer (class in cytopy.flow.transform)

M

mappings (cytopy.data.experiment.Panel attribute) marker (cytopy.data.mapping.ChannelMap attribute) markers (cytopy.data.experiment.Panel attribute) match_landmarks() (in module cytopy.flow.fda_norm) merge_gate_populations() (cytopy.data.fcs.FileGroup method) (in module cytopy.data.population) merge_multiple_gate_populations() (in module cytopy.data.population) merge_non_geom_populations() (cytopy.data.fcs.FileGroup method) (in module cytopy.data.population) merge_populations() (cytopy.data.experiment.Experiment method) meta_cluster() (cytopy.flow.clustering.flowsom.FlowSOM method) method (cytopy.flow.transform.Scaler attribute) missing_channels() (in module cytopy.data.experiment) MissingControlError MissingExperimentError MissingPopulationError MissingSampleError MissingSubjectError module cytopy.data.errors cytopy.data.experiment cytopy.data.fcs cytopy.data.geometry cytopy.data.mapping cytopy.data.population cytopy.data.project cytopy.data.read_write cytopy.data.setup cytopy.data.subject cytopy.flow.build_models cytopy.flow.cell_classifier.cell_classifier cytopy.flow.cell_classifier.keras_classifier cytopy.flow.cell_classifier.sklearn_classifier cytopy.flow.cell_classifier.utils cytopy.flow.clustering.flowsom cytopy.flow.fda_norm cytopy.flow.neighbours cytopy.flow.sampling cytopy.flow.transform cytopy.flow.tree

multilabel() (in module cytopy.flow.cell_classifier.utils)

N

n (cytopy.data.population.Population attribute) Normalise (class in cytopy.flow.transform) NormalisedName (class in cytopy.data.experiment)

notes (cytopy.data.experiment.Experiment attribute) (cytopy.data.fcs.FileGroup attribute) (cytopy.data.subject.Subject attribute)

O

original_functions (cytopy.flow.fda_norm.LandmarkReg attribute)

overwrite_or_create() (in module cytopy.data.fcs) owner (cytopy.data.project.Project attribute)

P

Panel (class in cytopy.data.experiment) panel (cytopy.data.experiment.Experiment attribute) parent (cytopy.data.population.Population attribute) peaks() (in module cytopy.flow.fda_norm) permutations (cytopy.data.experiment.NormalisedName attribute) plot_confusion_matrix() (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier method) plot_learning_curve() (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier method) plot_shift() (cytopy.flow.fda_norm.LandmarkReg method) plot_warping() (cytopy.flow.fda_norm.LandmarkReg method) polygon_overlap() (in module cytopy.data.geometry) PolygonGeom (class in cytopy.data.geometry) Population (class in cytopy.data.population) population_in_file() (in module cytopy.data.fcs) population_name (cytopy.data.population.Population attribute) population_statistics() (cytopy.data.experiment.Experiment method)

population_stats() (cytopy.data.fcs.FileGroup method) (in module cytopy.data.fcs) PopulationGeometry (class in cytopy.data.geometry) populations (cytopy.data.fcs.FileGroup attribute) predict() (cytopy.flow.clustering.flowsom.FlowSOM method) primary_id (cytopy.data.fcs.FileGroup attribute) print_population_tree() (cytopy.data.fcs.FileGroup method) prob_downsample() (in module cytopy.flow.sampling) probablistic_ellipse() (in module cytopy.data.geometry) processing_datetime (cytopy.data.fcs.FileGroup attribute) Project (class in cytopy.data.project) Project.DoesNotExist Project.MultipleObjectsReturned project_id (cytopy.data.project.Project attribute) prop_of_parent (cytopy.data.population.Population attribute) prop_of_total (cytopy.data.population.Population attribute)

Q

quantile_clean() (cytopy.data.fcs.FileGroup method)

query() (cytopy.data.experiment.NormalisedName method) query_normalised_list() (in module cytopy.data.experiment)

R

regex_str (cytopy.data.experiment.NormalisedName attribute)

remove_negative_values() (in module cytopy.flow.transform) remove_sample() (cytopy.data.experiment.Experiment method)

S

safe_range() (in module cytopy.flow.transform) sample_exists() (cytopy.data.experiment.Experiment method) save() (cytopy.data.fcs.FileGroup method) save_model() (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier method) scale() (cytopy.flow.transform.LogTransformer method) (cytopy.flow.transform.Transformer method) Scaler (class in cytopy.flow.transform) scaler (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute) set_column_names() (in module cytopy.data.fcs) set_params() (cytopy.flow.transform.Scaler method) shift_data() (cytopy.flow.fda_norm.LandmarkReg method)

signature (cytopy.data.population.Population attribute) singlelabel() (in module cytopy.flow.cell_classifier.utils) SklearnCellClassifier (class in cytopy.flow.cell_classifier.sklearn_classifier) source (cytopy.data.population.Population attribute) standard (cytopy.data.experiment.NormalisedName attribute) standardise_names() (in module cytopy.data.experiment) start_date (cytopy.data.project.Project attribute) Subject (class in cytopy.data.subject) subject (cytopy.data.fcs.FileGroup attribute) Subject.DoesNotExist Subject.MultipleObjectsReturned subject_id (cytopy.data.subject.Subject attribute) subjects (cytopy.data.project.Project attribute) subtract_populations() (cytopy.data.fcs.FileGroup method)

T

target_populations (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute) ThresholdGeom (class in cytopy.data.geometry) to_dict() (cytopy.data.mapping.ChannelMap method) train() (cytopy.flow.clustering.flowsom.FlowSOM method) transform (cytopy.flow.transform.Transformer attribute) transform_to_linear() (cytopy.data.geometry.PolygonGeom method) (cytopy.data.geometry.ThresholdGeom method)

transform_x (cytopy.data.geometry.PopulationGeometry attribute) transform_x_kwargs (cytopy.data.geometry.PopulationGeometry attribute) transform_y (cytopy.data.geometry.PopulationGeometry attribute) transform_y_kwargs (cytopy.data.geometry.PopulationGeometry attribute) Transformer (class in cytopy.flow.transform) transformer (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute) TransformError

U

uniform_downsampling() (in module cytopy.flow.sampling) unique_clusters_filter_nearest_centroid() (in module cytopy.flow.fda_norm) update_data_directory() (cytopy.data.project.Project method)

update_population() (cytopy.data.fcs.FileGroup method) upsample_density() (in module cytopy.flow.sampling) upsample_knn() (in module cytopy.flow.sampling)

V

valid (cytopy.data.fcs.FileGroup attribute)

W

warnings (cytopy.data.population.Population attribute)

warping_function (cytopy.flow.fda_norm.LandmarkReg attribute)

X

x (cytopy.data.geometry.PopulationGeometry attribute) (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute)

x_threshold (cytopy.data.geometry.ThresholdGeom attribute) x_values (cytopy.data.geometry.PolygonGeom attribute)

Y

y (cytopy.data.geometry.PopulationGeometry attribute) (cytopy.flow.cell_classifier.cell_classifier.CellClassifier attribute) (cytopy.flow.cell_classifier.keras_classifier.KerasCellClassifier attribute) (cytopy.flow.cell_classifier.sklearn_classifier.SklearnCellClassifier attribute)

y_threshold (cytopy.data.geometry.ThresholdGeom attribute) y_values (cytopy.data.geometry.PolygonGeom attribute)

Z

zero_entropy_clusters() (in module cytopy.flow.fda_norm)