Index

A

analysis_mode (pandora.pandora.PandoraConfig attribute) AnalysisMode (class in pandora.custom_types)

ANCESTRYMAP (pandora.custom_types.FileFormat attribute) argument_parser() (in module pandora.main)

B

BatchEmbeddingComparison (class in pandora.embedding_comparison) BOOTSTRAP (pandora.custom_types.AnalysisMode attribute) bootstrap() (pandora.dataset.EigenDataset method) (pandora.dataset.NumpyDataset method) bootstrap_and_embed_multiple() (in module pandora.bootstrap)

bootstrap_and_embed_multiple_numpy() (in module pandora.bootstrap) bootstrap_convergence_check (pandora.pandora.PandoraConfig attribute) bootstrap_convergence_tolerance (pandora.pandora.PandoraConfig attribute) bootstrap_embeddings() (pandora.pandora.Pandora method) bootstrap_result_dir (pandora.pandora.PandoraConfig property)

C

check_files() (pandora.dataset.EigenDataset method) check_smartpca_results() (in module pandora.embedding) cluster() (pandora.embedding.Embedding method) compare() (pandora.embedding_comparison.BatchEmbeddingComparison method) (pandora.embedding_comparison.EmbeddingComparison method)

compare_clustering() (pandora.embedding_comparison.BatchEmbeddingComparison method) (pandora.embedding_comparison.EmbeddingComparison method) configfile (pandora.pandora.PandoraConfig property) convert_to_eigenstrat_format() (in module pandora.pandora) convertf (pandora.pandora.PandoraConfig attribute) convertf_result_dir (pandora.pandora.PandoraConfig property)

D

dataset_prefix (pandora.pandora.PandoraConfig attribute)

E

EigenDataset (class in pandora.dataset) EIGENSTRAT (pandora.custom_types.FileFormat attribute) embed_dataset() (pandora.pandora.Pandora method) Embedding (class in pandora.embedding) embedding_algorithm (pandora.pandora.PandoraConfig attribute)

embedding_populations (pandora.pandora.PandoraConfig attribute) EmbeddingAlgorithm (class in pandora.custom_types) EmbeddingComparison (class in pandora.embedding_comparison) euclidean_population_distance() (in module pandora.distance_metrics) euclidean_sample_distance() (in module pandora.distance_metrics)

F

file_format (pandora.pandora.PandoraConfig attribute) FileFormat (class in pandora.custom_types) files_exist() (pandora.dataset.EigenDataset method)

fmt_message() (in module pandora.logger) from_smartpca() (in module pandora.embedding) fst_population_distance() (in module pandora.distance_metrics) (pandora.dataset.EigenDataset method)

G

get_configuration() (pandora.pandora.PandoraConfig method) get_distinct_colors() (in module pandora.plotting) get_filenames() (in module pandora.converter) get_header() (in module pandora.main) get_optimal_kmeans_k() (pandora.embedding.Embedding method) get_pairwise_cluster_stabilities() (pandora.embedding_comparison.BatchEmbeddingComparison method) get_pairwise_stabilities() (pandora.embedding_comparison.BatchEmbeddingComparison method)

get_population_info() (pandora.dataset.EigenDataset method) get_projected_samples() (pandora.dataset.EigenDataset method) get_rdylgr_color_scale() (in module pandora.plotting) get_sample_info() (pandora.dataset.EigenDataset method) get_sample_support_values() (pandora.embedding_comparison.BatchEmbeddingComparison method) get_sequence_length() (pandora.dataset.EigenDataset method) get_windows() (pandora.dataset.EigenDataset method) (pandora.dataset.NumpyDataset method)

H

hamming_sample_distance() (in module pandora.distance_metrics)

I

improve_plotly_text_position() (in module pandora.plotting)

impute_data() (in module pandora.imputation)

K

keep_replicates (pandora.pandora.PandoraConfig attribute)

kmeans_k (pandora.pandora.PandoraConfig attribute)

L

log_and_save_replicates_results() (pandora.pandora.Pandora method)

log_results_files() (pandora.pandora.PandoraConfig method) loglevel (pandora.pandora.PandoraConfig property)

M

main() (in module pandora.main) manhattan_population_distance() (in module pandora.distance_metrics) manhattan_sample_distance() (in module pandora.distance_metrics) match_and_transform() (in module pandora.embedding_comparison) MDS (pandora.custom_types.EmbeddingAlgorithm attribute) mds_from_dataframe() (in module pandora.embedding) missing_corrected_hamming_sample_distance() (in module pandora.distance_metrics) model_config (pandora.pandora.PandoraConfig attribute) module pandora pandora.bootstrap pandora.converter pandora.custom_errors pandora.custom_types pandora.dataset pandora.distance_metrics pandora.embedding pandora.embedding_comparison pandora.imputation pandora.logger pandora.main pandora.pandora pandora.plotting pandora.sliding_window

multiprocessing_process_cleanup() (in module pandora)

N

n_components (pandora.pandora.PandoraConfig attribute) n_replicates (pandora.pandora.PandoraConfig attribute)

numpy_dataset_from_eigenfiles() (in module pandora.dataset) NumpyDataset (class in pandora.dataset)

P

PACKEDANCESTRYMAP (pandora.custom_types.FileFormat attribute) PACKEDPED (pandora.custom_types.FileFormat attribute) pairwise_stability_result_file (pandora.pandora.PandoraConfig property) pandora module Pandora (class in pandora.pandora) pandora.bootstrap module pandora.converter module pandora.custom_errors module pandora.custom_types module pandora.dataset module pandora.distance_metrics module pandora.embedding module pandora.embedding_comparison module pandora.imputation module pandora.logger module

pandora.main module pandora.pandora module pandora.plotting module pandora.sliding_window module pandora_config_from_configfile() (in module pandora.pandora) pandora_logfile (pandora.pandora.PandoraConfig property) PandoraConfig (class in pandora.pandora) PandoraConfigException PandoraException PCA (pandora.custom_types.EmbeddingAlgorithm attribute) PED (pandora.custom_types.FileFormat attribute) plot_clusters() (in module pandora.plotting) plot_dim_x (pandora.pandora.PandoraConfig attribute) plot_dim_y (pandora.pandora.PandoraConfig attribute) plot_dir (pandora.pandora.PandoraConfig property) plot_embedding_comparison() (in module pandora.plotting) plot_embedding_comparison_rogue_samples() (in module pandora.plotting) plot_populations() (in module pandora.plotting) plot_projections() (in module pandora.plotting) plot_results (pandora.pandora.PandoraConfig attribute) plot_support_values() (in module pandora.plotting) population_distance() (in module pandora.distance_metrics) projected_sample_support_values_csv (pandora.pandora.PandoraConfig property)

R

redo (pandora.pandora.PandoraConfig attribute) remove_input_files() (pandora.dataset.EigenDataset method) result_decimals (pandora.pandora.PandoraConfig attribute) result_dir (pandora.pandora.PandoraConfig attribute) result_file (pandora.pandora.PandoraConfig property)

run_convertf() (in module pandora.converter) run_mds() (pandora.dataset.EigenDataset method) (pandora.dataset.NumpyDataset method) run_pca() (pandora.dataset.EigenDataset method) (pandora.dataset.NumpyDataset method)

S

sample_support_values_csv (pandora.pandora.PandoraConfig property) save_config() (pandora.pandora.PandoraConfig method) seed (pandora.pandora.PandoraConfig attribute) SLIDING_WINDOW (pandora.custom_types.AnalysisMode attribute) sliding_window() (pandora.pandora.Pandora method)

sliding_window_embedding() (in module pandora.sliding_window) sliding_window_embedding_numpy() (in module pandora.sliding_window) sliding_window_result_dir (pandora.pandora.PandoraConfig property) smartpca (pandora.pandora.PandoraConfig attribute) smartpca_optional_settings (pandora.pandora.PandoraConfig attribute) support_value_rogue_cutoff (pandora.pandora.PandoraConfig attribute)

T

threads (pandora.pandora.PandoraConfig attribute)

V

verbosity (pandora.pandora.PandoraConfig attribute)