Index

Symbols

--alpha decompose command line option rank_select command line option --beta_loss decompose command line option rank_select command line option regu_select command line option --compress decompose command line option --delimiter decompose command line option rank_select command line option regu_select command line option --design rank_select command line option regu_select command line option --hard_mapping reapply command line option --init decompose command line option rank_select command line option regu_select command line option --input decompose command line option rank_select command line option reapply command line option regu_select command line option --l1_ratio decompose command line option rank_select command line option regu_select command line option --log_debug decompose command line option rank_select command line option regu_select command line option --log_info decompose command line option rank_select command line option regu_select command line option --log_warning decompose command line option rank_select command line option regu_select command line option --max_iter decompose command line option rank_select command line option regu_select command line option --model reapply command line option --n_runs decompose command line option --no-progress decompose command line option rank_select command line option regu_select command line option --no-rollup reapply command line option --no-scale regu_select command line option --no-symlink decompose command line option --no_compress decompose command line option --output_dir decompose command line option rank_select command line option reapply command line option regu_select command line option

--progress decompose command line option rank_select command line option regu_select command line option --rank regu_select command line option --rank_max rank_select command line option --rank_min rank_select command line option --rank_step rank_select command line option --rollup reapply command line option --scale regu_select command line option --seed decompose command line option rank_select command line option regu_select command line option --separator reapply command line option --shuffles rank_select command line option regu_select command line option --symlink decompose command line option --top_criteria decompose command line option --top_n decompose command line option -d decompose command line option rank_select command line option regu_select command line option -h reapply command line option -i decompose command line option rank_select command line option reapply command line option regu_select command line option -k regu_select command line option -l rank_select command line option -m reapply command line option -n rank_select command line option -o decompose command line option rank_select command line option reapply command line option regu_select command line option -s rank_select command line option reapply command line option regu_select command line option -u rank_select command line option

A

A (cvanmf.denovo.BicvFold attribute) a (cvanmf.denovo.BicvResult attribute) add() (cvanmf.reapply.FeatureMapping method) add_models() (cvanmf.combine.Cohort method) add_signatures() (cvanmf.combine.Model method)

align_signatures() (in module cvanmf.stability) ALPHA regu_select command line option alpha (cvanmf.denovo.NMFParameters attribute) as_dataframe() (cvanmf.combine.Cluster static method)

B

B (cvanmf.denovo.BicvFold attribute) beta_divergence (cvanmf.denovo.Decomposition property) beta_loss (cvanmf.denovo.NMFParameters attribute)

bicv() (in module cvanmf.denovo) BicvFold (class in cvanmf.denovo) BicvResult (class in cvanmf.denovo) BicvSplit (class in cvanmf.denovo)

C

C (cvanmf.denovo.BicvFold attribute) ch (in module cvanmf) citation (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) (cvanmf.models.Signatures attribute) cli() (in module cvanmf.reapply) cli_decompose() (in module cvanmf.denovo) cli_rank_selection() (in module cvanmf.denovo) cli_regu_selection() (in module cvanmf.denovo) Cluster (class in cvanmf.combine) clusters (cvanmf.combine.Combiner property) Cohort (class in cvanmf.combine) cohort (cvanmf.combine.Model property) cohort_data (cvanmf.combine.Combiner property) cohort_model_count (cvanmf.combine.Cluster property) cohorts (cvanmf.combine.Combiner property) col() (cvanmf.denovo.BicvSplit method) col_metadata (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) color_scale (cvanmf.denovo.Decomposition property) colors (cvanmf.denovo.Decomposition property) (cvanmf.models.Signatures attribute) combine_signatures() (in module cvanmf.combine) Combiner (class in cvanmf.combine)

Comparable (in module cvanmf.stability) compare_signatures() (cvanmf.denovo.Decomposition method) (in module cvanmf.stability) conflicts (cvanmf.reapply.FeatureMapping property) consensus_matrix() (cvanmf.denovo.Decomposition method) cophenetic_correlation() (in module cvanmf.denovo) cosine_similarity (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.Decomposition property) cosine_similarity() (cvanmf.combine.Cluster static method) cvanmf module cvanmf.combine module cvanmf.data module cvanmf.data.utils module cvanmf.denovo module cvanmf.models module cvanmf.reapply module cvanmf.stability module

D

D (cvanmf.denovo.BicvFold attribute) data (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) decompose command line option --alpha --beta_loss --compress --delimiter --init --input --l1_ratio --log_debug --log_info --log_warning --max_iter --n_runs --no-progress --no-symlink --no_compress --output_dir --progress --seed --symlink --top_criteria --top_n -d -i -o RANKS

decompose() (in module cvanmf.denovo) Decomposition (class in cvanmf.denovo) decompositions() (in module cvanmf.denovo) description (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) design (cvanmf.denovo.BicvSplit property) discrete_signature_scale() (cvanmf.denovo.Decomposition method) dispersion() (in module cvanmf.denovo) doi (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute)

E

example_abundance() (in module cvanmf.data) (in module cvanmf.data.utils)

example_cohort_structure() (in module cvanmf.combine) ExampleData (class in cvanmf.data) (class in cvanmf.data.utils)

F

feature_mapping (cvanmf.denovo.Decomposition property) feature_match (cvanmf.models.Signatures attribute) FeatureMapping (class in cvanmf.reapply) FeatureMatch (class in cvanmf.reapply) fill_scale (cvanmf.denovo.Decomposition property) five_es() (in module cvanmf.models) FIVE_ES_COLORS (in module cvanmf.models)

fm (in module cvanmf) fold() (cvanmf.denovo.BicvSplit method) folds (cvanmf.denovo.BicvSplit property) from_comparable() (cvanmf.combine.Model static method) (cvanmf.combine.Signature static method) from_comparables() (cvanmf.combine.Cohort static method) from_matrix() (cvanmf.denovo.BicvSplit static method)

G

get_signatures_from_comparable() (in module cvanmf.stability)

H

h (cvanmf.denovo.Decomposition property)

I

i (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.BicvSplit property) identify_cohort_specific() (cvanmf.combine.Combiner method)

init (cvanmf.denovo.NMFParameters attribute) input_hash (cvanmf.denovo.Decomposition property) input_validation (cvanmf.models.Signatures attribute) InputValidation (class in cvanmf.reapply)

J

join_folds() (cvanmf.denovo.BicvResult static method)

K

keep_mats (cvanmf.denovo.NMFParameters attribute)

L

l1_ratio (cvanmf.denovo.NMFParameters attribute) l2_norm (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.Decomposition property) label (cvanmf.combine.Cluster property) label_by_match() (cvanmf.combine.Combiner method) leukemia() (in module cvanmf.data) (in module cvanmf.data.utils) load() (cvanmf.denovo.Decomposition static method) load_all_npz() (cvanmf.denovo.BicvSplit static method) load_decompositions() (cvanmf.denovo.Decomposition static method)

LOAD_FILES (cvanmf.denovo.Decomposition attribute) load_npz() (cvanmf.denovo.BicvSplit static method) log_str (cvanmf.denovo.NMFParameters property) logger (in module cvanmf) (in module cvanmf.data.utils) (in module cvanmf.denovo) (in module cvanmf.models) (in module cvanmf.reapply) (in module cvanmf.stability) lung_cancer_cells() (in module cvanmf.data) (in module cvanmf.data.utils)

M

mapping (cvanmf.reapply.FeatureMapping property) match_genera() (in module cvanmf.reapply) match_identical() (in module cvanmf.reapply) match_signatures() (cvanmf.denovo.Decomposition method) (in module cvanmf.stability) max_iter (cvanmf.denovo.NMFParameters attribute) mds() (cvanmf.combine.Signature static method) mean_signature (cvanmf.combine.Cluster property) member_data (cvanmf.combine.Cluster property) member_feature_weights() (cvanmf.combine.Cluster method) member_similarity() (cvanmf.combine.Cluster method) merge() (cvanmf.combine.Cluster static method) merge_similar() (cvanmf.combine.Combiner method) missing() (cvanmf.reapply.FeatureMapping method)

Model (class in cvanmf.combine) model (cvanmf.combine.Signature property) model_fit (cvanmf.denovo.Decomposition property) models (cvanmf.combine.Cohort property) module cvanmf cvanmf.combine cvanmf.data cvanmf.data.utils cvanmf.denovo cvanmf.models cvanmf.reapply cvanmf.stability monodominant_samples() (cvanmf.denovo.Decomposition method) mx (cvanmf.denovo.BicvSplit property)

N

name (cvanmf.combine.Cohort property) (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) name_signatures_by_weight() (cvanmf.denovo.Decomposition method)

names (cvanmf.denovo.Decomposition property) nmf_transform() (in module cvanmf.reapply) NMFParameters (class in cvanmf.denovo) num_folds (cvanmf.denovo.BicvSplit property) Numeric (in module cvanmf.denovo)

O

other_metadata (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute)

P

parameters (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.Decomposition property) pcoa() (cvanmf.denovo.Decomposition method) PcoaMatrices (in module cvanmf.denovo) plot_feature_variance() (cvanmf.combine.Cluster method) (cvanmf.combine.Combiner method) plot_feature_weight() (cvanmf.denovo.Decomposition method) plot_mds() (cvanmf.combine.Cluster method) (cvanmf.combine.Combiner method) plot_member_similarity() (cvanmf.combine.Cluster method) (cvanmf.combine.Combiner method)

plot_metadata() (cvanmf.denovo.Decomposition method) plot_modelfit() (cvanmf.denovo.Decomposition method) plot_modelfit_point() (cvanmf.denovo.Decomposition method) plot_pcoa() (cvanmf.denovo.Decomposition method) plot_rank_selection() (in module cvanmf.denovo) plot_regu_selection() (in module cvanmf.denovo) plot_relative_weight() (cvanmf.denovo.Decomposition method) plot_signature_stability() (in module cvanmf.stability) plot_stability_rank_selection() (in module cvanmf.denovo) plot_weight_distribution() (cvanmf.denovo.Decomposition method) primary_signature (cvanmf.denovo.Decomposition property)

Q

quality_series (cvanmf.denovo.Decomposition property)

R

r_squared (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.Decomposition property) rank (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) (cvanmf.denovo.NMFParameters attribute) rank_select command line option --alpha --beta_loss --delimiter --design --init --input --l1_ratio --log_debug --log_info --log_warning --max_iter --no-progress --output_dir --progress --rank_max --rank_min --rank_step --seed --shuffles -d -i -l -n -o -s -u rank_selection() (in module cvanmf.denovo) RANKS decompose command line option reapply command line option --hard_mapping --input --model --no-rollup --output_dir --rollup --separator -h -i -m -o -s

reapply() (cvanmf.denovo.Decomposition method) (cvanmf.models.Signatures method) (in module cvanmf.reapply) reconstruction_error (cvanmf.denovo.BicvResult attribute) regu_select command line option --beta_loss --delimiter --design --init --input --l1_ratio --log_debug --log_info --log_warning --max_iter --no-progress --no-scale --output_dir --progress --rank --scale --seed --shuffles -d -i -k -o -s ALPHA regu_selection() (in module cvanmf.denovo) remove_linear_combinations() (cvanmf.combine.Combiner method) remove_linear_combinations_2() (cvanmf.combine.Combiner method) remove_low_support() (cvanmf.combine.Combiner method) removed_clusters (cvanmf.combine.Combiner property) representative_signatures() (cvanmf.denovo.Decomposition method) results_to_table() (cvanmf.denovo.BicvResult static method) row() (cvanmf.denovo.BicvSplit method) row_metadata (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) rss (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.Decomposition property)

S

save() (cvanmf.denovo.Decomposition method) save_all_npz() (cvanmf.denovo.BicvSplit static method) save_decompositions() (cvanmf.denovo.Decomposition static method) save_npz() (cvanmf.denovo.BicvSplit method) scaled() (cvanmf.denovo.Decomposition method) seed (cvanmf.denovo.NMFParameters attribute) shape (cvanmf.denovo.BicvSplit property) short_name (cvanmf.data.ExampleData attribute) (cvanmf.data.utils.ExampleData attribute) Signature (class in cvanmf.combine) signature_similarity() (in module cvanmf.denovo) signature_stability() (in module cvanmf.stability), [1] Signatures (class in cvanmf.models) signatures (cvanmf.combine.Cluster property) (cvanmf.combine.Cohort property) (cvanmf.combine.Model property)

significance_format() (cvanmf.denovo.Decomposition static method) size (cvanmf.denovo.BicvSplit property) sparsity_h (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.Decomposition property) sparsity_w (cvanmf.denovo.BicvResult attribute) (cvanmf.denovo.Decomposition property) split_dataframe_to_cohorts() (in module cvanmf.combine) suggest_alpha() (in module cvanmf.denovo) suggest_rank() (in module cvanmf.denovo) suggest_rank_stability() (in module cvanmf.denovo) support() (cvanmf.combine.Cluster method) swimmer() (in module cvanmf.data) (in module cvanmf.data.utils) synthetic_blocks() (in module cvanmf.data) (in module cvanmf.data.utils) synthetic_dense() (in module cvanmf.data) (in module cvanmf.data.utils)

T

to_df() (cvanmf.reapply.FeatureMapping method) to_series() (cvanmf.denovo.BicvResult method) to_yaml() (cvanmf.denovo.NMFParameters method)

TOP_CRITERIA (cvanmf.denovo.Decomposition attribute) transform_abundance() (cvanmf.reapply.FeatureMapping method) transform_w() (cvanmf.reapply.FeatureMapping method)

U

univariate_tests() (cvanmf.denovo.Decomposition method)

V

validate_genus_table() (in module cvanmf.reapply)

W

w (cvanmf.denovo.Decomposition property) (cvanmf.models.Signatures attribute)

wh (cvanmf.denovo.Decomposition property)

X

x (cvanmf.combine.Cohort property) (cvanmf.denovo.BicvSplit property) (cvanmf.denovo.NMFParameters attribute)