Index

A

add_cmap() (pymaftools.plot.ColorManager.ColorManager method) add_feature_metadata() (pymaftools.core.PivotTable.PivotTable method) add_freq() (pymaftools.core.PivotTable.PivotTable method) add_legend() (pymaftools.plot.LegendManager.LegendManager method) add_numeric_colorbar() (pymaftools.plot.LegendManager.LegendManager method) add_numeric_legend() (pymaftools.plot.LegendManager.LegendManager method) add_sample_metadata() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method) add_shape_legend() (pymaftools.plot.LegendManager.LegendManager method)

add_table() (pymaftools.core.Cohort.Cohort method) add_xticklabel() (pymaftools.plot.OncoPlot.OncoPlot method) adjust_color_brightness() (pymaftools.plot.ColorManager.ColorManager method) align_cluster_label_dict() (in module pymaftools.core.Clustering) align_clusters() (in module pymaftools.core.Clustering) ALL_MUTATION_CMAP (pymaftools.plot.ColorManager.ColorManager attribute) analyze_similarity() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) apply_cmap_to_data() (pymaftools.plot.ColorManager.ColorManager method) ASCStackingModel (class in pymaftools.model.StackingModel)

B

build_model() (pymaftools.model.StackingModel.OmicsStackingModel method)

C

calculate_ari_matrix() (in module pymaftools.core.Clustering) calculate_feature_frequency() (pymaftools.core.PivotTable.PivotTable method) calculate_group_similarity_pvalues() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) calculate_TMB() (pymaftools.core.PivotTable.PivotTable method) CancerCellFractionTable (class in pymaftools.core.CancerCellFractionTable) capture_size() (in module pymaftools.core.PivotTable) categorical_heatmap() (pymaftools.plot.OncoPlot.OncoPlot static method) change_index_level() (pymaftools.core.MAF.MAF method) clear_legends() (pymaftools.plot.LegendManager.LegendManager method) CNV_CMAP (pymaftools.plot.ColorManager.ColorManager attribute) Cohort (class in pymaftools.core.Cohort) ColorManager (class in pymaftools.plot.ColorManager)

compare_group_pairs() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) compute_similarity() (pymaftools.core.PivotTable.PivotTable method) confusion_matrix() (pymaftools.model.StackingModel.OmicsStackingModel method) convert_ndarray_to_list() (in module pymaftools.core.Clustering) CooccurrenceMatrix (class in pymaftools.core.PairwiseMatrix) copy() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method) CopyNumberVariationTable (class in pymaftools.core.CopyNumberVariationTable) count_legends() (pymaftools.plot.LegendManager.LegendManager method) create_from_dict() (pymaftools.plot.LegendManager.LegendManager static method) create_matplotlib_cmap() (pymaftools.plot.ColorManager.ColorManager method) cross_validate_importance() (in module pymaftools.model.modelUtils)

D

decode_y() (pymaftools.model.StackingModel.OmicsStackingModel method)

default_oncoplot() (pymaftools.plot.OncoPlot.OncoPlot static method) draw_cube() (pymaftools.plot.MethodsPlot.MethodsPlot static method)

E

encode_y() (pymaftools.model.StackingModel.OmicsStackingModel method) entry_equal_properties() (pymaftools.plot.FontManager.FontManager method)

evaluate() (pymaftools.model.StackingModel.OmicsStackingModel method) evaluate_model() (in module pymaftools.model.modelUtils) ExpressionTable (class in pymaftools.core.ExpressionTable)

F

feature_metadata (pymaftools.core.PivotTable.PivotTable attribute) fetch_msigdb_geneset() (in module pymaftools.utils.geneset) filter_by_freq() (pymaftools.core.PivotTable.PivotTable method) filter_by_statistical_test() (pymaftools.core.PivotTable.PivotTable method) filter_by_variance() (pymaftools.core.PivotTable.PivotTable method)

filter_maf() (pymaftools.core.MAF.MAF method) fit() (pymaftools.model.StackingModel.OmicsStackingModel method) fit_transform() (pymaftools.utils.reduction.PCA_CCA method) FontManager (class in pymaftools.plot.FontManager) from_pivot_table() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable class method)

G

generate_categorical_cmap() (pymaftools.plot.ColorManager.ColorManager method) generate_cmap_from_list() (pymaftools.plot.ColorManager.ColorManager method) generate_permutation_list() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) get_available_fonts() (pymaftools.plot.FontManager.FontManager method) get_cmap() (pymaftools.plot.ColorManager.ColorManager method) get_domain_info() (pymaftools.core.MAF.MAF static method) get_gene_description_df() (in module pymaftools.utils.geneinfo) get_gene_info_json() (in module pymaftools.utils.geneinfo) get_importance() (in module pymaftools.model.modelUtils) get_legend_dict() (pymaftools.plot.LegendManager.LegendManager method) get_legend_info() (pymaftools.plot.LegendManager.LegendManager method)

get_legend_names() (pymaftools.plot.LegendManager.LegendManager method) get_mean_group_similarity() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) get_ncbi_gene_ID() (in module pymaftools.utils.geneinfo) get_ncbi_gene_IDs() (in module pymaftools.utils.geneinfo) get_omics_feature_importance() (pymaftools.model.StackingModel.OmicsStackingModel method) get_omics_weights() (pymaftools.model.StackingModel.OmicsStackingModel method) get_pairs_subset() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) get_protein_info() (pymaftools.core.MAF.MAF method) get_target_sample_ID() (in module pymaftools.core.CopyNumberVariationTable) get_weights() (pymaftools.utils.reduction.PCA_CCA method) gpt_known_genes_summary() (in module pymaftools.core.Clustering)

H

has_legend() (pymaftools.plot.LegendManager.LegendManager method)

head() (pymaftools.core.PivotTable.PivotTable method) heatmap_rectangle() (pymaftools.plot.OncoPlot.OncoPlot method)

I

index_col (pymaftools.core.MAF.MAF attribute), [1]

info() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method)

K

k_fold_clustering_evaluation() (in module pymaftools.core.Clustering)

L

LegendManager (class in pymaftools.plot.LegendManager)

LollipopPlot (class in pymaftools.plot.LollipopPlot)

M

MAF (class in pymaftools.core.MAF) merge() (pymaftools.core.PivotTable.PivotTable static method) merge_mafs() (pymaftools.core.MAF.MAF static method) merge_mutations() (pymaftools.core.MAF.MAF static method) MethodsPlot (class in pymaftools.plot.MethodsPlot) ModelPlot (class in pymaftools.plot.ModelPlot) module pymaftools.core.CancerCellFractionTable pymaftools.core.Clustering pymaftools.core.Cohort pymaftools.core.CopyNumberVariationTable pymaftools.core.ExpressionTable pymaftools.core.MAF pymaftools.core.PairwiseMatrix pymaftools.core.PivotTable pymaftools.core.SignatureTable pymaftools.model.modelUtils pymaftools.model.StackingModel pymaftools.plot.ColorManager pymaftools.plot.FontManager pymaftools.plot.LegendManager pymaftools.plot.LollipopPlot pymaftools.plot.MethodsPlot pymaftools.plot.ModelPlot pymaftools.plot.OncoPlot pymaftools.plot.PivotTablePlot pymaftools.utils.geneinfo pymaftools.utils.geneset pymaftools.utils.reduction

mutation_enrichment_test() (pymaftools.core.PivotTable.PivotTable method) mutation_heatmap() (pymaftools.plot.OncoPlot.OncoPlot method) mutations_count (pymaftools.core.MAF.MAF property)

N

NONSYNONYMOUS_CMAP (pymaftools.plot.ColorManager.ColorManager attribute) nonsynonymous_types (pymaftools.core.MAF.MAF attribute), [1]

normalize_weight() (pymaftools.plot.FontManager.FontManager static method) numeric_heatmap() (pymaftools.plot.OncoPlot.OncoPlot method)

O

OmicsStackingModel (class in pymaftools.model.StackingModel)

OncoPlot (class in pymaftools.plot.OncoPlot) order() (pymaftools.core.PivotTable.PivotTable method)

P

paired_similarity_utest() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) PairwiseMatrix (class in pymaftools.core.PairwiseMatrix) parse_gene_info() (in module pymaftools.utils.geneinfo) PCA() (pymaftools.core.PivotTable.PivotTable method) PCA_CCA (class in pymaftools.utils.reduction) PivotTable (class in pymaftools.core.PivotTable) PivotTablePlot (class in pymaftools.plot.PivotTablePlot) plot (pymaftools.core.PivotTable.PivotTable property) plot() (pymaftools.plot.LollipopPlot.LollipopPlot method) plot_ari_matrix() (in module pymaftools.core.Clustering) plot_bar() (pymaftools.plot.OncoPlot.OncoPlot method) plot_boxplot_with_annot() (pymaftools.plot.PivotTablePlot.PivotTablePlot method) plot_categorical_metadata() (pymaftools.plot.OncoPlot.OncoPlot method) plot_cluster_feature_importance() (in module pymaftools.core.Clustering) plot_cluster_feature_importance_boxplot() (in module pymaftools.core.Clustering) plot_clustering_metrics_and_find_best_k() (in module pymaftools.core.Clustering) plot_cnv_band_ratio() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) plot_cohort_demo() (pymaftools.plot.MethodsPlot.MethodsPlot method) plot_color_heatmap() (pymaftools.plot.OncoPlot.OncoPlot static method) plot_feature_importance_distribution() (pymaftools.plot.ModelPlot.ModelPlot method) plot_final_coefficients() (pymaftools.model.StackingModel.OmicsStackingModel method) plot_freq() (pymaftools.plot.OncoPlot.OncoPlot method) plot_group_heatmap() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) plot_heatmap() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) plot_horizontal_legend() (pymaftools.plot.LegendManager.LegendManager method) plot_legends() (pymaftools.plot.LegendManager.LegendManager method) plot_metric_comparison_with_annotation() (in module pymaftools.model.modelUtils) (pymaftools.plot.ModelPlot.ModelPlot method) plot_multi_cohort() (pymaftools.plot.LollipopPlot.LollipopPlot class method) plot_numeric_metadata() (pymaftools.plot.OncoPlot.OncoPlot method) plot_pca_legends() (pymaftools.plot.LegendManager.LegendManager method) plot_pca_samples() (pymaftools.plot.PivotTablePlot.PivotTablePlot method) plot_permutation_distribution() (pymaftools.core.PairwiseMatrix.SimilarityMatrix static method) plot_rfecv_curve() (pymaftools.plot.ModelPlot.ModelPlot method) plot_similarity() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) plot_similarity_matrix() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) plot_top_feature_importance_heatmap() (in module pymaftools.model.modelUtils) (pymaftools.plot.ModelPlot.ModelPlot method) predefined_cmaps (pymaftools.plot.ColorManager.ColorManager attribute) predict() (pymaftools.model.StackingModel.OmicsStackingModel method) predict_proba() (pymaftools.model.StackingModel.OmicsStackingModel method) prepare_data() (pymaftools.core.PivotTable.PivotTable static method) pyclone_to_sorted_table() (pymaftools.core.CancerCellFractionTable.CancerCellFractionTable static method)

pymaftools.core.CancerCellFractionTable module pymaftools.core.Clustering module pymaftools.core.Cohort module pymaftools.core.CopyNumberVariationTable module pymaftools.core.ExpressionTable module pymaftools.core.MAF module pymaftools.core.PairwiseMatrix module pymaftools.core.PivotTable module pymaftools.core.SignatureTable module pymaftools.model.modelUtils module pymaftools.model.StackingModel module pymaftools.plot.ColorManager module pymaftools.plot.FontManager module pymaftools.plot.LegendManager module pymaftools.plot.LollipopPlot module pymaftools.plot.MethodsPlot module pymaftools.plot.ModelPlot module pymaftools.plot.OncoPlot module pymaftools.plot.PivotTablePlot module pymaftools.utils.geneinfo module pymaftools.utils.geneset module pymaftools.utils.reduction module

R

read_all_gistic() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable static method) read_cnv_files() (in module pymaftools.core.CopyNumberVariationTable) read_csv() (pymaftools.core.MAF.MAF class method) read_gistic_arm_level() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable class method) read_gistic_gene_level() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable class method) read_GMT() (in module pymaftools.utils.geneset) read_hdf5() (pymaftools.core.Cohort.Cohort class method) read_maf() (pymaftools.core.MAF.MAF class method) read_sample_cutoff_file() (in module pymaftools.core.CopyNumberVariationTable) read_signature() (pymaftools.core.SignatureTable.SignatureTable class method) read_sqlite() (pymaftools.core.Cohort.Cohort class method) (pymaftools.core.PivotTable.PivotTable class method)

read_TCGA_ASCAT3_CNV_file_sheet() (in module pymaftools.core.CopyNumberVariationTable) register_fonts_from_directory() (pymaftools.plot.FontManager.FontManager method) register_local_font() (pymaftools.plot.FontManager.FontManager method) reindex() (pymaftools.core.PivotTable.PivotTable method) remove_legend() (pymaftools.plot.LegendManager.LegendManager method) remove_table() (pymaftools.core.Cohort.Cohort method) rename_index_and_columns() (pymaftools.core.PivotTable.PivotTable method) run_feature_clustering() (in module pymaftools.core.Clustering) run_model_evaluation() (in module pymaftools.model.modelUtils) run_random_forest_cv() (in module pymaftools.core.Clustering) run_random_forest_multiple_seeds() (in module pymaftools.core.Clustering) run_rfecv_feature_selection() (in module pymaftools.model.modelUtils)

S

sample_metadata (pymaftools.core.PivotTable.PivotTable attribute) select_samples() (pymaftools.core.MAF.MAF method) set_axis() (pymaftools.plot.LegendManager.LegendManager method) set_config() (pymaftools.plot.OncoPlot.OncoPlot method) setup_matplotlib_fonts() (pymaftools.plot.FontManager.FontManager method) show() (pymaftools.plot.LollipopPlot.LollipopPlot method) SignatureTable (class in pymaftools.core.SignatureTable) SimilarityMatrix (class in pymaftools.core.PairwiseMatrix)

simulate_alpha_blend() (pymaftools.plot.ColorManager.ColorManager method) soft_score() (pymaftools.model.StackingModel.ASCStackingModel method) sort_by_chrom() (pymaftools.core.MAF.MAF method) sort_by_chromosome() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) sort_features() (pymaftools.core.PivotTable.PivotTable method) sort_samples_by_group() (pymaftools.core.PivotTable.PivotTable method) sort_samples_by_mutations() (pymaftools.core.PivotTable.PivotTable method) subset() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method)

T

table_to_distance() (in module pymaftools.core.Clustering) tail() (pymaftools.core.PivotTable.PivotTable method) TCGA_sample_type() (in module pymaftools.core.CopyNumberVariationTable) to_base_change_pivot_table() (pymaftools.core.MAF.MAF method) to_binary_table() (pymaftools.core.PivotTable.PivotTable method) to_cluster_table() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) (pymaftools.core.ExpressionTable.ExpressionTable method) to_cnv_table() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable static method) to_cooccur_matrix() (pymaftools.core.PivotTable.PivotTable method) to_csv() (pymaftools.core.MAF.MAF method) to_edges_dataframe() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method)

to_hdf5() (pymaftools.core.Cohort.Cohort method) to_hierarchical_clustering() (pymaftools.core.PivotTable.PivotTable method) to_importance_table() (in module pymaftools.model.modelUtils) to_MAF() (pymaftools.core.MAF.MAF method) to_mutation_table() (pymaftools.core.MAF.MAF method) to_networkx_graph() (pymaftools.core.PairwiseMatrix.SimilarityMatrix method) to_pivot_table() (pymaftools.core.MAF.MAF method) to_sql_registry() (pymaftools.core.Cohort.Cohort method) to_sqlite() (pymaftools.core.Cohort.Cohort method) (pymaftools.core.PivotTable.PivotTable method) to_thresholded_cnv() (pymaftools.core.CopyNumberVariationTable.CopyNumberVariationTable method) transform() (pymaftools.utils.reduction.PCA_CCA method)

U

update_layout() (pymaftools.plot.OncoPlot.OncoPlot method)

update_legend_colors() (pymaftools.plot.LegendManager.LegendManager method)

V

vaild_variant_classfication (pymaftools.core.MAF.MAF attribute), [1]

W

WEIGHT_MAP (pymaftools.plot.FontManager.FontManager attribute), [1]

write_maf() (pymaftools.core.MAF.MAF method) write_SigProfilerMatrixGenerator_format() (pymaftools.core.MAF.MAF method)