Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V _ __init__() (_Assay method) (BarGraph method) (Cnv method) (COMPASS method) (CopyNumber method) (Dna method) (Fishplot method) (GroupByGenotype method) (Heatmap method) (LinePlot method) (MultiHeatmap method) (NSP method) (Protein method) (Sample method) (SampleGroup method) (TreeGraph method) (VariantSubcloneTable method) _Assay (class in missionbio.mosaic.assay) A add_col_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) add_extension() (_Assay class method) (Cnv class method) (Dna class method) (Protein class method) add_hrect() (LinePlot method) add_layer() (_Assay method) (Cnv method) (Dna method) (Protein method) add_metadata() (_Assay method) (Cnv method) (Dna method) (Protein method) add_row_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) ADO_PARENTS (in module missionbio.mosaic.constants) ADO_SCORE (in module missionbio.mosaic.constants) ADO_SISTERS (in module missionbio.mosaic.constants) AF_FILTERED (in module missionbio.mosaic.constants) AF_MISSING (in module missionbio.mosaic.constants) all_points_trace() (LinePlot method) AMBIGUOUS (COMPASS attribute) amp_uniformity() (Cnv method) ANNOTATED (in module missionbio.mosaic.constants) annotation() (Heatmap static method) ANNOTATION_COLUMNS (in module missionbio.mosaic.constants) apply() (SampleGroup method) assay_color (Cnv attribute) (Dna attribute) (Protein attribute) (Sample attribute) assay_scatter() (Sample method) assays() (Sample method) AttributeType (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) B barcodes() (_Assay method) (Cnv method) (Dna method) (Protein method) BarGraph (class in missionbio.mosaic.plots.bargraph) barplot() (SampleGroup method) C callback_create_figure() (CopyNumber method) (VariantSubcloneTable method) callback_filter_and_normalize() (CopyNumber method) callback_sort_variants_table() (VariantSubcloneTable method) callback_subclone_table_modifications() (VariantSubcloneTable method) callback_update_feature_options() (CopyNumber method) cell_uniformity() (Cnv method) cells_per_ab() (Protein method) clipped_values() (in module missionbio.mosaic.utils) clone_vs_analyte() (Sample method) cluster() (_Assay method) (Cnv method) (Dna method) (Protein method) clustered_barcodes() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) clustered_ids() (_Assay method) (Cnv method) (Dna method) (Protein method) Cnv (class in missionbio.mosaic.cnv) col_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) coloraxis() (Heatmap method) COLORS (in module missionbio.mosaic.constants) command_name (COMPASS attribute) common_barcodes() (Sample method) COMPASS (class in missionbio.mosaic.algorithms.compass) compute_ploidy() (Cnv method) convolve() (_Assay static method) (Cnv static method) (Dna static method) (Protein static method) copy() (_Assay method) (Cnv method) (Dna method) (Protein method) CopyNumber (class in missionbio.mosaic.workflows.copy_number) create() (_Assay class method) (Cnv class method) (Dna class method) (Protein class method) create_conditional_style() (VariantSubcloneTable static method) crosstab() (_Assay method) (Cnv method) (Dna method) (Protein method) crosstabmap() (_Assay method) (Cnv method) (Dna method) (Protein method) D data_lines_trace() (Heatmap method) DATA_TRACE (Heatmap attribute) data_trace() (Heatmap method) del_col_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) del_layer() (_Assay method) (Cnv method) (Dna method) (Protein method) del_metadata() (_Assay method) (Cnv method) (Dna method) (Protein method) del_row_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) disable_logging() (in module missionbio.mosaic.utils) Dna (class in missionbio.mosaic.dna) dna_modified() (CopyNumber method) draw() (BarGraph method) (Fishplot method) (Heatmap method) (LinePlot method) (MultiHeatmap method) (TreeGraph method) drop() (_Assay method) (Cnv method) (Dna method) (Protein method) E expected_fig_size() (TreeGraph method) extend_docs() (in module missionbio.mosaic.utils) extensions (Cnv attribute) (Dna attribute) (Protein attribute) extract_output() (COMPASS method) F feature_scatter() (_Assay method) (Cnv method) (Dna method) (Protein method) filter_amplicons() (Cnv method) filter_barcodes() (Dna method) filter_options (CopyNumber attribute) filter_variants() (Dna method) filter_variants_consecutive() (Dna method) find_clones() (Dna method) find_relevant_variants() (Dna method) Fishplot (class in missionbio.mosaic.plots.fishplot) fishplot() (SampleGroup method) FONT_ASPECT (TreeGraph attribute) FONT_LINESPACE (TreeGraph attribute) format_subclone_df() (VariantSubcloneTable static method) G ga() (_Assay method) (Cnv method) (Dna method) (Protein method) GENE_NAME (in module missionbio.mosaic.constants) get_ado_scores() (GroupByGenotype method) get_annotations() (Dna method) get_attribute() (_Assay method) (Cnv method) (Dna method) (Protein method) get_clones() (VariantSubcloneTable method) get_gene_and_gt_names() (VariantSubcloneTable method) get_gene_names() (Cnv method) get_indexes() (in module missionbio.mosaic.utils) get_labels() (_Assay method) (Cnv method) (Dna method) (GroupByGenotype method) (Protein method) get_layout() (CopyNumber method) (VariantSubcloneTable method) get_palette() (_Assay method) (Cnv method) (Dna method) (Protein method) get_row_ids() (_Assay method) (Cnv method) (Dna method) (Protein method) get_variant_bulk_metrics() (Dna method) get_variants_df() (VariantSubcloneTable method) getassays() (SampleGroup method) group_by_genotype() (Dna method) group_clusters() (_Assay method) (Cnv method) (Dna method) (Protein method) GroupByGenotype (class in missionbio.mosaic.algorithms.group_by_genotype) groups_median_trace() (LinePlot method) H hasassay() (SampleGroup method) Heatmap (class in missionbio.mosaic.plots.heatmap) heatmap() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) hierarchical_cluster() (_Assay class method) (Cnv class method) (Dna class method) (Protein class method) highlight_heatmap() (_Assay method) (Cnv method) (Dna method) (Protein method) HLINE_DATA_TRACE (Heatmap attribute) HLINE_LABEL_TRACE (Heatmap attribute) human_readable_variant_name() (COMPASS static method) I ids() (_Assay method) (Cnv method) (Dna method) (Protein method) is_contiguous() (Heatmap static method) is_port_in_use() (CopyNumber static method) (VariantSubcloneTable static method) L LABEL (in module missionbio.mosaic.constants) label_lines_trace() (Heatmap method) label_trace() (Heatmap method) labels_ (COMPASS attribute) LABELS_TRACE (Heatmap attribute) layers (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) LinePlot (class in missionbio.mosaic.plots.lineplot) lines_trace() (LinePlot method) load() (in module missionbio.mosaic.io) load_example_dataset() (in module missionbio.mosaic.io) M MARKER_TEXTSPACE (TreeGraph attribute) MAX_CELLS_TO_SHOW_POINTS (VariantSubcloneTable attribute) MAX_NAME_LENGTH (VariantSubcloneTable attribute) merge() (SampleGroup method) merge_assay() (SampleGroup method) merge_similar_clusters() (Dna method) metadata (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) missionbio.mosaic.constants module missionbio.mosaic.io module missionbio.mosaic.utils module MIXED (COMPASS attribute) module missionbio.mosaic.constants missionbio.mosaic.io missionbio.mosaic.utils MultiHeatmap (class in missionbio.mosaic.plots.multi_heatmap) mutated_cells() (Dna method) N name (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) name_id_by_pos() (Cnv method) NAN_L2 (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) NGT_FILTERED (in module missionbio.mosaic.constants) node_descriptions() (COMPASS method) node_genotypes_ (COMPASS attribute) nodes_ (COMPASS attribute) normalize_barcodes() (_Assay method) (Cnv method) (Dna method) (Protein method) normalize_reads() (Cnv method) (Protein method) NORMALIZED_READS (in module missionbio.mosaic.constants) NSP (class in missionbio.mosaic.algorithms.nsp) O ORG_BARCODE (in module missionbio.mosaic.constants) ORIGINAL_ID (in module missionbio.mosaic.constants) P PALETTE (in module missionbio.mosaic.constants) parse_var_id() (COMPASS static method) pathscale() (Dna method) PCA_LABEL (in module missionbio.mosaic.constants) PLOIDY (in module missionbio.mosaic.constants) plot() (GroupByGenotype method) (NSP method) plot_options() (CopyNumber method) plot_ploidy() (Cnv method) plot_tree() (COMPASS method) plot_variant_correlation() (Dna method) prep_amplicon_reads() (COMPASS method) prep_variants() (COMPASS method) prepare_input() (COMPASS method) probability_ (COMPASS attribute) Protein (class in missionbio.mosaic.protein) R raw_counts() (Sample method) raw_heatmaps() (Sample method) read_data() (Sample method) read_distribution() (_Assay method) (Cnv method) (Dna method) (Protein method) READS (in module missionbio.mosaic.constants) reads_to_ab() (Protein method) rename_clones() (VariantSubcloneTable method) rename_labels() (_Assay method) (Cnv method) (Dna method) (GroupByGenotype method) (Protein method) rename_sample() (_Assay method) (Cnv method) (Dna method) (Protein method) reset() (Sample method) reset_cnv_assay() (CopyNumber method) reset_ids() (_Assay method) (Cnv method) (Dna method) (Protein method) ridgeplot() (_Assay method) (Cnv method) (Dna method) (Protein method) row_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) run() (COMPASS method) (CopyNumber method) (VariantSubcloneTable method) run_lda() (_Assay method) (Cnv method) (Dna method) (Protein method) run_pca() (_Assay method) (Cnv method) (Dna method) (Protein method) run_umap() (_Assay method) (Cnv method) (Dna method) (Protein method) S Sample (class in missionbio.mosaic.sample) SampleGroup (class in missionbio.mosaic.samplegroup) samples() (_Assay method) (Cnv method) (Dna method) (Protein method) save() (in module missionbio.mosaic.io) scale_data() (_Assay method) (Cnv method) (Dna method) (Protein method) SCALED_LABEL (in module missionbio.mosaic.constants) scaling_factor() (NSP method) scatterplot() (_Assay method) (Cnv method) (Dna method) (Protein method) select_columns() (_Assay method) (Cnv method) (Dna method) (Protein method) select_rows() (_Assay method) (Cnv method) (Dna method) (Protein method) selected_bars (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) selected_ids (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) selected_variants (VariantSubcloneTable attribute) set_ids_from_cols() (_Assay method) (Cnv method) (Dna method) (Protein method) set_labels() (_Assay method) (Cnv method) (Dna method) (Protein method) set_layout() (LinePlot method) set_palette() (_Assay method) (Cnv method) (Dna method) (Protein method) set_port() (CopyNumber class method) (VariantSubcloneTable class method) set_random_seed() (in module missionbio.mosaic.utils) set_selected_labels() (_Assay method) (Cnv method) (Dna method) (Protein method) set_ticks() (Heatmap static method) (LinePlot static method) set_xticks() (Heatmap method) (LinePlot method) set_yticks() (Heatmap method) setup_callbacks() (CopyNumber method) (VariantSubcloneTable method) shape (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) signature() (_Assay method) (Cnv method) (Dna method) (Protein method) signaturemap() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) somatic_variants (COMPASS attribute) sort_columns() (_Assay method) (Cnv method) (Dna method) (Protein method) sort_ids() (Dna method) sort_rows() (_Assay method) (Cnv method) (Dna method) (Protein method) split() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) static_fig() (in module missionbio.mosaic.utils) stop() (CopyNumber method) (VariantSubcloneTable method) stripplot() (_Assay method) (Cnv method) (Dna method) (Protein method) subclone_options_layout (VariantSubcloneTable attribute) subclone_table() (GroupByGenotype method) subclone_table_component (VariantSubcloneTable attribute) T test_signature() (_Assay method) (Cnv method) (Dna method) (Protein method) to_zip() (in module missionbio.mosaic.io) trace() (BarGraph method) transform() (NSP method) tree_ (COMPASS attribute) TreeGraph (class in missionbio.mosaic.plots.fishplot) U UMAP_LABEL (in module missionbio.mosaic.constants) umaps() (Sample method) update_coloraxis() (_Assay static method) (Cnv static method) (Dna static method) (Protein static method) V VARIANT_CLONE_ERROR_RATE (COMPASS attribute) variants_table_component (VariantSubcloneTable attribute) VariantSubcloneTable (class in missionbio.mosaic.workflows.variant_subclone_table) violin_options_layout (VariantSubcloneTable attribute) violinplot() (_Assay method) (Cnv method) (Dna method) (Protein method) VLINE_DATA_TRACE (Heatmap attribute)