Index

A

alpha_ (mutopia.model.base.TopographyModel property) annot_component_distributions() (mutopia.model.base.TopographyModel method) annot_component_rates() (in module mutopia.analysis.topography_umap) annot_components() (mutopia.model.base.TopographyModel method) annot_contributions() (mutopia.model.base.TopographyModel method) annot_data() (mutopia.model.base.TopographyModel method)

annot_empirical_marginal() (in module mutopia.gtensor.gtensor) annot_marginal_prediction() (mutopia.model.base.TopographyModel method) annot_SHAP_values() (mutopia.model.base.TopographyModel method) apply_rows() (in module mutopia.plot.track_plot.transforms) apply_to_samples() (in module mutopia.gtensor.gtensor) available_components (mutopia.modalities.sbs.sbs.SBSMode property)

B

bar_plot() (in module mutopia.plot.track_plot.track_plot)

build_features() (mutopia.analysis.topography_umap.TopographyUMAP method)

C

categorical_plot() (in module mutopia.plot.track_plot.track_plot) center_at_zero() (in module mutopia.plot.track_plot.track_plot) clip() (in module mutopia.plot.track_plot.transforms) columns() (in module mutopia.plot.track_plot.track_plot)

component_names (mutopia.model.base.TopographyModel property) component_spectra() (mutopia.modalities.sbs.sbs.SBSMode method) components_ (mutopia.analysis.topography_umap.TopographyUMAP attribute) coords (mutopia.modalities.sbs.sbs.SBSMode property) custom_plot() (in module mutopia.plot.track_plot.track_plot)

D

DATABASE (mutopia.modalities.sbs.sbs.SBSMode attribute), [1]

dims (mutopia.modalities.sbs.sbs.SBSMode property) dims_except_for() (in module mutopia.gtensor.gtensor)

E

eager_load() (in module mutopia.gtensor.gtensor) eager_train_test_load() (in module mutopia.gtensor.gtensor)

embedding_ (mutopia.analysis.topography_umap.TopographyUMAP attribute) equal_size_quantiles() (in module mutopia.gtensor.gtensor) excel_report() (in module mutopia.gtensor.gtensor)

F

feature_matrix() (in module mutopia.plot.track_plot.transforms) features_from_model() (mutopia.analysis.topography_umap.TopographyUMAP method) fetch_component() (in module mutopia.gtensor.gtensor) fetch_features() (in module mutopia.gtensor.gtensor) fetch_interactions() (in module mutopia.gtensor.gtensor)

fetch_shared_effects() (in module mutopia.gtensor.gtensor) fetch_source() (in module mutopia.gtensor.gtensor) fill_plot() (in module mutopia.plot.track_plot.track_plot) fit() (mutopia.analysis.topography_umap.TopographyUMAP method) (mutopia.model.base.TopographyModel method) (mutopia.plot.track_plot.transforms.TopographyTransformer method)

G

get_context_frequencies() (mutopia.modalities.sbs.sbs.SBSMode class method) get_explanation() (in module mutopia.gtensor.gtensor)

get_shap_summary() (in module mutopia.gtensor.gtensor) GT (mutopia.model.base.TopographyModel attribute) GTensor() (in module mutopia.gtensor.gtensor)

H

heatmap_plot() (in module mutopia.plot.track_plot.track_plot)

I

ideogram() (in module mutopia.plot.track_plot.track_plot) infer_source_celltypes() (in module mutopia.gtensor.gtensor) ingest_observations() (mutopia.modalities.sbs.sbs.SBSMode method)

ingest_uncollaposed() (mutopia.modalities.sbs.sbs.SBSMode method) init_model() (mutopia.model.base.TopographyModel method) is_mixture_dataset() (in module mutopia.gtensor.gtensor)

K

kneighbors() (mutopia.analysis.topography_umap.TopographyUMAP method)

kneighbors_model() (mutopia.analysis.topography_umap.TopographyUMAP method)

L

labels (mutopia.plot.track_plot.transforms.TopographyTransformer property) lazy_load() (in module mutopia.gtensor.gtensor) lazy_train_test_load() (in module mutopia.gtensor.gtensor) line_plot() (in module mutopia.plot.track_plot.track_plot) list_components() (in module mutopia.gtensor.gtensor)

list_sources() (in module mutopia.gtensor.gtensor) load() (mutopia.analysis.topography_umap.TopographyUMAP class method) load_components() (mutopia.modalities.sbs.sbs.SBSMode method) load_dataset() (in module mutopia.gtensor.gtensor) load_reference_coordinates() (in module mutopia.analysis.topography_umap) load_reference_umap() (in module mutopia.analysis.topography_umap)

M

make_mixture_dataset() (in module mutopia.gtensor.gtensor) make_view() (in module mutopia.plot.track_plot.track_plot) match_components() (mutopia.modalities.sbs.sbs.SBSMode method) match_dims() (in module mutopia.gtensor.gtensor) metadata_ (mutopia.analysis.topography_umap.TopographyUMAP attribute) minmax_scale() (in module mutopia.plot.track_plot.transforms) modality (mutopia.model.base.TopographyModel property) MODE_ID (mutopia.modalities.sbs.sbs.SBSMode attribute), [1] module mutopia.gtensor.gtensor mutopia.plot mutopia.plot.track_plot mutopia.plot.track_plot.track_plot mutopia.plot.track_plot.tracks mutopia.plot.track_plot.transforms

mutate_method() (in module mutopia.gtensor.gtensor) mutopia.gtensor.gtensor module mutopia.plot module mutopia.plot.track_plot module mutopia.plot.track_plot.track_plot module mutopia.plot.track_plot.tracks module mutopia.plot.track_plot.transforms module MUTOPIA_TO_COSMIC_IDX (mutopia.modalities.sbs.sbs.SBSMode attribute), [1]

N

n_components (mutopia.model.base.TopographyModel property)

needs_setup() (mutopia.model.base.TopographyModel method) num_sources() (in module mutopia.gtensor.gtensor)

O

order_components() (in module mutopia.plot.track_plot.tracks)

P

PALETTE (mutopia.modalities.sbs.sbs.SBSMode attribute), [1] passthrough() (in module mutopia.plot.track_plot.transforms) pipeline() (in module mutopia.plot.track_plot.transforms) plot() (mutopia.modalities.sbs.sbs.SBSMode class method) plot_component() (in module mutopia.plot) plot_component_rates() (in module mutopia.plot.track_plot.tracks) plot_empirical_topography() (in module mutopia.plot.track_plot.tracks) plot_gene_annotation() (in module mutopia.plot.track_plot.tracks) plot_gene_expression_strip() (in module mutopia.plot.track_plot.tracks)

plot_gene_expression_track() (in module mutopia.plot.track_plot.tracks) plot_interaction_matrix() (in module mutopia.plot) plot_marginal_observed_vs_expected() (in module mutopia.plot.track_plot.tracks) plot_shap_summary() (in module mutopia.plot) plot_signature_panel() (in module mutopia.plot) plot_signature_report() (in module mutopia.plot) plot_spectrum() (in module mutopia.plot) plot_topography() (in module mutopia.plot.track_plot.tracks) plot_view() (in module mutopia.plot.track_plot.track_plot) predict_cluster() (mutopia.analysis.topography_umap.TopographyUMAP method)

R

reducer_ (mutopia.analysis.topography_umap.TopographyUMAP attribute) rename_components() (in module mutopia.gtensor.gtensor)

renorm() (in module mutopia.plot.track_plot.transforms) reorder_df() (in module mutopia.plot.track_plot.transforms)

S

sample_params() (mutopia.model.base.TopographyModel method) save() (mutopia.analysis.topography_umap.TopographyUMAP method) (mutopia.model.base.TopographyModel method) SBSMode (class in mutopia.modalities.sbs.sbs) scale_bar() (in module mutopia.plot.track_plot.track_plot) scatterplot() (in module mutopia.plot.track_plot.track_plot) score() (mutopia.model.base.TopographyModel method) select() (in module mutopia.plot.track_plot.transforms) set_fit_request() (mutopia.analysis.topography_umap.TopographyUMAP method) (mutopia.model.base.TopographyModel method)

set_score_request() (mutopia.model.base.TopographyModel method) set_spread() (mutopia.analysis.topography_umap.TopographyUMAP static method) set_transform_request() (mutopia.analysis.topography_umap.TopographyUMAP method) setup_corpus() (mutopia.model.base.TopographyModel method) sizes (mutopia.modalities.sbs.sbs.SBSMode property) slice_regions() (in module mutopia.gtensor.gtensor) slice_samples() (in module mutopia.gtensor.gtensor) spacer() (in module mutopia.plot.track_plot.track_plot) stack_plots() (in module mutopia.plot.track_plot.track_plot) static_track() (in module mutopia.plot.track_plot.track_plot)

T

text_banner() (in module mutopia.plot.track_plot.track_plot) TopographyModel (class in mutopia.model.base) (mutopia.modalities.sbs.sbs.SBSMode property) TopographyTransformer (class in mutopia.plot.track_plot.transforms)

TopographyUMAP (class in mutopia.analysis.topography_umap) train_test_split() (in module mutopia.gtensor.gtensor) transform() (mutopia.analysis.topography_umap.TopographyUMAP method) (mutopia.plot.track_plot.transforms.TopographyTransformer method) transform_model() (mutopia.analysis.topography_umap.TopographyUMAP method)

U

umap_params (mutopia.analysis.topography_umap.TopographyUMAP property)

unstack_regions() (in module mutopia.gtensor.gtensor)

V

validate_observations() (mutopia.modalities.sbs.sbs.SBSMode class method)

validate_signatures() (mutopia.modalities.sbs.sbs.SBSMode class method)

W

write_coordinates() (mutopia.analysis.topography_umap.TopographyUMAP method)

X

X_LABELS (mutopia.modalities.sbs.sbs.SBSMode attribute), [1]

X_ref_ (mutopia.analysis.topography_umap.TopographyUMAP attribute) xaxis_plot() (in module mutopia.plot.track_plot.track_plot)