Index

A

align_plot_stability() (cell2location.models.base.base_model.BaseModel static method) annotate_adata() (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method)

apply_fact_filt() (cell2location.models.base.base_model.BaseModel method) ArchetypalAnalysis (class in cell2location.models.downstream.ArchetypalAnalysis) AutoGuideMixinModule (class in cell2location.models.base._pyro_mixin) AutoNormalEncoder (class in cell2location.distributions.AutoNormalEncoder)

B

BaseModel (class in cell2location.models.base.base_model)

bootstrap_data() (cell2location.models.base.base_model.BaseModel method)

C

Cell2location (class in cell2location.models) cell2location.cluster_averages.cluster_averages module cell2location.cluster_averages.markers_by_hierarhy module cell2location.cluster_averages.select_features module cell2location.distributions module cell2location.models.base._pyro_mixin module cell2location.models.base.base_model module cell2location.models.downstream.ArchetypalAnalysis module cell2location.models.downstream.CoLocatedGroupsSklearnNMF module cell2location.plt module cell2location.plt.mapping_video module cell2location.plt.plot_expected_vs_obs module cell2location.plt.plot_factor_spatial module cell2location.plt.plot_heatmap module

cell2location.plt.RotateCrop module cell2location.utils.filtering module Cell2locationBaseModule (class in cell2location.models.base._pyro_base_loc_module) change_requires_grad() (cell2location.models.base._pyro_mixin.PyroAggressiveTrainingPlan1 method) clustermap() (in module cell2location.plt.plot_heatmap) CoLocatedGroupsSklearnNMF (class in cell2location.models.downstream.CoLocatedGroupsSklearnNMF) compute_cluster_averages() (in module cell2location.cluster_averages.cluster_averages) compute_distances() (cell2location.plt.RotateCrop.RotateCrop method) compute_expected() (cell2location.models._cell2location_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method) (cell2location.models.reference._reference_module.RegressionBackgroundDetectionTechPyroModel method), [1] (cell2location.models.simplified._cell2location_v3_no_factorisation_module.LocationModelMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.simplified._cell2location_v3_no_mg_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelNoMGPyroModel method) compute_expected_fact() (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method) compute_expected_per_cell_type() (cell2location.models._cell2location_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) compute_expected_subset() (cell2location.models.reference._reference_module.RegressionBackgroundDetectionTechPyroModel method), [1] create_plates() (cell2location.models._cell2location_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.reference._reference_module.RegressionBackgroundDetectionTechPyroModel method), [1] (cell2location.models.simplified._cell2location_v3_no_factorisation_module.LocationModelMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.simplified._cell2location_v3_no_mg_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelNoMGPyroModel method) crop_rotate() (cell2location.plt.RotateCrop.RotateCrop method)

D

dotplot() (in module cell2location.plt.plot_heatmap)

E

encode() (cell2location.distributions.AutoNormalEncoder.AutoNormalEncoder method) evaluate_stability() (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method) expand_1by1() (in module cell2location.plt.mapping_video)

export2adata() (cell2location.models.base.base_model.BaseModel method) export_posterior() (cell2location.models.Cell2location method) (cell2location.models.reference._reference_model.RegressionModel method) (cell2location.models.RegressionModel method)

F

factor_expressed_plot() (cell2location.models.base.base_model.BaseModel method) filter_genes() (in module cell2location.utils.filtering) find_rectangle_corners() (in module cell2location.plt.RotateCrop) fit() (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method)

forward() (cell2location.distributions.AutoNormalEncoder.AutoNormalEncoder method) (cell2location.models._cell2location_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.reference._reference_module.RegressionBackgroundDetectionTechPyroModel method), [1] (cell2location.models.simplified._cell2location_v3_no_factorisation_module.LocationModelMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.simplified._cell2location_v3_no_mg_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelNoMGPyroModel method)

G

generate_cv_data() (cell2location.models.base.base_model.BaseModel method) get_cluster_averages_df() (in module cell2location.cluster_averages.cluster_averages) get_cluster_variances() (in module cell2location.cluster_averages.cluster_averages)

get_cluster_variances_df() (in module cell2location.cluster_averages.cluster_averages) get_rotation_matrix() (cell2location.plt.RotateCrop.RotateCrop method) guide() (cell2location.models.base._pyro_base_loc_module.Cell2locationBaseModule property)

H

heatmap() (in module cell2location.plt.plot_heatmap)

I

init_to_value() (cell2location.models.base._pyro_base_loc_module.Cell2locationBaseModule method) (in module cell2location.models.base._pyro_mixin)

interpolate_coord() (in module cell2location.plt.mapping_video) is_amortised() (cell2location.models.base._pyro_base_loc_module.Cell2locationBaseModule property)

L

list_obs_plate_vars() (cell2location.models._cell2location_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.base._pyro_base_loc_module.Cell2locationBaseModule property) (cell2location.models.reference._reference_module.RegressionBackgroundDetectionTechPyroModel method), [1] (cell2location.models.simplified._cell2location_v3_no_factorisation_module.LocationModelMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel method) (cell2location.models.simplified._cell2location_v3_no_mg_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelNoMGPyroModel method)

LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel (class in cell2location.models._cell2location_module) LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelNoMGPyroModel (class in cell2location.models.simplified._cell2location_v3_no_mg_module) LocationModelMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel (class in cell2location.models.simplified._cell2location_v3_no_factorisation_module)

M

markers_by_hierarhy() (in module cell2location.cluster_averages.markers_by_hierarhy) median() (cell2location.distributions.AutoNormalEncoder.AutoNormalEncoder method) model() (cell2location.models.base._pyro_base_loc_module.Cell2locationBaseModule property) module cell2location.cluster_averages.cluster_averages cell2location.cluster_averages.markers_by_hierarhy cell2location.cluster_averages.select_features cell2location.distributions cell2location.models.base._pyro_mixin cell2location.models.base.base_model cell2location.models.downstream.ArchetypalAnalysis cell2location.models.downstream.CoLocatedGroupsSklearnNMF cell2location.plt cell2location.plt.mapping_video cell2location.plt.plot_expected_vs_obs cell2location.plt.plot_factor_spatial cell2location.plt.plot_heatmap cell2location.plt.RotateCrop cell2location.utils.filtering

N

normalise() (cell2location.models.reference._reference_module.RegressionBackgroundDetectionTechPyroModel method), [1]

O

on_train_epoch_end() (cell2location.models.base._pyro_mixin.PyroAggressiveConvergence method)

P

plot_absolute_abundances_1D() (in module cell2location.plt) plot_categ_spatial() (in module cell2location.plt) (in module cell2location.plt.plot_factor_spatial) plot_cell_type_loadings() (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method) plot_density_1D() (in module cell2location.plt) plot_expected_vs_obs() (in module cell2location.plt.plot_expected_vs_obs) plot_factor_spatial() (in module cell2location.plt.plot_factor_spatial) plot_gene_loadings() (cell2location.models.base.base_model.BaseModel method) plot_history() (cell2location.models.base._pyro_mixin.PltExportMixin method) (cell2location.models.base.base_model.BaseModel method) plot_loading_distribution() (cell2location.models.base.base_model.BaseModel method) plot_posterior_mu_vs_data() (cell2location.models.base._pyro_mixin.PltExportMixin static method) (cell2location.models.base.base_model.BaseModel method) (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method) plot_posterior_vs_data() (cell2location.models.base.base_model.BaseModel method)

plot_prior_vs_data() (cell2location.models.base.base_model.BaseModel method) plot_QC() (cell2location.models.base._pyro_mixin.PltExportMixin method) (cell2location.models.reference._reference_model.RegressionModel method) (cell2location.models.RegressionModel method) plot_reconstruction_history() (cell2location.models.base.base_model.BaseModel method) plot_spatial() (in module cell2location.plt) plot_spatial_general() (in module cell2location.plt.plot_spatial) plot_spatial_QC_across_batches() (cell2location.models.Cell2location method) plot_validation_history() (cell2location.models.base.base_model.BaseModel method) plot_video_mapping() (in module cell2location.plt.mapping_video) PltExportMixin (class in cell2location.models.base._pyro_mixin) posterior_quantile() (cell2location.models.base._pyro_mixin.QuantileMixin method) print_gene_loadings() (cell2location.models.base.base_model.BaseModel method) PyroAggressiveConvergence (class in cell2location.models.base._pyro_mixin) PyroAggressiveTrainingPlan (class in cell2location.models.base._pyro_mixin) PyroAggressiveTrainingPlan1 (class in cell2location.models.base._pyro_mixin) PyroTrainingPlan (class in cell2location.models.base._pyro_mixin)

Q

QuantileMixin (class in cell2location.models.base._pyro_mixin)

quantiles() (cell2location.distributions.AutoNormalEncoder.AutoNormalEncoder method)

R

RegressionBackgroundDetectionTechPyroModel (class in cell2location.models.reference._reference_module), [1] RegressionModel (class in cell2location.models) (class in cell2location.models.reference._reference_model)

rotate_points() (cell2location.plt.RotateCrop.RotateCrop method) RotateCrop (class in cell2location.plt.RotateCrop)

S

sample2df() (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method) sample2df_obs() (cell2location.models.base._pyro_mixin.PltExportMixin method) sample2df_vars() (cell2location.models.base._pyro_mixin.PltExportMixin method) sample_posterior() (cell2location.models.downstream.ArchetypalAnalysis.ArchetypalAnalysis method) (cell2location.models.downstream.CoLocatedGroupsSklearnNMF.CoLocatedGroupsSklearnNMF method) select_features() (in module cell2location.cluster_averages.select_features)

select_slide() (in module cell2location.utils) set_fact_filt() (cell2location.models.base.base_model.BaseModel method) setup_anndata() (cell2location.models.Cell2location class method) (cell2location.models.reference._reference_model.RegressionModel class method) (cell2location.models.RegressionModel class method) spatial_neighbours() (in module cell2location.utils) sum_neighbours() (in module cell2location.utils)

T

train() (cell2location.models.Cell2location method) (cell2location.models.reference._reference_model.RegressionModel method) (cell2location.models.RegressionModel method) train_aggressive() (cell2location.models.Cell2location method)

training_epoch_end() (cell2location.models.base._pyro_mixin.PyroAggressiveTrainingPlan1 method) (cell2location.models.base._pyro_mixin.PyroTrainingPlan method) training_step() (cell2location.models.base._pyro_mixin.PyroAggressiveTrainingPlan1 method) training_wo_initial (cell2location.models._cell2location_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel attribute) training_wo_observed (cell2location.models._cell2location_module.LocationModelLinearDependentWMultiExperimentLocationBackgroundNormLevelGeneAlphaPyroModel attribute)