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Tutorials
Command-line interface: Factorization workflow
Command-line interface: Integration workflow
Configuring
mosaicmpi
integrate
using a config.toml file
Command-line interface: Integration workflow
Python factorization tutorial
Python integration tutorial
API
mosaicmpi.Dataset
mosaicmpi.Dataset.has_cnmf_results
mosaicmpi.Dataset.hvf
mosaicmpi.Dataset.hvf_stats
mosaicmpi.Dataset.is_imputed
mosaicmpi.Dataset.is_normalized
mosaicmpi.Dataset.mosaicmpi_version
mosaicmpi.Dataset.patient_id_col
mosaicmpi.Dataset.add_cnmf_results
mosaicmpi.Dataset.append_to_history
mosaicmpi.Dataset.calculate_cnmf_prediction_error
mosaicmpi.Dataset.cross_validate_imputation
mosaicmpi.Dataset.from_anndata
mosaicmpi.Dataset.from_df
mosaicmpi.Dataset.from_h5ad
mosaicmpi.Dataset.get_approximation
mosaicmpi.Dataset.get_category_overrepresentation
mosaicmpi.Dataset.get_history
mosaicmpi.Dataset.get_metadata_correlation
mosaicmpi.Dataset.get_metadata_df
mosaicmpi.Dataset.get_printable_metadata_type_summary
mosaicmpi.Dataset.get_programs
mosaicmpi.Dataset.get_usages
mosaicmpi.Dataset.impute_knn
mosaicmpi.Dataset.impute_zeros
mosaicmpi.Dataset.initialize_cnmf
mosaicmpi.Dataset.map_gene_ids
mosaicmpi.Dataset.remove_cnmf_results
mosaicmpi.Dataset.remove_unfactorizable_features
mosaicmpi.Dataset.remove_unfactorizable_observations
mosaicmpi.Dataset.select_hvf
mosaicmpi.Dataset.select_hvf_cnmf
mosaicmpi.Dataset.select_hvf_stdeconvolve
mosaicmpi.Dataset.to_df
mosaicmpi.Dataset.update_obs
mosaicmpi.Dataset.validate_cnmf_prediction_errors
mosaicmpi.Dataset.validate_feature_stats
mosaicmpi.Dataset.write_h5ad
mosaicmpi.Integration
mosaicmpi.Integration.n_datasets
mosaicmpi.Integration.sample_to_patient
mosaicmpi.Integration.selected_k
mosaicmpi.Integration.compute_corr
mosaicmpi.Integration.compute_pairwise_thresholds
mosaicmpi.Integration.filter_programs_rank_reduction
mosaicmpi.Integration.get_category_overrepresentation
mosaicmpi.Integration.get_corr_matrix_lowertriangle
mosaicmpi.Integration.get_features_overlap_table
mosaicmpi.Integration.get_hvf_overlap_table
mosaicmpi.Integration.get_metadata_correlation
mosaicmpi.Integration.get_metadata_df
mosaicmpi.Integration.get_node_table
mosaicmpi.Integration.get_programs
mosaicmpi.Integration.get_usages
mosaicmpi.Integration.select_k_values
mosaicmpi.Network
mosaicmpi.Network.n_communities
mosaicmpi.Network.node_to_community
mosaicmpi.Network.ordered_community_names
mosaicmpi.Network.programs_in_graph
mosaicmpi.Network.add_community_weights_to_graph
mosaicmpi.Network.community_search
mosaicmpi.Network.compute_community_network_layout
mosaicmpi.Network.compute_layout
mosaicmpi.Network.consensus
mosaicmpi.Network.count_intracommunity_edges
mosaicmpi.Network.create_community_network
mosaicmpi.Network.create_program_network
mosaicmpi.Network.from_pkl
mosaicmpi.Network.get_community_category_overrepresentation
mosaicmpi.Network.get_community_metadata_correlation
mosaicmpi.Network.get_lowest_rank_programs
mosaicmpi.Network.get_max_corr_communities
mosaicmpi.Network.get_median_community_usage
mosaicmpi.Network.get_node_table
mosaicmpi.Network.get_representative_program_ids
mosaicmpi.Network.get_representative_program_usage
mosaicmpi.Network.get_representative_programs
mosaicmpi.Network.get_sample_entropy
mosaicmpi.Network.get_selected_rank_program_ids
mosaicmpi.Network.get_vectorized_community_sort_key
mosaicmpi.Network.most_correlated_edge_between_datasets
mosaicmpi.Network.prune_communities
mosaicmpi.Network.read_communities_from_toml
mosaicmpi.Network.to_pkl
mosaicmpi.Network.transfer_labels
mosaicmpi.Network.write_communities_toml
mosaicmpi.Network.write_community_network_graphml
mosaicmpi.Network.write_program_network_graphml
mosaicmpi.Colors
mosaicmpi.Colors.ordered_community_names
mosaicmpi.Colors.add_missing_community_colors
mosaicmpi.Colors.add_missing_dataset_colors
mosaicmpi.Colors.add_missing_metadata_colors
mosaicmpi.Colors.from_config
mosaicmpi.Colors.from_dataset
mosaicmpi.Colors.from_integration
mosaicmpi.Colors.from_named_datasets
mosaicmpi.Colors.from_network
mosaicmpi.Colors.from_toml
mosaicmpi.Colors.get_metadata_colors
mosaicmpi.Colors.plot_community_colors_legend
mosaicmpi.Colors.plot_dataset_colors_legend
mosaicmpi.Colors.plot_metadata_colors_legend
mosaicmpi.Colors.reset_community_colors
mosaicmpi.Colors.to_toml
mosaicmpi.plots
mosaicmpi.plots.draw_circle_bar_plot
mosaicmpi.plots.draw_circle_bar_scale
mosaicmpi.plots.plot_community_contribution
mosaicmpi.plots.plot_community_network_summary
mosaicmpi.plots.plot_community_usage_per_sample
mosaicmpi.plots.plot_compare_integrations
mosaicmpi.plots.plot_feature_mean_variance
mosaicmpi.plots.plot_feature_missingness
mosaicmpi.plots.plot_feature_statistic_histogram
mosaicmpi.plots.plot_features_upset
mosaicmpi.plots.plot_geneset_heatmap
mosaicmpi.plots.plot_integration_hvf_upset
mosaicmpi.plots.plot_metadata_correlation_community_bar
mosaicmpi.plots.plot_metadata_correlation_community_network
mosaicmpi.plots.plot_metadata_correlation_program_bar
mosaicmpi.plots.plot_metadata_correlation_program_network
mosaicmpi.plots.plot_metadata_transfer
mosaicmpi.plots.plot_overrepresentation_community_bar
mosaicmpi.plots.plot_overrepresentation_community_heatmap
mosaicmpi.plots.plot_overrepresentation_community_network
mosaicmpi.plots.plot_overrepresentation_heatmap
mosaicmpi.plots.plot_overrepresentation_program_bar
mosaicmpi.plots.plot_overrepresentation_program_network
mosaicmpi.plots.plot_pairwise_corr
mosaicmpi.plots.plot_pairwise_corr_overlaid
mosaicmpi.plots.plot_program_correlation_matrix
mosaicmpi.plots.plot_program_network_communities
mosaicmpi.plots.plot_program_network_datasets
mosaicmpi.plots.plot_program_network_npatients
mosaicmpi.plots.plot_program_network_nsamples
mosaicmpi.plots.plot_rank_reduction
mosaicmpi.plots.plot_representative_community_usage_heatmap
mosaicmpi.plots.plot_representative_program_nes
mosaicmpi.plots.plot_sample_entropy
mosaicmpi.plots.plot_sample_numbers
mosaicmpi.plots.plot_stability_error
mosaicmpi.plots.plot_stratified_hvf_upset
mosaicmpi.plots.plot_usage_heatmap
mosaicmpi
mosaicmpi.biomart
mosaicmpi.biomart.BiomartAttribute
mosaicmpi.biomart.BiomartAttributePage
mosaicmpi.biomart.BiomartDatabase
mosaicmpi.biomart.BiomartDataset
mosaicmpi.biomart.BiomartFilter
mosaicmpi.biomart.BiomartServer
mosaicmpi.cli
mosaicmpi.cli.post_cli
mosaicmpi.cli.NullableInt
mosaicmpi.cnmf
mosaicmpi.cnmf.fast_ols_all_cols
mosaicmpi.cnmf.get_highvar_genes
mosaicmpi.cnmf.get_highvar_genes_sparse
mosaicmpi.cnmf.cNMF
mosaicmpi.colors
mosaicmpi.colors.Colors
mosaicmpi.config
mosaicmpi.config.recursive_update
mosaicmpi.config.Config
mosaicmpi.dataset
mosaicmpi.dataset.to_array
mosaicmpi.dataset.Dataset
mosaicmpi.genesets
mosaicmpi.genesets.order_genesets
mosaicmpi.genesets.program_gprofiler
mosaicmpi.genesets.program_ssgsea
mosaicmpi.integration
mosaicmpi.integration.Integration
mosaicmpi.nancorrmp
mosaicmpi.nancorrmp.NaNCorrMp
mosaicmpi.network
mosaicmpi.network.compare_community_jaccard_similarity
mosaicmpi.network.Network
mosaicmpi.orphan
mosaicmpi.plots
mosaicmpi.plots.draw_circle_bar_plot
mosaicmpi.plots.draw_circle_bar_scale
mosaicmpi.plots.plot_community_contribution
mosaicmpi.plots.plot_community_network_summary
mosaicmpi.plots.plot_community_usage_per_sample
mosaicmpi.plots.plot_compare_integrations
mosaicmpi.plots.plot_feature_mean_variance
mosaicmpi.plots.plot_feature_missingness
mosaicmpi.plots.plot_feature_statistic_histogram
mosaicmpi.plots.plot_features_upset
mosaicmpi.plots.plot_geneset_heatmap
mosaicmpi.plots.plot_integration_hvf_upset
mosaicmpi.plots.plot_metadata_correlation_community_bar
mosaicmpi.plots.plot_metadata_correlation_community_network
mosaicmpi.plots.plot_metadata_correlation_program_bar
mosaicmpi.plots.plot_metadata_correlation_program_network
mosaicmpi.plots.plot_metadata_transfer
mosaicmpi.plots.plot_overrepresentation_community_bar
mosaicmpi.plots.plot_overrepresentation_community_heatmap
mosaicmpi.plots.plot_overrepresentation_community_network
mosaicmpi.plots.plot_overrepresentation_heatmap
mosaicmpi.plots.plot_overrepresentation_program_bar
mosaicmpi.plots.plot_overrepresentation_program_network
mosaicmpi.plots.plot_pairwise_corr
mosaicmpi.plots.plot_pairwise_corr_overlaid
mosaicmpi.plots.plot_program_correlation_matrix
mosaicmpi.plots.plot_program_network_communities
mosaicmpi.plots.plot_program_network_datasets
mosaicmpi.plots.plot_program_network_npatients
mosaicmpi.plots.plot_program_network_nsamples
mosaicmpi.plots.plot_rank_reduction
mosaicmpi.plots.plot_representative_community_usage_heatmap
mosaicmpi.plots.plot_representative_program_nes
mosaicmpi.plots.plot_sample_entropy
mosaicmpi.plots.plot_sample_numbers
mosaicmpi.plots.plot_stability_error
mosaicmpi.plots.plot_stratified_hvf_upset
mosaicmpi.plots.plot_usage_heatmap
mosaicmpi.utils
mosaicmpi.utils.get_adjusted_dpi
mosaicmpi.utils.load_df_from_npz
mosaicmpi.utils.newline_wrap
mosaicmpi.utils.node_to_program
mosaicmpi.utils.program_to_node
mosaicmpi.utils.save_df_to_npz
mosaicmpi.utils.save_df_to_text
mosaicmpi.utils.save_fig
mosaicmpi.utils.start_logging
Module Index
.rst
.pdf
mosaicmpi.network.Network.read_communities_from_toml
Contents
Network.read_communities_from_toml()
mosaicmpi.network.Network.read_communities_from_toml
#
Network.
read_communities_from_toml
(
toml_file
)
#
Contents
Network.read_communities_from_toml()
